Index (biojava-structure 5.0.0-alpha2 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

aaScore(char, char) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
absolutePercentialRNAsuiteness - Variable in class org.biojava.nbio.structure.validation.Entry
absolutePercentileClashscore - Variable in class org.biojava.nbio.structure.validation.Entry
absolutePercentileDCCRfree - Variable in class org.biojava.nbio.structure.validation.Entry
absolutePercentilePercentRamaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
absolutePercentilePercentRotaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
absolutePercentilePercentRSRZOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
AbstractBean - Class in org.biojava.nbio.structure.io.mmcif.model: a generic class that implements the toString method for a bean
AbstractBean() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AbstractBean
AbstractScoresCache - Class in org.biojava.nbio.structure.align.multiple: Abstact implementation of the ScoresCache with the shared code used in all objects with a variables cache.
AbstractScoresCache() - Constructor for class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
AbstractScoresCache(AbstractScoresCache) - Constructor for class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
AbstractStructureAlignment - Class in org.biojava.nbio.structure.align
AbstractStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.AbstractStructureAlignment
AbstractUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce: Base class for a new structure alignment CLI.
AbstractUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
acentricOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
AD - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
add(int, int, int, int) - Method in class org.biojava.nbio.structure.align.helper.JointFragments
add(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: add two atoms ( a + b).
add(AtomContact) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
add(GroupContact) - Method in class org.biojava.nbio.structure.contact.GroupContactSet
add(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
addAlgorithm(StructureAlignment) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory: Adds a new StructureAlignment algorithm to the list.
addAlignmentProgressListener(AlignmentProgressListener) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
addAlignmentProgressListener(AlignmentProgressListener) - Method in class org.biojava.nbio.structure.align.FarmJob
addAll(Collection<AtomContact>) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
addAltLoc(Group) - Method in interface org.biojava.nbio.structure.Group: Add a group that is an alternate location for this group.
addAltLoc(Group) - Method in class org.biojava.nbio.structure.HetatomImpl
addAtom(Atom) - Method in interface org.biojava.nbio.structure.Group: Add an atom to this group.
addAtom(Atom) - Method in class org.biojava.nbio.structure.HetatomImpl: Add an atom to this group.
addAtomAsaC(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
addAtomAsaU(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
addAtomContact(AtomContact) - Method in class org.biojava.nbio.structure.contact.GroupContact
addAtoms(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.contact.Grid: Adds the i and j atoms and fills the grid.
addAtoms(Atom[], BoundingBox, Atom[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid: Adds the i and j atoms and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
addAtoms(Atom[]) - Method in class org.biojava.nbio.structure.contact.Grid: Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts.
addAtoms(Atom[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid: Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts.
addAxis(Matrix4d, List<List<Integer>>, List<Integer>, Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes: Adds a new axis of symmetry.
addBond(Bond) - Method in interface org.biojava.nbio.structure.Atom: Add a bond
addBond(Bond) - Method in class org.biojava.nbio.structure.AtomImpl
addBridge(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState: Adds a Bridge to the residue.
addChain(Chain) - Method in class org.biojava.nbio.structure.EntityInfo: Add new Chain to this Compound
addChain(Chain) - Method in interface org.biojava.nbio.structure.Structure: Add a new chain.
addChain(Chain, int) - Method in interface org.biojava.nbio.structure.Structure: Add a new chain, if several models are available.
addChain(Chain) - Method in class org.biojava.nbio.structure.StructureImpl: Add a new chain.
addChain(Chain, int) - Method in class org.biojava.nbio.structure.StructureImpl: Add a new chain, if several models are available.
addCharges() - Method in class org.biojava.nbio.structure.io.ChargeAdder
addChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary: add a new component to the dictionary
addCompound(EntityInfo) - Method in interface org.biojava.nbio.structure.Structure: Add a Compound to this Structure
addCompound(EntityInfo) - Method in class org.biojava.nbio.structure.StructureImpl: Add a Compound to this Structure
addExtension(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.
addExtension(String) - Method in interface org.biojava.nbio.structure.io.StructureIOFile: Associates a file extension with this particular StructureIOFile, indicating that files of that type can be parsed.
addGroup(Group) - Method in interface org.biojava.nbio.structure.Chain: add a group to the list of ATOM record group of this chain.
addGroup(Group) - Method in class org.biojava.nbio.structure.ChainImpl: add a group to the list of ATOM record group of this chain.
addHelix(Helix) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
addIindex(int) - Method in class org.biojava.nbio.structure.contact.GridCell
addJindex(int) - Method in class org.biojava.nbio.structure.contact.GridCell
addLigand(RCSBLigand) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigands
addMatrixListener(MatrixListener) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
addMatrixListener(MatrixListener) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
addMember(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
addMirror(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
addMMcifConsumer(MMcifConsumer) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser: Add a MMcifConsumer that listens to even being triggered by the parser and processes the data into a backend provided by the Consumer.
addMMcifConsumer(MMcifConsumer) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
addModel(List<Chain>) - Method in interface org.biojava.nbio.structure.Structure: Add a new model.
addModel(List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl: Add a new model.
addMultipleAlignment(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Add a new MultipleAlignment to the end of the ensemble and set its parent ensemble to this.
addMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
addPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
addPoint(Point3d, T) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
addPoint(Point3d, double) - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
addPolymer(RCSBPolymer) - Method in class org.biojava.nbio.structure.rcsb.RCSBDescription
addProgressListener(AlignmentProgressListener) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
addResidue(SiftsResidue) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
addRotation(Rotation) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
addSegment(SiftsSegment) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
addSeqResGroup(Group) - Method in class org.biojava.nbio.structure.ChainImpl
addSSBond(Bond) - Method in interface org.biojava.nbio.structure.Structure: Add a single disulfide Bond to this structure
addSSBond(Bond) - Method in class org.biojava.nbio.structure.StructureImpl: Adds a single disulfide Bond to this structure
addTransformation(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
addUniqueSequenceList(UniqueSequenceList) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
AFP - Class in org.biojava.nbio.structure.align.model: A class to represent a FATCAT AFP
AFP() - Constructor for class org.biojava.nbio.structure.align.model.AFP
afp2Res(AFPChain, int, int[], int) - Static method in class org.biojava.nbio.structure.align.AFPTwister: Set the list of equivalent residues in the two proteins given a list of AFPs WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in afpChain!
AFPAlignmentDisplay - Class in org.biojava.nbio.structure.align.util
AFPAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
AFPCalculator - Class in org.biojava.nbio.structure.align.fatcat.calc: a class that performs calculations on AFPCHains
AFPCalculator() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
AFPChain - Class in org.biojava.nbio.structure.align.model: A bean to contain the core of a structure alignment.
AFPChain(String) - Constructor for class org.biojava.nbio.structure.align.model.AFPChain: Construction of an AFPChain needs the algorithm name, since downstream analysis methods (scores, display, etc) behave differently if the alignment is flexible (created with FatCat).
AFPChain() - Constructor for class org.biojava.nbio.structure.align.model.AFPChain: Deprecated.
AFPChain(AFPChain) - Constructor for class org.biojava.nbio.structure.align.model.AFPChain: Copy constructor
AFPChainer - Class in org.biojava.nbio.structure.align.fatcat.calc: a class to chain AFPs to an alignment
AFPChainer() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
AFPChainFlipper - Class in org.biojava.nbio.structure.align.xml
AFPChainFlipper() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainFlipper
AFPChainScorer - Class in org.biojava.nbio.structure.align.util
AFPChainScorer() - Constructor for class org.biojava.nbio.structure.align.util.AFPChainScorer
AfpChainWriter - Class in org.biojava.nbio.structure.align.model: A class to convert the data in an AfpChain object to various String outputs.
AfpChainWriter() - Constructor for class org.biojava.nbio.structure.align.model.AfpChainWriter
AFPChainXMLConverter - Class in org.biojava.nbio.structure.align.xml
AFPChainXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
AFPChainXMLParser - Class in org.biojava.nbio.structure.align.xml
AFPChainXMLParser() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
AFPOptimizer - Class in org.biojava.nbio.structure.align.fatcat.calc
AFPOptimizer() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
afpPairConn(int, int, FatCatParameters, AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer: //Key function: calculate the connectivity of AFP pairs //no compatibility criteria is executed //note: afp1 is previous to afp2 in terms of the position //this module must be optimized
AFPPostProcessor - Class in org.biojava.nbio.structure.align.fatcat.calc: does post processing after alignment chaingin
AFPPostProcessor() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
AFPTwister - Class in org.biojava.nbio.structure.align
AFPTwister() - Constructor for class org.biojava.nbio.structure.align.AFPTwister
algorithmName - Static variable in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeCPMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeSideChainMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat
algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
algorithmName - Static variable in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
algorithmName - Static variable in class org.biojava.nbio.structure.symmetry.internal.CeSymm
ALIGFACTOR - Static variable in class org.biojava.nbio.structure.align.pairwise.Gotoh
AligMatEl - Class in org.biojava.nbio.structure.align.helper
AligMatEl() - Constructor for class org.biojava.nbio.structure.align.helper.AligMatEl
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.CeCPMain: Aligns ca1 and ca2 using a heuristic to check for CPs.
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.CeMain: Align ca2 onto ca1.
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeMain
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain: Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
align(Atom[], Atom[], boolean, FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
align(Atom[], Atom[], FatCatParameters, boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
align(List<Atom[]>, Object) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
align(List<Atom[]>) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
align(List<Atom[]>) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner: Run an alignment while specifying the atoms to be aligned.
align(List<Atom[]>, Object) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner: Run an alignment and also send a bean containing the parameters.
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
align(Atom[], Atom[]) - Method in interface org.biojava.nbio.structure.align.StructureAlignment: Run an alignment while specifying the atoms to be aligned.
align(Atom[], Atom[], Object) - Method in interface org.biojava.nbio.structure.align.StructureAlignment: run an alignment and also send a bean containing the parameters.
align(Structure, Structure) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Calculate the alignment between the two full structures with default parameters
align(Structure, Structure, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Calculate the alignment between the two full structures with user provided parameters
align(Structure, String, Structure, String) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Align two chains from the structures.
align(Structure, String, Structure, String, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Aligns two chains from the structures using user provided parameters.
align(Atom[], Atom[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: calculate the protein structure superimposition, between two sets of atoms.
align(Structure, List<Chain>) - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
align(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
align_NPE(Matrix, StrucAligParameters) - Static method in class org.biojava.nbio.structure.align.pairwise.AligNPE: Align without penalizing end-gaps.
Alignable - Interface in org.biojava.nbio.structure.align.pairwise
alignFlexible(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
alignmentAsMap(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Creates a Map specifying the alignment as a mapping between residue indices of protein 1 and residue indices of protein 2.
alignmentEnded() - Method in class org.biojava.nbio.structure.align.client.CountProgressListener
alignmentEnded() - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener
AlignmentProgressListener - Interface in org.biojava.nbio.structure.align.events
AlignmentProgressListener - Class in org.biojava.nbio.structure.align.pairwise: A class to listen to progress of the structure alignment calculations
AlignmentProgressListener() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
AlignmentResult - Class in org.biojava.nbio.structure.align.pairwise: A class to track the alignment results in a flat file
AlignmentResult() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlignmentResult
alignmentStarted(String, String) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener
alignmentStarted(String, String) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener
AlignmentTools - Class in org.biojava.nbio.structure.align.util: Methods for analyzing and manipulating AFPChains and for other pairwise alignment utilities.
AlignmentTools() - Constructor for class org.biojava.nbio.structure.align.util.AlignmentTools
AlignmentTools.IdentityMap<K> - Class in org.biojava.nbio.structure.align.util: A Map can be viewed as a function from K to V.
alignmentToSIF(Writer, AFPChain, Atom[], Atom[], String, String) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Creates a simple interaction format (SIF) file for an alignment.
alignOptimal(Atom[], Atom[], Object, AFPChain[]) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain: Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
alignPair(String, String) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
alignPair(String, String, String) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
AligNPE - Class in org.biojava.nbio.structure.align.pairwise
AligNPE() - Constructor for class org.biojava.nbio.structure.align.pairwise.AligNPE
alignPermuted(Atom[], Atom[], Object, int) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain: Aligns ca1 with ca2 permuted by cp residues.
alignRigid(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
alignRigid(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
alignSuperfamily() - Method in class demo.DemoSCOP
AlignTools - Class in org.biojava.nbio.structure.align.helper
AlignTools() - Constructor for class org.biojava.nbio.structure.align.helper.AlignTools
ALL_POLYMER_TYPES - Static variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType: Convenience Set of all polymer types.
AllChemCompProvider - Class in org.biojava.nbio.structure.io.mmcif: A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.
AllChemCompProvider() - Constructor for class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider
AltAligComparator - Class in org.biojava.nbio.structure.align.pairwise: a comparator to sort AlternativeAlignments based on their number of equivalent residues and RMSD.
AltAligComparator() - Constructor for class org.biojava.nbio.structure.align.pairwise.AltAligComparator
altcode - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
AlternativeAlignment - Class in org.biojava.nbio.structure.align.pairwise: Implements a class which handles one possible (alternative) solution.
AlternativeAlignment() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
AMINO_ACID_MATCHER - Static variable in class org.biojava.nbio.structure.AtomPositionMap: Matches CA atoms of protein groups
AminoAcid - Interface in org.biojava.nbio.structure: A Group that represents an AminoAcid.
AminoAcidImpl - Class in org.biojava.nbio.structure: AminoAcid inherits most from Hetatom.
AminoAcidImpl() - Constructor for class org.biojava.nbio.structure.AminoAcidImpl: inherits most from Hetero and has just a few extensions.
amount(Atom) - Static method in class org.biojava.nbio.structure.Calc: Gets the length of the vector (2-norm)
analyze(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm: Analyze the symmetries of the input Atom array using the DEFAULT parameters.
analyze(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm: Analyze the symmetries of the input Atom array using the provided parameters.
analyzeLevel(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm: Analyze a single level of symmetry.
angle(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: Gets the angle between two vectors
angleCheckOk(FragmentPair, FragmentPair, float) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
AngleOrderDetectorPlus - Class in org.biojava.nbio.structure.symmetry.internal: Guesses an order of rotational symmetry from the angle.
AngleOrderDetectorPlus(double) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
AngleOrderDetectorPlus(int) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
AngleOrderDetectorPlus(int, double) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
AngleOrderDetectorPlus(int, double, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus: Determine order by finding the order (up to the maxOrder) which has the closest rotation angle to the observed rotation.
AngleOutlier - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
AngleOutlier() - Constructor for class org.biojava.nbio.structure.validation.AngleOutlier
angleOutlier - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
ANYTHING_MATCHER - Static variable in class org.biojava.nbio.structure.AtomPositionMap: Matches all atoms
apairs_from_idxlst(JointFragments) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: Set apairs according to a list of (i,j) tuples.
apairs_from_seed(int, int, int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: Set apairs according to a seed position.
applyAlignment(Map<T, T>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Applies an alignment k times.
applyAlignment(Map<S, T>, Map<T, S>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Applies an alignment k times.
approach_ap3(Atom[], Atom[], FragmentPair[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
areInSameAxis(int, int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Returns true if both given transform ids belong to the same crystallographic axis (a, b or c) For two non-rotation transformations (i.e.
arrayLeftDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element left division, C = A.\B
arrayLeftDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element left division in place, A = A.\B
arrayRightDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element right division, C = A./B
arrayRightDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element right division in place, A = A./B
arrayTimes(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element multiplication, C = A.*B
arrayTimesEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element multiplication in place, A = A.*B
AsaCalculator - Class in org.biojava.nbio.structure.asa: Class to calculate Accessible Surface Areas based on the rolling ball algorithm by Shrake and Rupley.
AsaCalculator(Structure, double, int, int, boolean) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator: Constructs a new AsaCalculator.
AsaCalculator(Atom[], double, int, int) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator: Constructs a new AsaCalculator.
assignment - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
AssignmentXMLSerializer - Class in org.biojava.nbio.structure.domain
AssignmentXMLSerializer() - Constructor for class org.biojava.nbio.structure.domain.AssignmentXMLSerializer
Astral - Class in org.biojava.nbio.structure.scop: Provides programmatic access to ASTRAL representative sets.
Astral(Astral.AstralSet) - Constructor for class org.biojava.nbio.structure.scop.Astral: Constructs a new Astral object.
Astral(String, URL) - Constructor for class org.biojava.nbio.structure.scop.Astral: Constructs a new Astral object.
Astral(String, Reader) - Constructor for class org.biojava.nbio.structure.scop.Astral: Constructs a new Astral object.
Astral.AstralSet - Enum in org.biojava.nbio.structure.scop: An ASTRAL sequence-identity cutoff with an identifier such as:
Atom - Interface in org.biojava.nbio.structure: A simple interface for an Atom.
atom - Variable in class org.biojava.nbio.structure.validation.Clash
atom - Variable in class org.biojava.nbio.structure.validation.SymmClash
atom0 - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
atom0 - Variable in class org.biojava.nbio.structure.validation.BondOutlier
atom1 - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
atom1 - Variable in class org.biojava.nbio.structure.validation.BondOutlier
atom2 - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
ATOM_CA_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.FileParsingParameters: The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
AtomCache - Class in org.biojava.nbio.structure.align.util: A utility class that provides easy access to Structure objects.
AtomCache() - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Default AtomCache constructor.
AtomCache(String) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
AtomCache(String, String) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
AtomCache(String, boolean) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
isSplit parameter is ignored (4.0.0)
AtomCache(String, String, boolean) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
isSplit parameter is ignored (4.0.0)
AtomCache(UserConfiguration) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Creates a new AtomCache object based on the provided UserConfiguration.
AtomContact - Class in org.biojava.nbio.structure.contact: A pair of atoms that are in contact
AtomContact(Pair<Atom>, double) - Constructor for class org.biojava.nbio.structure.contact.AtomContact
AtomContactSet - Class in org.biojava.nbio.structure.contact: A set of atom-atom contacts to hold the results of intra and inter-chain contact calculations
AtomContactSet(double) - Constructor for class org.biojava.nbio.structure.contact.AtomContactSet
AtomIdentifier - Class in org.biojava.nbio.structure.contact
AtomIdentifier(int, String) - Constructor for class org.biojava.nbio.structure.contact.AtomIdentifier
AtomImpl - Class in org.biojava.nbio.structure: Implementation of an Atom of a PDB file.
AtomImpl() - Constructor for class org.biojava.nbio.structure.AtomImpl
AtomIterator - Class in org.biojava.nbio.structure: an iterator over all atoms of a structure / group.
AtomIterator(Structure) - Constructor for class org.biojava.nbio.structure.AtomIterator: Constructs an AtomIterator object.
AtomIterator(Group) - Constructor for class org.biojava.nbio.structure.AtomIterator: Constructs an AtomIterator object.
AtomPositionMap - Class in org.biojava.nbio.structure: A map from ResidueNumbers to ATOM record positions in a PDB file.
AtomPositionMap(Atom[]) - Constructor for class org.biojava.nbio.structure.AtomPositionMap: Creates a new AtomPositionMap containing peptide alpha-carbon atoms
AtomPositionMap(Atom[], AtomPositionMap.GroupMatcher) - Constructor for class org.biojava.nbio.structure.AtomPositionMap: Creates a new AtomPositionMap containing only atoms matched by matcher.
AtomPositionMap(Structure) - Constructor for class org.biojava.nbio.structure.AtomPositionMap: Creates a new AtomPositionMap containing representative atoms from a structure.
AtomPositionMap.GroupMatcher - Interface in org.biojava.nbio.structure: Used as a Predicate to indicate whether a particular Atom should be mapped
ATOMRECORD - Static variable in interface org.biojava.nbio.structure.AminoAcid: Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
atoms - Variable in class org.biojava.nbio.structure.HetatomImpl
atoms - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier
atoms - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier
AtomSite - Class in org.biojava.nbio.structure.io.mmcif.model
AtomSite() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AtomSite
atomsToPoints(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Convert an array of atoms into an array of vecmath points
attemptedValidationSteps - Variable in class org.biojava.nbio.structure.validation.Entry
AuditAuthor - Class in org.biojava.nbio.structure.io.mmcif.model
AuditAuthor() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
AugmentedResidueRange - Class in org.biojava.nbio.structure: Created by douglas on 1/23/15.
AugmentedResidueRange(String, ResidueNumber, ResidueNumber, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
AugmentedResidueRange(String, String, String, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
Author - Class in org.biojava.nbio.structure: Describes author attributes for author information in a PDB file.
Author() - Constructor for class org.biojava.nbio.structure.Author
avgoccu - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
AVGTM_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
AxisAligner - Class in org.biojava.nbio.structure.symmetry.core
AxisAligner() - Constructor for class org.biojava.nbio.structure.symmetry.core.AxisAligner

B

baseURL - Static variable in class org.biojava.nbio.structure.rcsb.RCSBUpdates
basicLoad(PDBFileReader, boolean, String) - Method in class demo.DemoChangeChemCompProvider
basicLoad(String) - Method in class demo.DemoDomainsplit
basicLoad() - Method in class demo.DemoLoadStructure
BerkeleyScopInstallation - Class in org.biojava.nbio.structure.scop: SCOPe: The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop.berkeley.edu/).
BerkeleyScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.BerkeleyScopInstallation
bestTrace1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTrace1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTrace2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTrace2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTraces1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTraces1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTraces2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTraces2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTraceScore - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTraceScore - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTracesN - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTracesN - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTracesScores - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTracesScores - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
BetaBridge - Class in org.biojava.nbio.structure.secstruc: Container that represents a beta Bridge between two residues.
BetaBridge(int, int, BridgeType) - Constructor for class org.biojava.nbio.structure.secstruc.BetaBridge
BIO_ASSEMBLY - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
BIO_NAME_PATTERN - Static variable in class org.biojava.nbio.structure.BioAssemblyIdentifier
BioAssemblyIdentifier - Class in org.biojava.nbio.structure
BioAssemblyIdentifier(String) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier
BioAssemblyIdentifier(String, int) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier
BioAssemblyInfo - Class in org.biojava.nbio.structure.quaternary: Representation of a Biological Assembly annotation as provided by the PDB.
BioAssemblyInfo() - Constructor for class org.biojava.nbio.structure.quaternary.BioAssemblyInfo: Empty constructor
BioAssemblyTools - Class in org.biojava.nbio.structure.quaternary
BioAssemblyTools() - Constructor for class org.biojava.nbio.structure.quaternary.BioAssemblyTools
BIOJAVA_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo: Secondary strucuture calculated and assigned by DSSP of BioJava
BioJavaStructureAlignment - Class in org.biojava.nbio.structure.align: Wrapper for the BioJava Structure Alignment Implementation
BioJavaStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.BioJavaStructureAlignment
BioJavaStructureDecoder - Class in org.biojava.nbio.structure.io.mmtf: A biojava specific structure inflator for MMTF.
BioJavaStructureDecoder() - Constructor for class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder: Instantiates a new bio java structure decoder.
BIOL_ASSEMBLY_IDENTIFIER - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
BiologicalAssemblyBuilder - Class in org.biojava.nbio.structure.quaternary: Reconstructs the quaternary structure of a protein from an asymmetric unit
BiologicalAssemblyBuilder() - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
BiologicalAssemblyTransformation - Class in org.biojava.nbio.structure.quaternary: The transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file.
BiologicalAssemblyTransformation() - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Default Constructor
BiologicalAssemblyTransformation(BiologicalAssemblyTransformation) - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Copy Constructor
BioUnitDataProvider - Interface in org.biojava.nbio.structure.quaternary.io: Provides access to the data that is needed in order to rebuild the correct biological assembly of a protein.
BioUnitDataProviderFactory - Class in org.biojava.nbio.structure.quaternary.io: Factory to create BioUnitDataProvider instances.
blankOutBreakFlag(AFPChain, Atom[], int, int, CECalculator, boolean[][], int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
blankOutCEOrig(Atom[], int, int, CECalculator, Matrix, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
blankOutPreviousAlignment(AFPChain, Atom[], int, int, CECalculator, Matrix, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
BlastClustReader - Class in org.biojava.nbio.structure.symmetry.utils
BlastClustReader(int) - Constructor for class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
Block - Interface in org.biojava.nbio.structure.align.multiple: A Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in a sequential order.
BlockImpl - Class in org.biojava.nbio.structure.align.multiple: General implementation of a Block that supports any type of sequential alignment with gaps.
BlockImpl(BlockSet) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl: Constructor.
BlockImpl(BlockImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl: Copy constructor.
blockInfo(AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer: get the afp list and residue list for each block
BlockSet - Interface in org.biojava.nbio.structure.align.multiple: A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment.
BlockSetImpl - Class in org.biojava.nbio.structure.align.multiple: A general implementation of a BlockSet to store a flexible part of a multiple alignment.
BlockSetImpl(MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl: Constructor.
BlockSetImpl(BlockSetImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl: Copy constructor.
Bond - Interface in org.biojava.nbio.structure: A simple bond -- it stores information about two atoms as well as information about its bond order.
BOND_TYPES_TO_PARSE - Static variable in class org.biojava.nbio.structure.io.BondMaker: The types of bonds that are read from struct_conn (type specified in field conn_type_id)
BondImpl - Class in org.biojava.nbio.structure: A simple bond -- it stores information about two atoms as well as information about its bond order.
BondImpl(Atom, Atom, int) - Constructor for class org.biojava.nbio.structure.BondImpl: Constructs a new bond from a pair of atoms and the bond order of the bond between them.
BondImpl(Atom, Atom, int, boolean) - Constructor for class org.biojava.nbio.structure.BondImpl: Constructs a new bond from a pair of atoms and the bond order of the bond between them.
BondMaker - Class in org.biojava.nbio.structure.io: Adds polymer bonds for peptides and nucleotides based on distance cutoffs and intra-group (residue) bonds based on data from the Chemical Component Dictionary to the Structure object.
BondMaker(Structure, FileParsingParameters) - Constructor for class org.biojava.nbio.structure.io.BondMaker
BondOutlier - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
BondOutlier() - Constructor for class org.biojava.nbio.structure.validation.BondOutlier
bondOutlier - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
BONDS_INITIAL_CAPACITY - Static variable in class org.biojava.nbio.structure.AtomImpl: The inital capacity of the bonds list.
BondType - Enum in org.biojava.nbio.structure: Work in progress - NOT final!
BoundingBox - Class in org.biojava.nbio.structure.contact: A bounding box for short cutting some geometrical calculations.
BoundingBox(double, double, double, double, double, double) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
BoundingBox(BoundingBox) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
BoundingBox(Atom[]) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox: Constructs a BoundingBox by calculating maxs and mins of given array of atoms.
BoundingBox(BoundingBox[]) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox: Given a set of bounding boxes returns a bounding box that bounds all of them.
BravaisLattice - Enum in org.biojava.nbio.structure.xtal: An enum to represent the 7 Bravais lattices
BridgeType - Enum in org.biojava.nbio.structure.secstruc: A bridge is formed by two non-overlapping stretches of three residues each (i-1,i,i+1) and (j-1,j,j+1), where i
buildSymmetryGraph(List<AFPChain>, Atom[], boolean) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Converts a set of AFP alignments into a Graph of aligned residues, where each vertex is a residue and each edge means the connection between the two residues in one of the alignments.
buildSymmetryGraph(AFPChain) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Converts a self alignment into a directed jGraphT of aligned residues, where each vertex is a residue and each edge means the equivalence between the two residues in the self-alignment.
bulkSolventB - Variable in class org.biojava.nbio.structure.validation.Entry
bulkSolventK - Variable in class org.biojava.nbio.structure.validation.Entry

C

c - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange: first allowed c-term
C1_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C1' in RNA
C2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C2' in RNA
C2RotationSolver - Class in org.biojava.nbio.structure.symmetry.core
C2RotationSolver(Subunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.C2RotationSolver
C3_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C3' in RNA
C4_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C4' in RNA
C_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name for the backbone carbonyl
CA_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C-alpha atom.
CA_MIN_DIST - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc: min distance of two CA atoms if H-bonds are allowed to form
cache - Variable in class org.biojava.nbio.structure.align.client.FarmJobRunnable
cache(K, V) - Method in class org.biojava.nbio.structure.domain.SerializableCache: This will not cache null values.
CachedRemoteScopInstallation - Class in org.biojava.nbio.structure.scop: An extension of the RemoteScopInstallation that caches some of the data locally.
CachedRemoteScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
CachedRemoteScopInstallation(boolean) - Constructor for class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
CacheFactory - Class in org.biojava.nbio.structure.align.util: provides a SoftHashMap singleton.
cacheFileName - Variable in class org.biojava.nbio.structure.domain.SerializableCache
CAConverter - Class in org.biojava.nbio.structure.io: Converts full atom representations to Calpha only ones.
CAConverter() - Constructor for class org.biojava.nbio.structure.io.CAConverter
calAfpRmsd(int, int[], int, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer: //return the rmsd of the residues from the segments that form the given AFP list //this value can be a measurement (1) for the connectivity of the AFPs
Calc - Class in org.biojava.nbio.structure: Utility operations on Atoms, AminoAcids, etc.
Calc() - Constructor for class org.biojava.nbio.structure.Calc
calc_rmsd(Atom[], Atom[], int, boolean, boolean) - Method in class org.biojava.nbio.structure.align.ce.CECalculator: Deprecated.
Use CECalculator.calc_rmsd(Atom[],Atom[],int,boolean) instead
calc_rmsd(Atom[], Atom[], int, boolean) - Method in class org.biojava.nbio.structure.align.ce.CECalculator: superimpose and get rmsd
calc_rmsd(Atom[], Atom[], int, boolean, boolean) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced: superimpose and get rmsd
calcAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together.
calcAsas(int, int, int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together.
calcCenterOfRotation() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
calcIdSimilarity(char[], char[], int) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
calcLength(List<ResidueRangeAndLength>) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength: Calculates the combined number of residues of the ResidueRanges in rrs.
calcPairwiseAlignments() - Method in class org.biojava.nbio.structure.symmetry.core.ClusterMerger: Aligns all pairs of input clusters, calculating their pairwise alignments
calcQuatSymmetry(Subunits, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
calcRotationAngleInDegrees(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: Calculates the angle from centerPt to targetPt in degrees.
calcScores(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: calculates scores for this alignment ( %id )
calcScores(Subunits, Matrix4d, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer: Returns minimum, mean, and maximum RMSD and TM-Score for two superimposed sets of subunits TM score: Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)
calcSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain
calculate(Structure, boolean) - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc: Predicts the secondary structure of this Structure object, using a DSSP implementation.
calculateAsas() - Method in class org.biojava.nbio.structure.asa.AsaCalculator: Calculates the Accessible Surface Areas for the atoms given in constructor and with parameters given.
calculateBlockGap(int[][][]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Method that calculates the number of gaps in each subunit block of an optimal AFP alignment.
calculatedFragmentPairs(List<FragmentPair>) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
calculateInterfaces(Structure) - Static method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Calculates the interfaces for a structure using default parameters
calculateMinCP(int[], int, int, int) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain: Finds the alignment index of the residues minCPlength before and after the duplication.
calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector
calculateOrder(AFPChain, Atom[]) - Method in interface org.biojava.nbio.structure.symmetry.internal.OrderDetector
calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector
calculateScores(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates and puts the RMSD and the average TM-Score of the MultipleAlignment.
calculateSuperpositionByIdx(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
calculator - Variable in class org.biojava.nbio.structure.align.ce.CeMain
call() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
call() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer
CallableStructureAlignment - Class in org.biojava.nbio.structure.align
CallableStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment: Default constructor.
CallableStructureAlignment(Atom[], Atom[], String, ConfigStrucAligParams) - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment: Constructor for all-to-all alignment calculation.
calNS(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
calSigAll(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
CartesianProduct<T> - Class in org.biojava.nbio.structure.quaternary: A cartesian product between two lists A and B is the set of all ordered pairs of the elements of both sets.
CartesianProduct(List<T>, List<T>) - Constructor for class org.biojava.nbio.structure.quaternary.CartesianProduct: Class constructor specifying the two lists of a cartesian product.
CATH_DOWNLOAD - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
CathCategory - Enum in org.biojava.nbio.structure.cath: The categories found within CATH.
CathDatabase - Interface in org.biojava.nbio.structure.cath: General API for interacting with CATH.
CathDomain - Class in org.biojava.nbio.structure.cath: A class which represents a single CATH domain.
CathDomain() - Constructor for class org.biojava.nbio.structure.cath.CathDomain
CathFactory - Class in org.biojava.nbio.structure.cath: Controls global CathDatabases being used.
CathFragment - Class in org.biojava.nbio.structure.cath
CathFragment() - Constructor for class org.biojava.nbio.structure.cath.CathFragment
CathInstallation - Class in org.biojava.nbio.structure.cath
CathInstallation(String, boolean, boolean) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
CathInstallation(String) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
CathInstallation() - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
CathNode - Class in org.biojava.nbio.structure.cath: Represents a node in the CATH hierarchy.
CathNode() - Constructor for class org.biojava.nbio.structure.cath.CathNode
CathSegment - Class in org.biojava.nbio.structure.cath
CathSegment() - Constructor for class org.biojava.nbio.structure.cath.CathSegment
CB_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the side-chain C-beta atom
ccp4Version - Variable in class org.biojava.nbio.structure.validation.Entry
CE_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
CECalculator - Class in org.biojava.nbio.structure.align.ce: This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
CECalculator(CeParameters) - Constructor for class org.biojava.nbio.structure.align.ce.CECalculator
CeCalculatorEnhanced - Class in org.biojava.nbio.structure.align.ce: This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
CeCalculatorEnhanced(CeParameters) - Constructor for class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
CeCPMain - Class in org.biojava.nbio.structure.align.ce: A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.
CeCPMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain
CeCPMain.CPRange - Class in org.biojava.nbio.structure.align.ce: Tiny wrapper for the disallowed regions of an alignment.
CECPParameters - Class in org.biojava.nbio.structure.align.ce: Provides parameters to CeCPMain
CECPParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CECPParameters
CECPParameters.DuplicationHint - Enum in org.biojava.nbio.structure.align.ce
CeCPStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
CeCPUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
CeCPUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
CeCPUserArgumentProcessor.CeCPStartupParams - Class in org.biojava.nbio.structure.align.ce
ceil(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable: Return the smallest key in the table >= k.
Cell - Class in org.biojava.nbio.structure.io.mmcif.model
Cell() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Cell
CeMain - Class in org.biojava.nbio.structure.align.ce: The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I.
CeMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeMain
center(Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
centerAtoms(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Center the atoms at the Centroid.
centerAtoms(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc: Center the atoms at the Centroid, if the centroid is already know.
centerOfMass(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
centerOfMass() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
centricOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
centroid(Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
CeParameters - Class in org.biojava.nbio.structure.align.ce: Contains the parameters that can be sent to CE
CeParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CeParameters
CeParameters.ScoringStrategy - Enum in org.biojava.nbio.structure.align.ce
CeSideChainMain - Class in org.biojava.nbio.structure.align.ce
CeSideChainMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainMain
CeSideChainUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
CeSideChainUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
CeStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
CeSymm - Class in org.biojava.nbio.structure.symmetry.internal: Identify the symmetries in a structure by running an alignment of the structure against itself disabling the diagonal of the identity alignment.
CeSymmIterative - Class in org.biojava.nbio.structure.symmetry.internal: Iterative version of CeSymm that aims at identifying all symmetry axis (internal or quaternary) of a particular structure.
CeSymmIterative(CESymmParameters) - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative: For the iterative algorithm to work properly the refinement and optimization options should be turned on, because the alignment has to be consistent at every recursive step.
CESymmParameters - Class in org.biojava.nbio.structure.symmetry.internal: Provides parameters to CeSymm.
CESymmParameters() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
CESymmParameters.OrderDetectorMethod - Enum in org.biojava.nbio.structure.symmetry.internal
CESymmParameters.RefineMethod - Enum in org.biojava.nbio.structure.symmetry.internal
CESymmParameters.SymmetryType - Enum in org.biojava.nbio.structure.symmetry.internal: The internal symmetry detection can be divided into two types: CLOSE: includes the circular and dihedral symmetries, and OPEN: includes the helical and protein repeats symmetries.
CeSymmResult - Class in org.biojava.nbio.structure.symmetry.internal: This Class stores all the relevant information of an internal symmetry result obtained with CeSymm.
CeSymmResult() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
CeUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce: process the arguments from command line
CeUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
CeUserArgumentProcessor.CeStartupParams - Class in org.biojava.nbio.structure.align.ce
Chain - Interface in org.biojava.nbio.structure: Defines the interface for a Chain.
chain - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
CHAIN_NR_SYMBOL - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
CHAIN_REGEX - Static variable in class org.biojava.nbio.structure.ResidueRange
CHAIN_SPLIT_SYMBOL - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
ChainClusterer - Class in org.biojava.nbio.structure.symmetry.core: Wraps a sequence clustering with structural information
ChainClusterer(List<SequenceAlignmentCluster>) - Constructor for class org.biojava.nbio.structure.symmetry.core.ChainClusterer
chainEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
chainId - Variable in class org.biojava.nbio.structure.align.client.StructureName
CHAINID_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier: URL parameter specifying a single chain to include; overridden by residues
ChainImpl - Class in org.biojava.nbio.structure: A Chain in a PDB file.
ChainImpl() - Constructor for class org.biojava.nbio.structure.ChainImpl: Constructs a ChainImpl object.
ChainSignature - Class in org.biojava.nbio.structure.symmetry.misc
ChainSignature(String, int, List<String>) - Constructor for class org.biojava.nbio.structure.symmetry.misc.ChainSignature
ChargeAdder - Class in org.biojava.nbio.structure.io
ChargeAdder(Structure) - Constructor for class org.biojava.nbio.structure.io.ChargeAdder
checkDoFirstInstall() - Method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider: Checks if the chemical components already have been installed into the PDB directory.
checkFileExists(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
checkScaleMatrix(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Given a scale matrix parsed from a PDB entry (SCALE1,2,3 records), compares it to our calculated Mtranspose matrix to see if they coincide and returns true if they do.
checkScaleMatrixConsistency(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Given a scale matrix parsed from the PDB entry (SCALE1,2,3 records), checks that the matrix is a consistent scale matrix by comparing the cell volume to the inverse of the scale matrix determinant (tolerance of 1/100).
CHEM_COMP_CACHE_DIRECTORY - Static variable in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
chem_comp_type - Variable in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType: String value of the type
ChemComp - Class in org.biojava.nbio.structure.io.mmcif.model: A definition for a Chemical Component, as maintained by the wwPDB.
ChemComp() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemComp
ChemCompAtom - Class in org.biojava.nbio.structure.io.mmcif.model: stores these fields: _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_residue_numbering _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_polymer_type _chem_comp_atom.pdbx_ref_id _chem_comp_atom.pdbx_component_id _chem_comp_atom.pdbx_ordinal
ChemCompAtom() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
ChemCompBond - Class in org.biojava.nbio.structure.io.mmcif.model
ChemCompBond() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
ChemCompConsumer - Class in org.biojava.nbio.structure.io.mmcif
ChemCompConsumer() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
ChemCompDescriptor - Class in org.biojava.nbio.structure.io.mmcif.model: Container object for _pdbx_chem_comp_descriptor
ChemCompDescriptor() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
ChemCompDistribution - Class in demo
ChemCompDistribution() - Constructor for class demo.ChemCompDistribution
ChemCompGroupFactory - Class in org.biojava.nbio.structure.io.mmcif
ChemCompGroupFactory() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
ChemCompProvider - Interface in org.biojava.nbio.structure.io.mmcif: Interface that is implemented by all classes that can provide ChemComp definitions.
ChemCompTools - Class in org.biojava.nbio.structure.io.mmcif.chem: Some tools for working with chemical compounds.
ChemCompTools() - Constructor for class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
ChemicalComponentDictionary - Class in org.biojava.nbio.structure.io.mmcif: A representation of the Chemical Component Dictionary.
ChemicalComponentDictionary() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
chol() - Method in class org.biojava.nbio.structure.jama.Matrix: Cholesky Decomposition
CholeskyDecomposition - Class in org.biojava.nbio.structure.jama: Cholesky Decomposition.
CholeskyDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.CholeskyDecomposition: Cholesky algorithm for symmetric and positive definite matrix.
cid - Variable in class org.biojava.nbio.structure.validation.Clash
claFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
Clash - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
Clash() - Constructor for class org.biojava.nbio.structure.validation.Clash
clash - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
clashmag - Variable in class org.biojava.nbio.structure.validation.Clash
clashmag - Variable in class org.biojava.nbio.structure.validation.SymmClash
clashscore - Variable in class org.biojava.nbio.structure.validation.Entry
cleanup() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
cleanup(List<Domain>) - Static method in class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
cleanUpStructure() - Method in class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder
clear() - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache: Clear the cached scores.
clear() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Clear scores and other properties which depend on the specific alignment.
clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
clear() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Clear scores and other properties which depend on the specific alignment.
clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Clear scores and other properties which depend on the specific alignment.
clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Clear scores and other properties which depend on the specific alignment.
clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
clear() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Clears all domains, requiring the file to be reparsed for subsequent accesses
clear() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
clearAlgorithms() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory: Removes all algorithms from the list
clearAtoms() - Method in interface org.biojava.nbio.structure.Group: Remove all atoms from this group.
clearAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl: remove all atoms
clearCache() - Static method in class org.biojava.nbio.structure.PDBStatus: The status of PDB IDs are cached to reduce server overload.
clearConsumers() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser: Remove all consumers from the parser.
clearConsumers() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
clearExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: clear the supported file extensions
clearListeners() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
clearListeners() - Method in class org.biojava.nbio.structure.align.FarmJob
clearListeners() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
CliTools - Class in org.biojava.nbio.structure.align.util: Utilities for autoconfiguring javabeans based on command line arguments.
clone() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Creates and returns a copy of this object.
clone(Object) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache: Subclasses should override clone and use the copy constructor.
clone() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Creates and returns an identical copy of this block.
clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
clone() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Creates and returns an identical copy of this blockset, including a deep copy of all constituent Blocks.
clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Creates and returns an identical copy of this alignment, including a deep copy of all constituent BlockSets.
clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Creates and returns an identical copy of this ensemble, including a deep clone of all constituent alignments.
clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
clone() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
clone() - Method in class org.biojava.nbio.structure.AminoAcidImpl: returns and identical copy of this Group object .
clone() - Method in class org.biojava.nbio.structure.asa.GroupAsa
clone() - Method in interface org.biojava.nbio.structure.Atom: Return an identical copy of this object .
clone() - Method in class org.biojava.nbio.structure.AtomImpl: returns and identical copy of this object .
clone() - Method in interface org.biojava.nbio.structure.Chain: returns an identical copy of this Chain.
clone() - Method in class org.biojava.nbio.structure.ChainImpl: Returns an identical copy of this Chain .
clone() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
clone() - Method in interface org.biojava.nbio.structure.Group: returns and identical copy of this Group object .
clone() - Method in class org.biojava.nbio.structure.GroupIterator: Creates and returns a copy of this object.
clone() - Method in class org.biojava.nbio.structure.HetatomImpl: returns and identical copy of this Group object .
clone() - Method in class org.biojava.nbio.structure.io.SSBondImpl
clone() - Method in class org.biojava.nbio.structure.jama.Matrix: Clone the Matrix object.
clone() - Method in class org.biojava.nbio.structure.NucleotideImpl
clone() - Method in class org.biojava.nbio.structure.scop.ScopDescription
clone() - Method in class org.biojava.nbio.structure.scop.ScopDomain
clone() - Method in class org.biojava.nbio.structure.secstruc.HBond
clone() - Method in interface org.biojava.nbio.structure.Structure: Return an identical copy of this Structure object
clone() - Method in class org.biojava.nbio.structure.StructureImpl: returns an identical copy of this structure .
clone() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
clone() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
clone() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
cloneAtomArray(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools: Provides an equivalent copy of Atoms in a new array.
cloneCAArray(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools: Deprecated.
Use the better-named StructureTools.cloneAtomArray(Atom[]) instead
cloneGroups(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools: Clone a set of representative Atoms, but returns the parent groups
clonePoint3dArray(Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
close() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile
cluster(AlternativeAlignment[]) - Static method in class org.biojava.nbio.structure.align.ClusterAltAligs
cluster(AlternativeAlignment[], int) - Static method in class org.biojava.nbio.structure.align.ClusterAltAligs
cluster(List<Domain>, PDPDistanceMatrix) - Static method in class org.biojava.nbio.structure.domain.pdp.ClusterDomains
ClusterAltAligs - Class in org.biojava.nbio.structure.align: A class that clusters alternative alignments according to their similarity.
ClusterAltAligs() - Constructor for class org.biojava.nbio.structure.align.ClusterAltAligs
ClusterDomains - Class in org.biojava.nbio.structure.domain.pdp
ClusterDomains() - Constructor for class org.biojava.nbio.structure.domain.pdp.ClusterDomains
ClusterMerger - Class in org.biojava.nbio.structure.symmetry.core: Merges clusters based on their sequence identity.
ClusterMerger(List<SequenceAlignmentCluster>, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ClusterMerger
ClusterProteinChains - Class in org.biojava.nbio.structure.symmetry.core: Clusters the chains of one or two structures by sequence.
ClusterProteinChains(Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
ClusterProteinChains(Structure, Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
CollectionTools - Class in org.biojava.nbio.structure.align.util: Utilities for working with collections.
CollectionTools() - Constructor for class org.biojava.nbio.structure.align.util.CollectionTools
CombinationGenerator - Class in org.biojava.nbio.structure.symmetry.utils
CombinationGenerator(int, int) - Constructor for class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
combine(BiologicalAssemblyTransformation, BiologicalAssemblyTransformation) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Returns the combination (product) of two biological assembly transformations.
combine(List<Integer>, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
combineWith(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup: Combine the ResidueGroup with the alignment block.
comFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
COMMENT_CHAR - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
compare(int[], int[]) - Method in class org.biojava.nbio.structure.align.helper.IdxComparator
compare(AlternativeAlignment, AlternativeAlignment) - Method in class org.biojava.nbio.structure.align.pairwise.AltAligComparator
compare(Segment, Segment) - Method in class org.biojava.nbio.structure.domain.pdp.SegmentComparator
compareTo(PdbPair) - Method in class org.biojava.nbio.structure.align.client.PdbPair
compareTo(StructureName) - Method in class org.biojava.nbio.structure.align.client.StructureName: Orders identifiers lexicographically by PDB ID and then full Identifier
compareTo(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterface
compareTo(Domain) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
compareTo(Segment) - Method in class org.biojava.nbio.structure.domain.pdp.Segment
compareTo(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
compareTo(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber
compareTo(Site) - Method in class org.biojava.nbio.structure.Site
compareTo(ChainSignature) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
complete() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
completeGroup() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup: Starts with an incomplete set of group generators in `permutations` and expands it to include all possible combinations.
COMPONENTS_FILE_LOCATION - Static variable in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider
CompoundFinder - Class in org.biojava.nbio.structure.io: Heuristical finding of Compounds (called Entities in mmCIF dictionary) in a given Structure.
CompoundFinder(Structure) - Constructor for class org.biojava.nbio.structure.io.CompoundFinder
cond() - Method in class org.biojava.nbio.structure.jama.Matrix: Matrix condition (2 norm)
cond() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition: Two norm condition number
ConfigStrucAligParams - Interface in org.biojava.nbio.structure.align.ce
ConfigurationException - Exception in org.biojava.nbio.structure.align.util
ConfigurationException(String) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException: Constructs a ConfigurationException object.
ConfigurationException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
ConfigurationException(Throwable) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException: Constructs a ConfigurationException object.
ConfigurationException() - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
configureBean(Object, String[]) - Static method in class org.biojava.nbio.structure.align.util.CliTools: Configure a JavaBean based on a set of command line arguments.
constructWithCopy(double[][]) - Static method in class org.biojava.nbio.structure.jama.Matrix: Construct a matrix from a copy of a 2-D array.
contacts(Point3d[], Point3d[], double) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
contains(ResidueNumber) - Method in class org.biojava.nbio.structure.AugmentedResidueRange
contains(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable: Is the key in the table?
contains(ResidueNumber, AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange
contains(Subunits) - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
containsChainId(String, String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
containsKey(Object) - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
containsUniProtId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
convert_3code_1code(String) - Static method in class org.biojava.nbio.structure.StructureTools: Deprecated.
Use StructureTools.get1LetterCodeAmino(String) instead
convertAfpChain(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator: copy data from this class into AFPChain container object.
convertAfpChain(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced: copy data from this class into AFPChain container object.
convertAtomsToSeq(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
convertAtomToAtomSite(Atom, int, String, String) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: Converts an Atom object to an AtomSite object.
convertAtomToAtomSite(Atom, int, String, String, int) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: Converts an Atom object to an AtomSite object.
convertChainToAtomSites(Chain, int, String, String) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: Converts a Chain into a List of AtomSite objects
convertCrystalCellToCell(CrystalCell) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: Converts a CrystalCell object to a Cell object.
convertPairsToXML(SortedSet<PdbPair>, String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
convertSpaceGroupToSymmetry(SpaceGroup) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: Converts a SpaceGroup object to a Symmetry object.
convertStreamToString(InputStream) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
convertStructureToAtomSites(Structure) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: Converts a Structure into a List of AtomSite objects
convertXMLtoPairs(String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
copy(File, File) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils: Copy the content of file src to dst TODO since java 1.7 this is provided in java.nio.file.Files
copy() - Method in class org.biojava.nbio.structure.jama.Matrix: Make a deep copy of a matrix
CoreSuperimposer - Class in org.biojava.nbio.structure.align.multiple.util: Superimposes the core aligned residues of every structure in a MultipleAlignment onto a reference structure.
CoreSuperimposer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer: Default Constructor.
CoreSuperimposer(int) - Constructor for class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer: Constructor using a specified structure as reference.
CountProgressListener - Class in org.biojava.nbio.structure.align.client
CountProgressListener() - Constructor for class org.biojava.nbio.structure.align.client.CountProgressListener
cpFastaToAfpChain(String, String, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
cpFastaToAfpChain(File, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
cpFastaToAfpChain(ProteinSequence, ProteinSequence, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
cpPoint - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters: The CP point, specified as a residue index
CPRange() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
createAFPChain(Atom[], Atom[], ResidueNumber[], ResidueNumber[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Fundamentally, an alignment is just a list of aligned residues in each protein.
createAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of AngleOutlier
createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
createBondOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of BondOutlier
createClash() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of Clash
createEntry() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of Entry
createModelledSubgroup() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of ModelledSubgroup
createMogAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of MogAngleOutlier
createMogBondOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of MogBondOutlier
createProgram() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of Program
createPrograms() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of Programs
createSymmClash() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of SymmClash
createVirtualCBAtom(AminoAcid) - Static method in class org.biojava.nbio.structure.Calc: creates a virtual C-beta atom.
createWwPDBValidationInformation() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of WwPDBValidationInformation
CrystalBuilder - Class in org.biojava.nbio.structure.xtal: A class containing methods to find interfaces in a given crystallographic Structure by reconstructing the crystal lattice through application of symmetry operators
CrystalBuilder(Structure) - Constructor for class org.biojava.nbio.structure.xtal.CrystalBuilder
CrystalCell - Class in org.biojava.nbio.structure.xtal: A crystal cell's parameters.
CrystalCell() - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell
CrystalCell(double, double, double, double, double, double) - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell
CrystalTransform - Class in org.biojava.nbio.structure.xtal: Representation of a transformation in a crystal: - a transformation id (each of the transformations in a space group, 0 to m) - a crystal translation The transformation matrix in crystal basis is stored, representing the basic transformation together with the crystal translation.
CrystalTransform(SpaceGroup) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform: Creates a new CrystalTransform representing the identity transform in cell (0,0,0)
CrystalTransform(SpaceGroup, int) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform: Represents the n-th transform
CrystalTransform(CrystalTransform) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform: Copy constructor
Cut - Class in org.biojava.nbio.structure.domain.pdp
Cut() - Constructor for class org.biojava.nbio.structure.domain.pdp.Cut
cut(Atom[], Domain, CutValues, int[][], PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.Cut
CUT_OFF_VALUE - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CUT_OFF_VALUE1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CUT_OFF_VALUE1M - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CUT_OFF_VALUE1S - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CUT_OFF_VALUE2 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CutDomain - Class in org.biojava.nbio.structure.domain.pdp
CutDomain(Atom[], PDPDistanceMatrix) - Constructor for class org.biojava.nbio.structure.domain.pdp.CutDomain
cutDomain(Domain, CutSites, PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.CutDomain
CutSites - Class in org.biojava.nbio.structure.domain.pdp
CutSites() - Constructor for class org.biojava.nbio.structure.domain.pdp.CutSites
CutValues - Class in org.biojava.nbio.structure.domain.pdp
CutValues() - Constructor for class org.biojava.nbio.structure.domain.pdp.CutValues

D

d2 - Static variable in class org.biojava.nbio.structure.io.FileConvert
d3 - Static variable in class org.biojava.nbio.structure.io.FileConvert
dataAnisotropy - Variable in class org.biojava.nbio.structure.validation.Entry
DatabasePDBremark - Class in org.biojava.nbio.structure.io.mmcif.model
DatabasePDBremark() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
DatabasePDBrev - Class in org.biojava.nbio.structure.io.mmcif.model
DatabasePDBrev() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
DatabasePdbrevRecord - Class in org.biojava.nbio.structure.io.mmcif.model
DatabasePdbrevRecord() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
dataCompleteness - Variable in class org.biojava.nbio.structure.validation.Entry
DBL - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
DBRef - Class in org.biojava.nbio.structure: A class to represent database cross references.
DBRef() - Constructor for class org.biojava.nbio.structure.DBRef
dccr - Variable in class org.biojava.nbio.structure.validation.Entry
dccRefinementProgram - Variable in class org.biojava.nbio.structure.validation.Entry
dccRfree - Variable in class org.biojava.nbio.structure.validation.Entry
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
debug - Static variable in class org.biojava.nbio.structure.align.util.AlignmentTools
DEF_NUM_CELLS - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder
DEFAULT - Static variable in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
DEFAULT - Static variable in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
DEFAULT_ALGORITHM_NAME - Static variable in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
DEFAULT_ASA_SPHERE_POINTS - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList: Default number of points to use when calculating ASAs
DEFAULT_BATCH_SIZE - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
DEFAULT_CHAIN_ID - Static variable in class org.biojava.nbio.structure.ChainImpl: The default chain identifier used to be an empty space
DEFAULT_CLUSTER_CUTOFF - Static variable in class org.biojava.nbio.structure.align.ClusterAltAligs
DEFAULT_CONNECTION_TIMEOUT - Static variable in class org.biojava.nbio.structure.align.util.HTTPConnectionTools
DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList: Any 2 interfaces with contact overlap score larger than this value will be considered to be clustered
DEFAULT_FRAGLEN - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
DEFAULT_GAP_EXTENSION - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
DEFAULT_GAP_OPEN - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
DEFAULT_INTERFACE_DISTANCE_CUTOFF - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder: Default maximum distance between two chains to be considered an interface.
DEFAULT_JOB_TIME - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
DEFAULT_METHOD_NAME - Static variable in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
DEFAULT_MIN_COFACTOR_SIZE - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList: Default minimum size of cofactor molecule (non-chain HET atoms) that will be used
DEFAULT_MIN_CP_LENGTH - Static variable in class org.biojava.nbio.structure.align.ce.CECPParameters
DEFAULT_MINIMUM_INTERFACE_AREA - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList: Default minimum area for a contact between two chains to be considered a valid interface.
DEFAULT_N_SPHERE_POINTS - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
DEFAULT_NR_ALIGNMENTS - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
DEFAULT_NR_THREADS - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
DEFAULT_NTHREADS - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
DEFAULT_oRmsdThr - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
DEFAULT_PDB_API_URL - Static variable in class org.biojava.nbio.structure.domain.PDBDomainProvider
DEFAULT_PDB_FILE_SERVER - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory: The default server name, prefixed by the protocol string (http:// or ftp://).
DEFAULT_PDB_HOST - Static variable in class org.biojava.nbio.structure.domain.PDBDomainProvider
DEFAULT_PDB_PATH - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
DEFAULT_PDB_SERVER - Static variable in class org.biojava.nbio.structure.PDBStatus
DEFAULT_PROBE_SIZE - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
DEFAULT_PROVIDER_CLASS - Static variable in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
DEFAULT_PROVIDER_CLASSNAME - Static variable in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
DEFAULT_RESOLUTION - Static variable in class org.biojava.nbio.structure.PDBHeader
DEFAULT_RFREE - Static variable in class org.biojava.nbio.structure.PDBHeader
DEFAULT_SCORING_STRATEGY - Static variable in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
DEFAULT_SERVER - Static variable in class org.biojava.nbio.structure.domain.RemotePDPProvider
DEFAULT_SERVER - Static variable in class org.biojava.nbio.structure.scop.RemoteScopInstallation
DEFAULT_SERVER_URL - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
DEFAULT_SERVERNAME - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
DEFAULT_SERVERNAME - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
DEFAULT_SUBSTITUTION_MATRIX - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
DEFAULT_SYMMETRY_THRESHOLD - Static variable in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathFactory
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.ecod.EcodFactory
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
delete(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable: Delete the key (and paired value) from table.
deleteStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Attempts to delete all versions of a structure from the local directory.
DELTA - Static variable in class org.biojava.nbio.structure.xtal.SpaceGroup
deltaComp(double, double, double) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
demo - package demo
DemoAsa - Class in demo
DemoAsa() - Constructor for class demo.DemoAsa
DemoAtomCache - Class in demo: Example of how to load PDB files using the AtomCache class.
DemoAtomCache() - Constructor for class demo.DemoAtomCache
DemoBerkeleyScop - Class in demo: A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP
DemoBerkeleyScop() - Constructor for class demo.DemoBerkeleyScop
DemoCATH - Class in demo: An example for how to access CATH data.
DemoCATH() - Constructor for class demo.DemoCATH
DemoCE - Class in demo: Example of how to run a structure alignment using the CE algorithm.
DemoCE() - Constructor for class demo.DemoCE
DemoCeSymm - Class in demo: Quick demo of how to call CE-Symm programmatically.
DemoCeSymm() - Constructor for class demo.DemoCeSymm
DemoChangeChemCompProvider - Class in demo: This demo shows how to use an alternative ChemCompProvider.
DemoChangeChemCompProvider() - Constructor for class demo.DemoChangeChemCompProvider
DemoCommandLineStartup - Class in demo
DemoCommandLineStartup() - Constructor for class demo.DemoCommandLineStartup
DemoContacts - Class in demo
DemoContacts() - Constructor for class demo.DemoContacts
DemoCrystalInterfaces - Class in demo
DemoCrystalInterfaces() - Constructor for class demo.DemoCrystalInterfaces
DemoDomainsplit - Class in demo
DemoDomainsplit() - Constructor for class demo.DemoDomainsplit
DemoFATCAT - Class in demo
DemoFATCAT() - Constructor for class demo.DemoFATCAT
DemoLoadSecStruc - Class in demo: Demonstration of how to load a Structure with the SS information, either from the PDB file annotation (Author's assignment) or from the DSSP file in the PDB servers (DSSP assignment).
DemoLoadSecStruc() - Constructor for class demo.DemoLoadSecStruc
DemoLoadStructure - Class in demo: Example for how to load protein structures (from PDB files).
DemoLoadStructure() - Constructor for class demo.DemoLoadStructure
DemoMMCIFReader - Class in demo: An example of how to read MMcif files
DemoMMCIFReader() - Constructor for class demo.DemoMMCIFReader
DemoMultipleMC - Class in demo: Demo for running the MultipleMC Algorithm on a protein family.
DemoMultipleMC() - Constructor for class demo.DemoMultipleMC
DemoSCOP - Class in demo: A class demonstrating the use of the SCOP parsing tools
DemoSCOP() - Constructor for class demo.DemoSCOP
DemoSecStrucCalc - Class in demo: Demonstration on how to use the Secondary Structure Prediction (DSSP) implementation in BioJava and obtain different SS representations and outputs.
DemoSecStrucCalc() - Constructor for class demo.DemoSecStrucCalc
deserialize(File) - Static method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
desFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
det() - Method in class org.biojava.nbio.structure.jama.LUDecomposition: Determinant
det() - Method in class org.biojava.nbio.structure.jama.Matrix: Matrix determinant
disableCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
dist - Variable in class org.biojava.nbio.structure.validation.Clash
dist - Variable in class org.biojava.nbio.structure.validation.SymmClash
DISTANCE_INCREMENT - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
DistanceBox<T> - Class in org.biojava.nbio.structure.symmetry.geometry
DistanceBox(double) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.DistanceBox: Creates a new instance of DistanceBox
distanceIncrement - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
DNA_ONLY - Static variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType: Convenience Set of polymer types classified as DNA.
doChainAfp(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer: // Key function: chain (assembly) the AFPs // a AFP (k) is defined as (i, j, k), with i and j are staring points // AFP extension (eg.
documentEnd() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
documentEnd() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer: called at end of document
documentEnd() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
documentStart() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
documentStart() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer: called at start of document
documentStart() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer: Start the parsing
doIter0(int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
doIter0(int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
Domain - Class in org.biojava.nbio.structure.domain.pdp
Domain() - Constructor for class org.biojava.nbio.structure.domain.pdp.Domain
domainDescriptionFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
domainListFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
DomainProvider - Interface in org.biojava.nbio.structure.domain: Decomposes a structure from the PDB into representative domains
DomainProviderFactory - Class in org.biojava.nbio.structure.domain: A simple factory object that returns the system wide default DomainProvider
DOMAINS_PATH - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
domallFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
doPOST(URL, String) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: do a POST to a URL and return the response stream for further processing elsewhere.
doPOST(URL, String, int) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: do a POST to a URL and return the response stream for further processing elsewhere.
doPOST(URL, String) - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: do a POST to a URL and return the response stream for further processing elsewhere.
doPrintConnections() - Method in class org.biojava.nbio.structure.io.FileConvert: Returns if the Connections should be added default is true;
dot(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseVector: Calculates the dot product of this vector a with b
DownloadChemCompProvider - Class in org.biojava.nbio.structure.io.mmcif: This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.
DownloadChemCompProvider() - Constructor for class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
DownloadChemCompProvider(String) - Constructor for class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
downloadClaFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
downloadComFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
downloadDesFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
downloadDomainDescriptionFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
downloadDomainListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
downloadDomallFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
downloadFile() - Static method in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider: Downloads the components.cif.gz file from the wwPDB site.
downloadFile(URL, File) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils: Download the content provided at URL url and store the result to a local file, using a temp file to cache the content in case something goes wrong in download
downloadFileFromRemote(URL, File) - Method in class org.biojava.nbio.structure.cath.CathInstallation
downloadFileFromRemote(URL, File) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
downloadHieFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
downloadingStructures(String) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener
downloadingStructures(String) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener
downloadNodeListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
downloadPDB(String) - Method in class org.biojava.nbio.structure.io.PDBFileReader: Deprecated.
downloadStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Downloads an MMCIF file from the PDB to the local path
DSSP_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo: Secondary strucuture parsed from a DSSP output file
DSSPParser - Class in org.biojava.nbio.structure.secstruc: Class to parse a DSSP file (output of the DSSP program), that contains the secondary structure assignment of a structure.
DSSPParser() - Constructor for class org.biojava.nbio.structure.secstruc.DSSPParser
duplicateCA2(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools: Utility method for working with circular permutations.
duplicationHint - Variable in class org.biojava.nbio.structure.align.ce.CECPParameters
duplicationHint - Variable in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

E

ECOD_RE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
ECOD_URL - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
EcodDatabase - Interface in org.biojava.nbio.structure.ecod: General API for interacting with CATH.
EcodDomain - Class in org.biojava.nbio.structure.ecod
EcodDomain() - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain: Default constructor with all null properties
EcodDomain(Long, String, Boolean, Integer, Integer, Integer, Integer, String, String, String, String, String, String, String, String, Long, Set<String>) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
EcodDomain(Long, String, Boolean, Integer, Integer, Integer, Integer, String, String, String, String, String, String, String, String, String, Long, Set<String>) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
EcodDomain(String) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
EcodDomain(EcodDomain) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
EcodFactory - Class in org.biojava.nbio.structure.ecod: Controls global CathDatabases being used.
EcodInstallation - Class in org.biojava.nbio.structure.ecod: Provides access to the Evolutionary Classification of Protein Domains (ECOD).
EcodInstallation(String, String) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation: Use EcodFactory to create instances.
EcodInstallation.EcodParser - Class in org.biojava.nbio.structure.ecod
EcodParser(String) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
EcodParser(File) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
EcodParser(Reader) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
EcodParser(BufferedReader) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
edsr - Variable in class org.biojava.nbio.structure.validation.Entry
edsResolution - Variable in class org.biojava.nbio.structure.validation.Entry
edsResolutionLow - Variable in class org.biojava.nbio.structure.validation.Entry
eig() - Method in class org.biojava.nbio.structure.jama.Matrix: Eigenvalue Decomposition
EigenvalueDecomposition - Class in org.biojava.nbio.structure.jama: Eigenvalues and eigenvectors of a real matrix.
EigenvalueDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.EigenvalueDecomposition: Check for symmetry, then construct the eigenvalue decomposition Structure to access D and V.
Element - Enum in org.biojava.nbio.structure: Element is an enumeration of the elements of the periodic table.
ElementType - Enum in org.biojava.nbio.structure: ElementType is an enumeration of the types of elements found in the periodic table.
enableCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
ENDS - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
ENDSEND - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
ensureClaInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
ensureComInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
ensureDesInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
ensureDomainDescriptionInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
ensureDomainListInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
ensureDomainsFileInstalled() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Blocks until ECOD domains file has been downloaded and parsed.
ensureDomallInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
ensureHieInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
ensureNodeListInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
ent - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
Entity - Class in org.biojava.nbio.structure.io.mmcif.model: A simple class to represent Entity records in mmCif files
Entity() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Entity
entity_poly_type - Variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType
EntityInfo - Class in org.biojava.nbio.structure: An object to contain the info from the PDB header for a Molecule.
EntityInfo() - Constructor for class org.biojava.nbio.structure.EntityInfo
EntityInfo(EntityInfo) - Constructor for class org.biojava.nbio.structure.EntityInfo: Constructs a new Compound copying all data from the given one but not setting the Chains
EntityPolySeq - Class in org.biojava.nbio.structure.io.mmcif.model: Container for _entity_poly_seq records
EntityPolySeq() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
EntitySrcGen - Class in org.biojava.nbio.structure.io.mmcif.model: Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated.
EntitySrcGen() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
EntitySrcNat - Class in org.biojava.nbio.structure.io.mmcif.model: Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural tissue.
EntitySrcNat() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
EntitySrcSyn - Class in org.biojava.nbio.structure.io.mmcif.model: PDBX_ENTITY_SRC_SYN records the details about each chemically synthesized molecule (entity) in the asymmetric unit.
EntitySrcSyn() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
Entry - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
Entry() - Constructor for class org.biojava.nbio.structure.validation.Entry
entry - Variable in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
entrySet() - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap: Always returns the empty set
equals(Object) - Method in class org.biojava.nbio.structure.align.client.PdbPair
equals(Object) - Method in class org.biojava.nbio.structure.align.client.StructureName
equals(Object) - Method in class org.biojava.nbio.structure.align.model.AFPChain: A week equality metric.
equals(Object) - Method in class org.biojava.nbio.structure.Author
equals(Object) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
equals(Object) - Method in class org.biojava.nbio.structure.contact.Pair
equals(Object) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
equals(Object) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
equals(Object) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
equals(Object) - Method in class org.biojava.nbio.structure.io.SSBondImpl
equals(PDBHeader) - Method in class org.biojava.nbio.structure.PDBHeader: Compare two PDBHeader objects
equals(Object) - Method in class org.biojava.nbio.structure.ResidueNumber
equals(Object) - Method in class org.biojava.nbio.structure.ResidueRange
equals(Object) - Method in class org.biojava.nbio.structure.ResidueRangeAndLength
equals(Object) - Method in class org.biojava.nbio.structure.scop.ScopDescription: Compares the fields sunID, category, classificationId, and name for equality
equals(Object) - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
equals(Object) - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc
equals(Object) - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
equals(Object) - Method in class org.biojava.nbio.structure.Site
equals(Object) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
equals(Object) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
EQUIVALENT_VERSIONS - Static variable in class org.biojava.nbio.structure.scop.BerkeleyScopInstallation: A map from SCOP version names which the Berkeley server offers as a download to an array of equivalent deprecated SCOP version names.
equivalentAxes(Matrix4d, Matrix4d, double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Determines if two symmetry axis are equivalent inside the error threshold.
execute(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative: This method uses iteratively CeSymm to calculate all symmetries in the input array of atoms and organize them in a multiple alignment of the repeats.
expandUserHome(String) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils: Expands ~ in paths to the user's home directory.
ExperimentalTechnique - Enum in org.biojava.nbio.structure: An enum to represent the experimental technique of a PDB structure
Exptl - Class in org.biojava.nbio.structure.io.mmcif.model
Exptl() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Exptl
extendFragments(Atom[], Atom[], JointFragments[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
extendFragments(Atom[], Atom[], JointFragments, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
extendHelix(int) - Method in class org.biojava.nbio.structure.symmetry.core.HelixExtender
extractAFPChains(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

F

F_UNCLASSIFIED - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser: String for unclassified F-groups
FarmJob - Class in org.biojava.nbio.structure.align: A job as it can be run on the farm.
FarmJob() - Constructor for class org.biojava.nbio.structure.align.FarmJob
FarmJobParameters - Class in org.biojava.nbio.structure.align.client
FarmJobParameters() - Constructor for class org.biojava.nbio.structure.align.client.FarmJobParameters
FarmJobRunnable - Class in org.biojava.nbio.structure.align.client: Contains the single thread for a job that can run multiple alignments.
FarmJobRunnable(FarmJobParameters) - Constructor for class org.biojava.nbio.structure.align.client.FarmJobRunnable
FastaAFPChainConverter - Class in org.biojava.nbio.structure.io: A collection of static utilities to convert between AFPChains and FastaSequences.
FastaAFPChainConverter() - Constructor for class org.biojava.nbio.structure.io.FastaAFPChainConverter
fastaFileToAfpChain(File, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Reads the file fastaFile, expecting exactly two sequences which give a pairwise alignment.
fastaStringToAfpChain(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
FastaStructureParser - Class in org.biojava.nbio.structure.io: Reads a protein sequence from a fasta file and attempts to match it to a 3D structure.
FastaStructureParser(InputStream, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
FastaStructureParser(File, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
FastaStructureParser(FastaReader<ProteinSequence, AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
fastaToAfpChain(Map<String, ProteinSequence>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Uses two sequences each with a corresponding structure to create an AFPChain corresponding to the alignment.
fastaToAfpChain(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: TODO Write comment
fastaToAfpChain(ProteinSequence, ProteinSequence, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>, AminoAcidCompound>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Provided only for convenience.
FatCat - Class in org.biojava.nbio.structure.align.fatcat
FatCat() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCat
FatCatAligner - Class in org.biojava.nbio.structure.align.fatcat.calc: A class that does calculations on an AFPChain
FatCatAligner() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
FatCatFlexible - Class in org.biojava.nbio.structure.align.fatcat
FatCatFlexible() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
FatCatParameters - Class in org.biojava.nbio.structure.align.fatcat.calc
FatCatParameters() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
FatCatRigid - Class in org.biojava.nbio.structure.align.fatcat
FatCatRigid() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatRigid
FatCatStartupParams() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
FatCatUserArgumentProcessor - Class in org.biojava.nbio.structure.align.fatcat
FatCatUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
FatCatUserArgumentProcessor.FatCatStartupParams - Class in org.biojava.nbio.structure.align.fatcat
FCAlignHelper - Class in org.biojava.nbio.structure.align.fatcat.calc
FCAlignHelper(double[][], int, int, double, double) - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper: do an alignment given the provided matrix sij0
fetch(String, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser: Fetch and parse the DSSP file of the specified pdb code from the PDB web server and return the secondary structure annotation as a List of SecStrucState objects.
FIELD_LINE - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
FileConvert - Class in org.biojava.nbio.structure.io: Methods to convert a structure object into different file formats.
FileConvert(Structure) - Constructor for class org.biojava.nbio.structure.io.FileConvert: Constructs a FileConvert object.
FileDownloadUtils - Class in org.biojava.nbio.structure.io.util
FileDownloadUtils() - Constructor for class org.biojava.nbio.structure.io.util.FileDownloadUtils
FileParsingParameters - Class in org.biojava.nbio.structure.io: A class that configures parameters that can be sent to the PDB file parsers FileParsingParameters.setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms FileParsingParameters.setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.
FileParsingParameters() - Constructor for class org.biojava.nbio.structure.io.FileParsingParameters
fileSeparator - Static variable in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
FILESPLIT - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
FILESPLIT - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
filterByCathCode(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return list of CATH descriptions whose CATH codes (e.g.
filterByCathCode(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
filterByClassificationId(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
filterByClassificationId(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
filterByClassificationId(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Get all scop descriptions that start with a classification ID, e.g.
filterByClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
filterByDescription(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return list of CATH descriptions whose descriptions (name field) starts with the query.
filterByDescription(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
filterByDescription(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Get all scop descriptions that start with a certain name.
filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
filterByDomainName(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
filterByDomainName(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
filterByDomainName(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: search through SCOP and filter based on domain name
filterByDomainName(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
filterByHierarchy(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase: Get a list of domains within a particular level of the hierarchy
filterByHierarchy(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Get a list of domains within a particular level of the hierarchy
filterByNodeName(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return list of CATH domains whose node name (e.g.
filterByNodeName(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain: Takes as input an AFPChain where ca2 has been artificially duplicated.
filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[], CECPParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
filterLigands(List<Group>) - Static method in class org.biojava.nbio.structure.StructureTools: Removes all polymeric and solvent groups from a list of groups
findChain(String) - Method in interface org.biojava.nbio.structure.Structure: Request a particular chain from a structure.
findChain(String, int) - Method in interface org.biojava.nbio.structure.Structure: Request a particular chain from a particular model
findChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl: Request a particular chain from a particular model
findChain(String) - Method in class org.biojava.nbio.structure.StructureImpl: Request a particular chain from a structure.
findCompounds() - Method in class org.biojava.nbio.structure.io.CompoundFinder: Utility method that employs some heuristics to find the Compounds for this Structure in case the information is missing in PDB/mmCIF file
findGroup(String, String) - Method in interface org.biojava.nbio.structure.Structure: Request a particular group from a structure.
findGroup(String, String, int) - Method in interface org.biojava.nbio.structure.Structure: Request a particular group from a structure.
findGroup(String, String, int) - Method in class org.biojava.nbio.structure.StructureImpl: Request a particular group from a structure.
findGroup(String, String) - Method in class org.biojava.nbio.structure.StructureImpl: Request a particular group from a structure.
finish(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
first_cut - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
flagLoading(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
flagLoadingFinished(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
flipAlignment(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser: Takes an XML representation of the alignment and flips the positions of name1 and name2
flipChain(AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainFlipper: Flip the position of name1 and name2 (as well as all underlying data) in an AFPChain.
flippableSidechain - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
floor(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable: Return the largest key in the table <= k.
flush() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile
flushCache() - Method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
flushCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
flushCache() - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
foFcCorrelation - Variable in class org.biojava.nbio.structure.validation.Entry
FORMAT_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier: URL parameter specifying the file format (PDB or CIF)
formBondsFromStructConn(List<StructConn>) - Method in class org.biojava.nbio.structure.io.BondMaker
formDisulfideBonds(List<SSBondImpl>) - Method in class org.biojava.nbio.structure.io.BondMaker: Creates disulfide bond objects and references in the corresponding Atoms objects, given a list of SSBondImpls parsed from a PDB/mmCIF file.
formLinkRecordBond(PDBTemporaryStorageUtils.LinkRecord) - Method in class org.biojava.nbio.structure.io.BondMaker: Creates bond objects from a LinkRecord as parsed from a PDB file
frag_pairwise_compat(FragmentPair[], int, float, int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner: Calculate the pairwise compatibility of fpairs.
FragmentJoiner - Class in org.biojava.nbio.structure.align.pairwise: Joins the initial Fragments together to larger Fragments
FragmentJoiner() - Constructor for class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
FragmentPair - Class in org.biojava.nbio.structure.align.pairwise: a pair of fragments of two protein structures
FragmentPair(int, int, int) - Constructor for class org.biojava.nbio.structure.align.pairwise.FragmentPair
fromAFP(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Converts a refined symmetry AFPChain alignment into the standard representation of symmetry in a MultipleAlignment, that contains the entire Atom array of the strcuture and the symmetric repeats are orgaized in different rows in a single Block.
fromCathCode(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory
fromCharacter(Character) - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType
fromCharacter(Character) - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType: Converts a Character representing a Secondary Structure type into the corresponding enum object.
fromConciseAlignmentString(String) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
fromMultiXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
fromStartupParams(StartupParameters) - Static method in class org.biojava.nbio.structure.align.util.UserConfiguration
fromString(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory
fromString(String) - Static method in enum org.biojava.nbio.structure.PDBStatus.Status
fromString(String) - Static method in class org.biojava.nbio.structure.ResidueNumber: Convert a string representation of a residue number to a residue number object.
fromString(String) - Static method in enum org.biojava.nbio.structure.scop.ScopCategory
fromXML(String, String, String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser: new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed
fromXML(String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
fromXML(String) - Method in class org.biojava.nbio.structure.align.xml.HasResultXMLConverter
fromXML(String) - Method in class org.biojava.nbio.structure.align.xml.PositionInQueueXMLConverter
fromXML(String) - Static method in class org.biojava.nbio.structure.align.xml.RepresentativeXMLConverter
fromXML(String) - Static method in class org.biojava.nbio.structure.domain.AssignmentXMLSerializer
fromXML(String) - Static method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
fromXML(String) - Static method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
fromXML(String) - Static method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
fromXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ListStringWrapper
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ScopDescriptions
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ScopDomains
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ScopNodes
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper
fromXML(String) - Static method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
fromXML(String) - Static method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

G

GAP_COVERAGE_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.CompoundFinder: Gap coverage value (num gaps over length of sequence) for each chain of the match: 2 chains with more gap coverage than this value will not be considered part of the same entity
GapArray - Class in org.biojava.nbio.structure.align.helper
GapArray() - Constructor for class org.biojava.nbio.structure.align.helper.GapArray
gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
get(Object) - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
get(int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Gets the interface corresponding to given id.
get(K) - Method in class org.biojava.nbio.structure.domain.SerializableCache
get(int, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Get a single element.
get(int, int) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix: access a value at i,j
get(int) - Method in class org.biojava.nbio.structure.math.SparseVector: get a value
get(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable: Return the value paired with given key; null if key is not in table.
get(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory
get(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory
get1LetterCode(String) - Static method in class org.biojava.nbio.structure.StructureTools: Convert a three letter amino acid or nucleotide code into a single character code.
get1LetterCodeAmino(String) - Static method in class org.biojava.nbio.structure.StructureTools: Convert three character amino acid codes into single character e.g.
GET_ASSEMBLY - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
GET_ASSEMBLY_GENS - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
GET_STRUCT_OPER - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getA() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
getA() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getAbsoluteMinimumSequenceLength() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getAbsolutePercentialRNAsuiteness() - Method in class org.biojava.nbio.structure.validation.Entry
getAbsolutePercentileClashscore() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the absolutePercentileClashscore property.
getAbsolutePercentileDCCRfree() - Method in class org.biojava.nbio.structure.validation.Entry
getAbsolutePercentilePercentRamaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the absolutePercentilePercentRamaOutliers property.
getAbsolutePercentilePercentRotaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the absolutePercentilePercentRotaOutliers property.
getAbsolutePercentilePercentRSRZOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the absolutePercentilePercentRSRZOutliers property.
getAbsorpt_coefficient_mu() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getAbsorpt_correction_T_max() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getAbsorpt_correction_T_min() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getAbsorpt_correction_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getAbsorpt_process_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getAccept1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getAccept2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getAcceptedAtomNames() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: By default the parser will read in all atoms (unless using the CAonly switch).
getAccessions() - Method in class org.biojava.nbio.structure.io.FastaStructureParser: Gets the protein accessions mapped from the Fasta file.
getAccessions() - Method in class org.biojava.nbio.structure.rcsb.RCSBMacromolecule
getAcentricOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the acentricOutliers property.
getAddress() - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
getAdjustedMinimumSequenceLength() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
getAfpAftIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpBefIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpChain() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
getAFPChainFromServer(String, String, String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
getAFPChainFromServer(String, String, String, String, Atom[], Atom[], int) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
getAfpChainLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpChainList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpChainTwiBin() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpChainTwiList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpChainTwiNum() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getAfpDisCut0() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getAfpIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpSet() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Get the set of AFPs for this alignment.
getAlgebraicFromMatrix(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
getAlgorithm() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
getAlgorithm() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getAlgorithm() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
getAlgorithm(String) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeCPMain
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeMain
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
getAlgorithmName() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getAlgorithmName() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner: Get the name of this Algorithm.
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
getAlgorithmName() - Method in interface org.biojava.nbio.structure.align.StructureAlignment: Get the name of the Algorithm
getAligMat() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getAligMat(int, int) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getAligMat() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getAlign(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay: Extract the alignment output
getAlign(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay: Sets the following properties: The alignment strings alnseq1, alnseq2, and alnsymb alnbeg1 and 2 alnLength and gapLen
getAlign_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getAlign_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getAlign_se1() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getAlign_se1() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getAlign_se2() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getAlign_se2() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getAlignedAtoms1(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
getAlignedAtoms2(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
getAlignedCalphaAtoms() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getAlignedResIndex(Group, Chain) - Method in class org.biojava.nbio.structure.EntityInfo: Given a Group g of Chain c (member of this Compound) return the corresponding position in the alignment of all member sequences (1-based numbering), i.e.
getAlignedStructure(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
getAlignedStructure(Structure, Structure) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: create an artifical Structure object that contains the two structures superimposed onto each other.
getAlignedUserCollection(String) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Takes a protein sequence string with capital and lowercase letters and sets its user collection to record which letters are uppercase (aligned) and which are lowercase (unaligned).
getAlignment() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
getAlignment1() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getAlignment2() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getAlignmentAtoms(Structure) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Returns the atoms that are being used for the alignment.
getAlignmentFractionThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getAlignmentLengthFraction() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
getAlignmentPairsFromServer() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable: talk to centralized server and fetch all alignments to run.
getAlignments() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getAlignments() - Method in class org.biojava.nbio.structure.align.StructurePairAligner: return the alternative alignments that can be found for the two structures
getAlignmentString() - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
getAlignPairs() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters: The file that contains a list of PDB pairs to be aligned
getAlignPos(int[][]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper: record the aligned pairs in alignList[][0], alignList[][1]; return the number of aligned pairs
getAlignRes() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Returns the double List containing the aligned residues for each structure.
getAlignRes() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getAlignScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlignScoreUpdate() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAll() - Static method in class org.biojava.nbio.structure.rcsb.GetRepresentatives: Returns the current list of all PDB IDs.
getAllAlgorithmNames() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
getAllAlgorithms() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
getAllAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Convert all atoms of the structure (first model) into an Atom array
getAllAtomArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Returns and array of all atoms of the chain (first model), including Hydrogens (if present) and all HETATOMs.
getAllDomains() - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase: Get all ECOD domains
getAllDomains() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Get all ECOD domains
getAllNonHAtomArray(Structure, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Returns and array of all non-Hydrogen atoms in the given Structure, optionally including HET atoms or not.
getAllNonHAtomArray(Chain, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Returns and array of all non-Hydrogen atoms in the given Chain, optionally including HET atoms or not Waters are not included.
getAllOxidationStates() - Method in enum org.biojava.nbio.structure.Element: Returns a list of all oxidation states the element is found in.
getAllPDBIDs() - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider: Returns a list of all PDB IDs that are available in this installation
getAllSpaceGroups() - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser
getAllViruses() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: Get the PDB IDs of all virus structures in the current PDB
getAlnbeg1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlnbeg2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlnLength() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlnseq1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlnseq2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlnsymb() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlpha() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
getAlpha() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getAlt_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getAltAligNumber() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: returns the sequential number of this alternative alignment
getAltcode() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the altcode property.
getAltLoc() - Method in interface org.biojava.nbio.structure.Atom: Get alternate Location.
getAltLoc() - Method in class org.biojava.nbio.structure.AtomImpl: Get alternate Location.
getAltLoc1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getAltLoc2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getAltLocGroup(Character) - Method in interface org.biojava.nbio.structure.Group: Gets the alternate location group to this group that has the alt-loc character code passed.
getAltLocGroup(Character) - Method in class org.biojava.nbio.structure.HetatomImpl
getAltLocs() - Method in interface org.biojava.nbio.structure.Group: Get the list of alternate locations.
getAltLocs() - Method in class org.biojava.nbio.structure.HetatomImpl
getAltShortSymbol() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets the alternative international short name (as sometimes used in PDB), e.g.
getAminoAcid(String) - Static method in class org.biojava.nbio.structure.StandardAminoAcid: get a standard amino acid.
getAminoOneLetter(String) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
getAminoThreeLetter(Character) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
getAminoType() - Method in interface org.biojava.nbio.structure.AminoAcid: Returns the name of the AA, in single letter code.
getAminoType() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Returns the name of the AA, in single letter code.
getAngle() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: The rotation angle
getAngle(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis: Calculate the rotation angle for a structure
getAngle(Matrix) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis: Calculate the rotation angle for a given matrix
getAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Helix: Returns the pitch angle of the helix
getAngle(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Returns the magnitude of the angle between the first and second blocks of afpChain, measured in degrees.
getAngle_alpha() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getAngle_alpha_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getAngle_beta() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getAngle_beta_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getAngle_gamma() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getAngle_gamma_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getAngleDiff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the angleOutlier property.
getAngleThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getAniso_B() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getArchitectureId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getArchitectureName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getArray() - Method in class org.biojava.nbio.structure.jama.Matrix: Access the internal two-dimensional array.
getArrayCopy() - Method in class org.biojava.nbio.structure.jama.Matrix: Copy the internal two-dimensional array.
getAsaC() - Method in class org.biojava.nbio.structure.asa.GroupAsa: Returns the ASA of the residue in the complexed state
getAsaU() - Method in class org.biojava.nbio.structure.asa.GroupAsa: Returns the ASA of the residue in the uncomplexed state
getAssembly_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
getAssemblyId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getAssignment() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
getAssignments() - Method in class org.biojava.nbio.structure.domain.AssignmentXMLSerializer
getAsym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getAsym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getAsym_id_list() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
getAsymmetryParameter(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getAsymUnit(String) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider: load the asym unit, but set the info how to re-create the bio unit in the PdbHeader object
getAsymUnit(String) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
getAsymUnit() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider: get the asym unit for this PDB ID
getAsymUnit(String) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
getAsymUnit(String) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
getAtcc() - Method in class org.biojava.nbio.structure.EntityInfo
getAtom(String) - Method in interface org.biojava.nbio.structure.Group: Get an atom given its PDB name.
getAtom(int) - Method in interface org.biojava.nbio.structure.Group: Get at atom by position.
getAtom(String) - Method in class org.biojava.nbio.structure.HetatomImpl: Get an atom given its PDB name.
getAtom(int) - Method in class org.biojava.nbio.structure.HetatomImpl: Get at atom by position.
getAtom() - Method in class org.biojava.nbio.structure.validation.Clash: Gets the value of the atom property.
getAtom() - Method in class org.biojava.nbio.structure.validation.SymmClash: Gets the value of the atom property.
getAtom0() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the atom0 property.
getAtom0() - Method in class org.biojava.nbio.structure.validation.BondOutlier: Gets the value of the atom0 property.
getAtom1() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the atom1 property.
getAtom1() - Method in class org.biojava.nbio.structure.validation.BondOutlier: Gets the value of the atom1 property.
getAtom2() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the atom2 property.
getAtom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getAtom_id_1() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getAtom_id_2() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getAtomA() - Method in interface org.biojava.nbio.structure.Bond: Gets atom 'A' of this bond.
getAtomA() - Method in class org.biojava.nbio.structure.BondImpl: Gets atom 'A' of this bond.
getAtomArray(Atom[], List<Group>, List<Group>) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
getAtomArray(Structure, String[]) - Static method in class org.biojava.nbio.structure.StructureTools: Returns an array of the requested Atoms from the Structure object.
getAtomArray(Chain, String[]) - Static method in class org.biojava.nbio.structure.StructureTools: Returns an array of the requested Atoms from the Chain object.
getAtomArrayAllModels(Structure, String[]) - Static method in class org.biojava.nbio.structure.StructureTools: Returns an array of the requested Atoms from the Structure object.
getAtomArrays() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the array of Atoms for each structure from its parent Ensemble.
getAtomArrays() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Get an array of representative atoms for each structure (CA atoms for proteins).
getAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getAtomAsaCs() - Method in class org.biojava.nbio.structure.asa.GroupAsa
getAtomAsaUs() - Method in class org.biojava.nbio.structure.asa.GroupAsa
getAtomB() - Method in interface org.biojava.nbio.structure.Bond: Gets atom 'B' of this bond.
getAtomB() - Method in class org.biojava.nbio.structure.BondImpl: Gets atom 'B' of this bond.
getAtomCAArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Returns an Atom array of the C-alpha atoms.
getAtomCAArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Return an Atom array of the C-alpha atoms.
getAtomCache() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getAtomCache() - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider
getAtomCache() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
getAtomCache() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getAtomCache() - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
getAtomCache() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
getAtomCaThreshold() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
getAtomContacts() - Method in class org.biojava.nbio.structure.contact.GroupContact
getAtomCoordinateBounds(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
getAtomForSequencePosition(MultipleAlignment, List<Integer>, int, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Returns the Atom of the specified structure that is aligned in the sequence alignment position specified.
getAtomGroup(int) - Method in interface org.biojava.nbio.structure.Chain: Return the Group at given position, from within Groups with observed density in the chain, i.e.
getAtomGroup(int) - Method in class org.biojava.nbio.structure.ChainImpl: Return the Group at given position, from within Groups with observed density in the chain, i.e.
getAtomGroups() - Method in interface org.biojava.nbio.structure.Chain: Return all Groups with observed density in the chain, i.e.
getAtomGroups(GroupType) - Method in interface org.biojava.nbio.structure.Chain: Return a List of all (observed) Groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
getAtomGroups(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl: Return a List of all (observed) Groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
getAtomGroups() - Method in class org.biojava.nbio.structure.ChainImpl: Return all Groups with observed density in the chain, i.e.
getAtomicMass() - Method in enum org.biojava.nbio.structure.Element: Returns the atomic mass for this Element.
getAtomicNumber() - Method in enum org.biojava.nbio.structure.Element: Returns the atomic number of this Element.
getAtomLength() - Method in interface org.biojava.nbio.structure.Chain: Returns the number of Groups with observed density in the chain, i.e.
getAtomLength() - Method in class org.biojava.nbio.structure.ChainImpl: Returns the number of Groups with observed density in the chain, i.e.
getAtomLigands() - Method in interface org.biojava.nbio.structure.Chain: Gets all groups that are not polymer groups and that are not solvent groups.
getAtomLigands() - Method in class org.biojava.nbio.structure.ChainImpl: Gets all groups that are not polymer groups and that are not solvent groups.
getAtoms(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the CA atoms for the provided name.
getAtoms(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache
getAtoms() - Method in interface org.biojava.nbio.structure.Group: Get list of atoms.
getAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl: Get list of atoms.
getAtoms() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getAtoms() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getAtoms() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the atoms property.
getAtoms() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the atoms property.
getAtomsCAInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools: Returns the set of intra-chain contacts for the given chain for C-alpha atoms (including non-standard aminoacids appearing as HETATM groups), i.e.
getAtomSequence() - Method in interface org.biojava.nbio.structure.Chain: Returns the sequence of amino acids as it has been provided in the ATOM records.
getAtomSequence() - Method in class org.biojava.nbio.structure.ChainImpl: Returns the sequence of amino acids as it has been provided in the ATOM records.
getAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
getAtomsInContact(Chain, String[], double) - Static method in class org.biojava.nbio.structure.StructureTools: Returns the set of intra-chain contacts for the given chain for given atom names, i.e.
getAtomsInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools: Returns the set of intra-chain contacts for the given chain for all non-H atoms of non-hetatoms, i.e.
getAtomsInContact(Chain, Chain, String[], double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Returns the set of inter-chain contacts between the two given chains for the given atom names.
getAtomsInContact(Chain, Chain, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Returns the set of inter-chain contacts between the two given chains for all non-H atoms.
getAtomSiteHeader() - Static method in class org.biojava.nbio.structure.io.FileConvert
getAttemptedValidationSteps() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the attemptedValidationSteps property.
getAuBoundingBox(int) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox: Get the AU BoundingBox for the given cell index (cellIdx=0 would be original AU) The AU BoundingBox is the BoundingBox that bounds all chains belonging to the AU
getAuth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getAuth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getAuth_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getAuth_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getAuth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getAuth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getAuth_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getAuth_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getAuth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getAuth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getAuth_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getAuth_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getAuthorList() - Method in class org.biojava.nbio.structure.JournalArticle: Get the list of Authors of the JournalArticle
getAuthors() - Method in class org.biojava.nbio.structure.PDBHeader: Return the names of the authors as listed in the AUTHORS section of a PDB file.
getAutoFetch() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration: Deprecated.
Use UserConfiguration.getFetchBehavior()
getAverageResidueDistances(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.
getAverageResidueDistances(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.
getAverageScore() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster: Returns the average similarity score between all pairs of members in the cluster
getAverageTraceRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Deprecated.
use QuatSymmetryResults.getScores() instead.
getAverageTraceTmScoreMin() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Deprecated.
use QuatSymmetryResults.getScores() instead.
getAvgoccu() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the avgoccu property.
getAvgTMScore(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the average TMScore of all the possible pairwise structure comparisons of the given alignment.
getAvgTMScore(List<Atom[]>, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the average TMScore all the possible pairwise structure comparisons of the given a set of superimposed Atoms and the original structure lengths.
getAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getAxisAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Helix: Returns the AxisAngle of the helix transformation
getAxisAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getAxisAngle(int, AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
getAxisAngle(int, AxisAngle4f) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
getAxisAngle(int, AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
getAxisAngle4d() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Returns the rotation axis and angle in a single javax.vecmath.AxisAngle4d object
getAxisFoldType(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Given a transformId returns the type of axis of rotation: 1 (no rotation), 2, 3, 4 or 6 -fold and for improper rotations: -1, -2, -3, -4 and -6
getAxisTypes() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getB() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
getB() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getB_iso_max() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getB_iso_mean() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getB_iso_min() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getB_iso_or_equiv() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getB_iso_or_equiv_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getBackboneAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Return an Atom array of the main chain atoms: CA, C, N, O Any group that contains those atoms will be included, be it a standard aminoacid or not
getBadRmsd() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getBaseIdentifier() - Method in class org.biojava.nbio.structure.align.client.StructureName: StructureName wraps another StructureIdentifier.
getBeta() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
getBeta() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getBinaryOperators() - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver: Returns a list of operators for this assembly.
getBioAssemblies() - Method in class org.biojava.nbio.structure.PDBHeader: Return the map of biological assemblies.
getBiojavaStruct(byte[], ParsingParams) - Method in class org.biojava.nbio.structure.io.mmtf.ParseUsingBioJava: Utility function to get a biojava structure from a byte array.
getBiol_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getBiolAssembly(String, int) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
getBiologicalAssembly(String, int, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Loads the biological assembly for a given PDB ID and bioAssemblyId.
getBiologicalAssembly(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Loads the default biological unit (e.g.
getBiologicalAssembly(String, int) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Loads the default biological unit (e.g.
getBiologicalAssembly(String) - Static method in class org.biojava.nbio.structure.StructureIO: Returns the first biologicalAssembly that is available for a protein structure.
getBiologicalAssembly(String, int) - Static method in class org.biojava.nbio.structure.StructureIO: By default the getStructure method loads asym units.
getBiologicalAssembly(String, int, AtomCache) - Static method in class org.biojava.nbio.structure.StructureIO
getBiologicalAssembly(String, int, AtomCache, BioUnitDataProvider) - Static method in class org.biojava.nbio.structure.StructureIO
getBiologicalMoleculeBounds(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
getBiologicalMoleculeCentroid(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools: Returns the centroid of the biological molecule.
getBiologicalMoleculeMaximumExtend(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools: Returns the maximum extend of the biological molecule in the x, y, or z direction.
getBiologicalUnit(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
Renamed to AtomCache.getBiologicalAssembly(String) in 4.2
getBiologicalUnit() - Method in class org.biojava.nbio.structure.EntityInfo
getBioUnitDataProvider() - Static method in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
getBioUnitDataProviderClass() - Static method in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory: Get the class of providers to be instantiated.
getBioUnitTransformationList(PdbxStructAssembly, List<PdbxStructAssemblyGen>, List<PdbxStructOperList>) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder: Returns a list of transformation matrices for the generation of a macromolecular assembly for the specified assembly Id.
getBioUnitTransformationList(String, int) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider: get the data for a particular assembly, counting starts at 1...
getBioUnitTransformationList(String, int) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
getBioUnitTransformationList(String, int) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
getBioUnitTransformationList(String, int) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
getBJSequence() - Method in interface org.biojava.nbio.structure.Chain: Converts the SEQRES groups of a Chain to a Biojava Sequence object.
getBJSequence() - Method in class org.biojava.nbio.structure.ChainImpl: Converts the SEQRES groups of a Chain to a Biojava Sequence object.
getBlock(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the Block with the specified index of the MultipleAlignment.
getBlock(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getBlock2Afp() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockForSequencePosition(MultipleAlignment, List<Integer>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Returns the block number of a specified position in the sequence alignment, given the mapping from structure to function.
getBlockGap() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockNrForAlignPos(AFPChain, int) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay: get the block number for an aligned position
getBlockNum() - Method in class org.biojava.nbio.structure.align.model.AFPChain: The number of blocks in the alignment
getBlockNumClu() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockNumIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockNumSpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockResList() - Method in class org.biojava.nbio.structure.align.model.AFPChain: tracks the residues of the initial blocks (before optimization)
getBlockResSize() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockRotationMatrix() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlocks() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Returns the List of alignment Blocks of the BlockSet.
getBlocks() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
getBlocks() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Convenience method to get a List of all Blocks from all BlockSets.
getBlocks() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getBlockScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockSequenceAlignment(MultipleAlignment, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
getBlockSequenceAlignment(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
getBlockSet() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Returns the parent BlockSet of the Block.
getBlockSet() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getBlockSet(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the BlockSet with the specified index of the MultipleAlignment.
getBlockSet(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getBlockSets() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the BlockSet List of the multiple structure alignment.
getBlockSets() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getBlockShiftVector() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockSize() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBondOrder() - Method in interface org.biojava.nbio.structure.Bond: Gets the bond order of this bond.
getBondOrder() - Method in class org.biojava.nbio.structure.BondImpl: Gets the bond order of this bond.
getBondOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the bondOutlier property.
getBonds() - Method in interface org.biojava.nbio.structure.Atom: Get all Bonds this atom is part of.
getBonds() - Method in class org.biojava.nbio.structure.AtomImpl: Get all Bonds this atom is part of.
getBonds() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getBravLattice() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getBridge1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getBridge2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getBsa() - Method in class org.biojava.nbio.structure.asa.GroupAsa: Returns the BSA value for this group, i.e.
getBsaToAsaRatio() - Method in class org.biojava.nbio.structure.asa.GroupAsa: Returns the bsa/asa(uncomplexed) ratio, i.e.
getBtype() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getBulkSolventB() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the bulkSolventB property.
getBulkSolventK() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the bulkSolventK property.
getByCategory(CathCategory) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return list of CATH descriptions for node representatives at a CATH category (e.g.
getByCategory(CathCategory) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getByCategory(ScopCategory) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Get all records of a particular classification.
getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getByChainId(String, String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
getByLargestContacts() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
getByLargestContactsNotLowestAngle() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
getByLowestAngle() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
getByName(String) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique: Returns the ExpTechnique given an experimental technique name as used in the PDB, e.g.
getByName(String) - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice
getByUniProtId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
getC() - Method in interface org.biojava.nbio.structure.AminoAcid: Get C atom.
getC() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Get C atom.
getC() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
getC() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getC2Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getC3Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getC4Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getCA() - Method in interface org.biojava.nbio.structure.AminoAcid: Get CA atom.
getCA() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Get CA atom.
getCa1() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
getCa1Length() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getCa2Length() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getCache() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
getCache() - Static method in class org.biojava.nbio.structure.align.util.CacheFactory
getCacheFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getCacheFilePath() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getCacheFilePath() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
getCacheLocation() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getCacheLocation() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Get the location of the cache directory (usually set to the PDB_CACHE_DIR property).
getCacheLocation() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getCachePath() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the path that contains the caching file for utility data, such as domain definitions.
getCalculationTime() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getCalculationTime() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the running time of the structure alignment calculation, in milliseconds.
getCalculationTime() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getCalculationTime() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getCalphaAtoms() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getCalphaCoordinates() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getCalphaCount() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getCalphaTraces() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getCalphaTraces() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
getCAOnly(List<Chain>) - Static method in class org.biojava.nbio.structure.io.CAConverter: Deprecated.
Use the more generic CAConverter.getRepresentativeAtomsOnly(List) instead
getCAOnly(Chain) - Static method in class org.biojava.nbio.structure.io.CAConverter: Deprecated.
Use the more generic CAConverter.getRepresentativeAtomsOnly(Chain) instead
getCartn_x() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getCartn_x_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getCartn_y() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getCartn_y_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getCartn_z() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getCartn_z_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getCategories() - Method in class demo.DemoSCOP: Get various categories
getCategory() - Method in class org.biojava.nbio.structure.cath.CathNode
getCategory() - Method in class org.biojava.nbio.structure.scop.ScopDescription
getCATH() - Method in class org.biojava.nbio.structure.cath.CathDomain
getCathDatabase() - Static method in class org.biojava.nbio.structure.cath.CathFactory: Returns the default (singleton) CathDatabase.
getCathDatabase(String) - Static method in class org.biojava.nbio.structure.cath.CathFactory: Returns a CATH database of the specified version.
getCathDownloadUrl() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getCathNode(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return the CathNode for a node ID.
getCathNode(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getCathVersion() - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return the CATH release version.
getCathVersion() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getCB() - Method in interface org.biojava.nbio.structure.AminoAcid: Get CB atom.
getCB() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Get CB atom.
getCCP4Version() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the ccp4Version property.
getCECalculator() - Method in class org.biojava.nbio.structure.align.ce.CeMain
getCell() - Method in class org.biojava.nbio.structure.EntityInfo
getCell_setting() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
getCellIndices(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Get the index of a unit cell to which the query point belongs.
getCellLine() - Method in class org.biojava.nbio.structure.EntityInfo
getCellTranslation(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getCellTranslations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getCellularLocation() - Method in class org.biojava.nbio.structure.EntityInfo
getCenter(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools: get the centroid for the set of atoms starting fromposition pos, length fragmentLenght
getCenter1() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getCenter2() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getCenters() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getCenterVector(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Returns the Vector that needs to be applied to shift a set of atoms to the Centroid.
getCenterVector(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc: Returns the Vector that needs to be applied to shift a set of atoms to the Centroid, if the centroid is already known
getCentricOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the centricOutliers property.
getCentroid(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Returns the center of mass of the set of atoms.
getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getChain() - Method in interface org.biojava.nbio.structure.Group: Returns the parent Chain of the Group.
getChain() - Method in class org.biojava.nbio.structure.HetatomImpl: Returns the parent Chain of the Group.
getChain(int) - Method in interface org.biojava.nbio.structure.Structure: Retrieve a chain by its position within the Structure .
getChain(int, int) - Method in interface org.biojava.nbio.structure.Structure: Retrieve a chain by its position within the Structure and model number.
getChain(int) - Method in class org.biojava.nbio.structure.StructureImpl: Retrieve a chain by its position within the Structure .
getChain(int, int) - Method in class org.biojava.nbio.structure.StructureImpl: Retrieve a chain by its position within the Structure and model number.
getChain() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the chain property.
getChain1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getChain2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getChainBoundingBox(int, int) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox: Get the chain BoundingBox for the given cell index (cellIdx=0 would be original AU) and chain index
getChainByPDB(String) - Method in interface org.biojava.nbio.structure.Structure: Request a chain by its PDB code by default takes only the first model
getChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure: Request a chain by its PDB code by default takes only the first model
getChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl: Request a chain by its PDB code by default takes only the first model
getChainByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl: Request a chain by its PDB code by default takes only the first model
getChainId() - Method in class org.biojava.nbio.structure.align.client.StructureName: Gets the chain ID, for structures where it is unique and well-defined.
getChainID() - Method in interface org.biojava.nbio.structure.Chain: Gets the name of this chain (Chain id in PDB file ).
getChainID() - Method in class org.biojava.nbio.structure.ChainImpl: Gets the name of this chain (Chain id in PDB file ).
getChainId() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
getChainId() - Method in class org.biojava.nbio.structure.DBRef: The chain ID of the corresponding chain.
getChainId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getChainId() - Method in interface org.biojava.nbio.structure.Group: Utility method for returning the chainId of the Group or null if no Chain has been set.
getChainId() - Method in class org.biojava.nbio.structure.HetatomImpl: Utility method for returning the chainId of the Group or null if no Chain has been set.
getChainId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getChainId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getChainId() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Returns the chain identifier this transformation should be applied to.
getChainId() - Method in class org.biojava.nbio.structure.ResidueNumber
getChainId() - Method in class org.biojava.nbio.structure.ResidueRange
getChainId() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getChainId1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getChainID1() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getChainID1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getChainId2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getChainID2() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getChainID2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getChainIds() - Method in class org.biojava.nbio.structure.EntityInfo: Return the list of member chain IDs that are described by this Compound, only unique chain IDs are contained in the list.
getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getChainIds() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
getChainIdsInEntry(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
getChainLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getChainRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getChains() - Method in class org.biojava.nbio.structure.cath.CathDomain: Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
getChains() - Method in class org.biojava.nbio.structure.EntityInfo: Get the list of chains that are part of this Compound.
getChains() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getChains() - Method in class org.biojava.nbio.structure.scop.ScopDomain: Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
getChains() - Method in interface org.biojava.nbio.structure.Structure: Retrieve all chains - if it is a NMR structure will return the chains of the first model.
getChains(int) - Method in interface org.biojava.nbio.structure.Structure: Retrieve all chains of a model.
getChains(int) - Method in class org.biojava.nbio.structure.StructureImpl: retrieve all chains of a model.
getChains() - Method in class org.biojava.nbio.structure.StructureImpl: Retrieve all chains - if it is a NMR structure will return the chains of the first model.
getCharge() - Method in interface org.biojava.nbio.structure.Atom: Get the charge of this atom
getCharge() - Method in class org.biojava.nbio.structure.AtomImpl
getCharge() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getChemComp() - Method in interface org.biojava.nbio.structure.Group: Get the chemical component that closer describes this group.
getChemComp() - Method in class org.biojava.nbio.structure.HetatomImpl
getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider: Returns a new instance of a chemical component definition.
getChemComp(String) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
getChemComp(String) - Method in interface org.biojava.nbio.structure.io.mmcif.ChemCompProvider: Returns a new instance of a chemical component definition.
getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider: Loads the definitions for this ChemComp from a local file and instantiates a new object.
getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider
getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider
getChemCompProvider() - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
getChildren() - Method in class org.biojava.nbio.structure.scop.ScopNode
getCid() - Method in class org.biojava.nbio.structure.validation.Clash: Gets the value of the cid property.
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron: Returns the radius of a circumscribed sphere, that goes through all vertices
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron: Returns the radius of a circumscribed sphere, that goes through all vertices
getCirumscribedRadius() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism: Returns the radius of a circumscribed sphere, that goes through all vertices
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism: Returns the radius of a circumscribed sphere (length of diagonal of rectangular prism/2, that goes through at least four vertices
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron: Returns the radius of a circumscribed sphere, that goes through all vertices
getClaFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getClash() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the clash property.
getClashmag() - Method in class org.biojava.nbio.structure.validation.Clash: Gets the value of the clashmag property.
getClashmag() - Method in class org.biojava.nbio.structure.validation.SymmClash: Gets the value of the clashmag property.
getClashscore() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the clashscore property.
getClassId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getClassId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getClassification() - Method in class org.biojava.nbio.structure.PDBHeader
getClassificationId(CathCategory) - Method in class org.biojava.nbio.structure.cath.CathDomain
getClassificationId() - Method in class org.biojava.nbio.structure.scop.ScopDescription
getClassificationId(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopDescription: Return a portion of the classificationID corresponding to the specified category (class, fold, superfamily, family).
getClassificationId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getClaURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
getCluster() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: get the number of the cluster this alignment belongs to
getCluster() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getCluster() - Method in class org.biojava.nbio.structure.contact.StructureInterface
getCluster1() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
getCluster2() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
getClusters() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Calculate the interface clusters for this StructureInterfaceList using a contact overlap score to measure the similarity of interfaces.
getClusters(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Calculate the interface clusters for this StructureInterfaceList using a contact overlap score to measure the similarity of interfaces.
getCode() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
getCol() - Method in class org.biojava.nbio.structure.align.helper.IndexPair
getCols() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getCols() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getColumnDimension() - Method in class org.biojava.nbio.structure.jama.Matrix: Get column dimension.
getColumnPackedCopy() - Method in class org.biojava.nbio.structure.jama.Matrix: Make a one-dimensional column packed copy of the internal array.
getComFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getComment() - Method in class org.biojava.nbio.structure.cath.CathDomain
getComments(int) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getComments(int) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getComments(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Get comments about a SCOP domain by its sunid
getComments(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getCommentsFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getCommentsXML(List<String>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getCommon_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getCommonValence() - Method in enum org.biojava.nbio.structure.Element: Returns the common valence for this Element.
getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
getComplexSignature() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
getComplexStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
getCompositionId() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
getCompositionId(String) - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
getCompound() - Method in interface org.biojava.nbio.structure.Chain: Returns the Compound for this chain.
getCompound() - Method in class org.biojava.nbio.structure.ChainImpl: Returns the Compound for this chain.
getCompoundById(int) - Method in interface org.biojava.nbio.structure.Structure: Request a particular compound by its molId (entity_id in mmCIF dictionary)
getCompoundById(int) - Method in class org.biojava.nbio.structure.StructureImpl: Request a particular compound by its molId (entity_id in mmCIF dictionary)
getComURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
getConn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getConn_type_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getConnectedFrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getConnectedTo() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getConnections() - Method in interface org.biojava.nbio.structure.Structure: Deprecated.
use Atom.getBonds() instead
getConnections() - Method in class org.biojava.nbio.structure.StructureImpl: Return the connections value.
getContact(Atom, Atom) - Method in class org.biojava.nbio.structure.contact.AtomContactSet: Returns the corresponding AtomContact or null if no contact exists between the 2 given atoms
getContact(Group, Group) - Method in class org.biojava.nbio.structure.contact.GroupContactSet: Returns the corresponding GroupContact or null if no contact exists between the 2 given groups
getContactOverlapScore(StructureInterface, boolean) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Calculates the contact overlap score between this StructureInterface and the given one.
getContacts() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getContacts() - Method in class org.biojava.nbio.structure.contact.Grid: Returns all contacts, i.e.
getContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface
getContacts() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getContactsToOtherCell(GridCell, Atom[], Atom[], double) - Method in class org.biojava.nbio.structure.contact.GridCell: Calculates all distances of atoms between this cell and the given cell returning those that are within the given cutoff as a list of AtomContacts
getContactsWithinCell(Atom[], Atom[], double) - Method in class org.biojava.nbio.structure.contact.GridCell: Calculates all distances of atoms within this cell returning those that are within the given cutoff as a list of AtomContacts
getContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContactSet: Returns the list of contacts from this set that are within the given distance.
getContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.GroupContact: Returns the list of atom contacts in this GroupContact that are within the given distance.
getContig() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
getConvergenceSteps() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getCoordpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getCoords() - Method in interface org.biojava.nbio.structure.Atom: Get the coordinates.
getCoords() - Method in class org.biojava.nbio.structure.AtomImpl: Get the coordinates.
getCoreElectronCount() - Method in enum org.biojava.nbio.structure.Element: Returns the number of core electrons for this Element.
getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Returns the number of aligned positions (columns) without gaps in the Block.
getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all Block core lengths.
getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all BlockSet core lengths.
getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getCorePositions(Block) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate a List of alignment indicies that correspond to the core of a Block, which means that all structures have a residue in that positon.
getCoreResidues(double, double) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns the residues belonging to the interface core, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is above the given bsaToAsaCutoff
getCorrelation_coeff_Fo_to_Fc() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getCorrelation_coeff_Fo_to_Fc_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getCovalentRadius() - Method in enum org.biojava.nbio.structure.Element: Returns the covalent radius of this Element.
getCoverage1() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Get the coverage of protein 1 with the alignment
getCoverage2() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Get the coverage of protein 2 with the alignment
getCovered() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getCPPoint() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
getCreate_co() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getCrystalCell() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo: Return the crystal cell
getCrystalIds() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns a pair of identifiers for each of the 2 member molecules that identify them uniquely in the crystal: <molecule id (asym unit id)>+<operator id>+<crystal translation>
getCrystallographicInfo() - Method in class org.biojava.nbio.structure.PDBHeader
getCrystallographicInfo() - Method in interface org.biojava.nbio.structure.Structure: Get crystallographic information for this structure
getCrystallographicInfo() - Method in class org.biojava.nbio.structure.StructureImpl: Gets crystallographic information for this structure
getCrystals_number() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getCrystalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
getCurrent(String) - Static method in class org.biojava.nbio.structure.PDBStatus: Gets the current version of a PDB ID.
getCurrentChain() - Method in class org.biojava.nbio.structure.AtomIterator: Get the chain that contains the current atom.
getCurrentChain() - Method in class org.biojava.nbio.structure.GroupIterator: Get the current Chain.
getCurrentModel() - Method in class org.biojava.nbio.structure.AtomIterator: Get the model number of the model containing the current atom.
getCurrentModel() - Method in class org.biojava.nbio.structure.GroupIterator: Get the model number of the current model.
getCurrentPDBIds() - Static method in class org.biojava.nbio.structure.PDBStatus: Returns a list of current PDB IDs
getCurrentPDBIds() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: get the list of current PDB IDs
getCustomChain1() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getCustomFile1() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getCut_sites() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
getCutoff() - Method in class org.biojava.nbio.structure.contact.Grid
getD() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition: Return the block diagonal eigenvalue matrix
getData() - Method in class org.biojava.nbio.structure.scop.server.ListStringWrapper
getData() - Method in class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper
getData() - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
getDataAnisotropy() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the dataAnisotropy property.
getDatabase() - Method in class org.biojava.nbio.structure.DBRef: The database of the db-ref.
getDataCompleteness() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the dataCompleteness property.
getDate() - Method in class org.biojava.nbio.structure.cath.CathDomain
getDate() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
getDate_original() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
getDb_align_beg() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getDb_align_end() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getDb_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getDb_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getDb_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getDbAccession() - Method in class org.biojava.nbio.structure.DBRef: Sequence database accession code.
getDbIdCode() - Method in class org.biojava.nbio.structure.DBRef: Sequence database identification code.
getDBRefs() - Method in interface org.biojava.nbio.structure.Structure: Get the list of database references
getDBRefs() - Method in class org.biojava.nbio.structure.StructureImpl: Get the list of database references
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
getDBSearchParameters() - Static method in class org.biojava.nbio.structure.align.StrucAligParameters
getDbSearchResult(AFPChain) - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
getDbSeqBegin() - Method in class org.biojava.nbio.structure.DBRef: Initial sequence number of the database seqment.
getDbSeqEnd() - Method in class org.biojava.nbio.structure.DBRef: Ending sequence position of the database segment.
getDCCR() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the dccr property.
getDCCRefinementProgram() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the dccRefinementProgram property.
getDCCRfree() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the dccRfree property.
getDefaultParameters() - Static method in class org.biojava.nbio.structure.align.StrucAligParameters
getDelta() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getDensityCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getDepDate() - Method in class org.biojava.nbio.structure.PDBHeader
getDescription() - Method in class org.biojava.nbio.structure.cath.CathNode
getDescription() - Method in class org.biojava.nbio.structure.EntityInfo
getDescription() - Method in class org.biojava.nbio.structure.PDBHeader
getDescription() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getDescription() - Method in class org.biojava.nbio.structure.scop.ScopDescription
getDescription() - Method in class org.biojava.nbio.structure.Site: gets the REMARK 800 description of the site
getDescription2() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Get a textual description for the protein 2 of the alignment.
getDescriptionByCathId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return CATH description for CATH domain ID.
getDescriptionByCathId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDescriptionByNodeId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return CATH description for node representative by node ID.
getDescriptionByNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDescriptor() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
getDescriptors() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getDesFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getDesURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
getDetails() - Method in class org.biojava.nbio.structure.EntityInfo
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getDetails() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getDetails() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getDiagonalAtK(Atom[], int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools
getDiagonalDistance() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getDiagonalDistance2() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getDictionary() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
getDimension() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getDimension() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getDimension() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getDimensions() - Method in class org.biojava.nbio.structure.contact.BoundingBox: Returns the dimensions of this bounding box.
getDir(String, boolean) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Gets the directory in which the file for a given MMCIF file would live, creating it if necessary.
getDirection() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters: Get the distance cutoff used during AFP chain connectivity checks
getDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
getDisFilter() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getDisSmooth() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getDist() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
getDist() - Method in class org.biojava.nbio.structure.validation.Clash: Gets the value of the dist property.
getDist() - Method in class org.biojava.nbio.structure.validation.SymmClash: Gets the value of the dist property.
getDist1() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getDist1() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getDist2() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getDist2() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getDisTable1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getDisTable2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getDistance(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: calculate distance between two atoms.
getDistance() - Method in class org.biojava.nbio.structure.contact.AtomContact
getDistanceCutoff() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getDistanceCutoff() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getDistanceFast(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: Will calculate the square of distances between two atoms.
getDistanceIncrement() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools: Matrix of all distances between two sets of Atoms.
getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.model.AFPChain: A matrix with ca1length rows and ca2length columns.
getDistanceMatrix() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the List containing the interatomic distance Matrix of each structure.
getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: The distance matrix this alignment is based on
GetDistanceMatrix - Class in org.biojava.nbio.structure.domain.pdp
GetDistanceMatrix() - Constructor for class org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix
getDistanceMatrix(Atom[]) - Method in class org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix: A set of Calpha atoms that are representing the protein
getDistMat() - Method in class org.biojava.nbio.structure.align.StructurePairAligner: return the difference of distance matrix between the two structures
getDkMatrix(Atom[], Atom[], int, double[], double[], int, int) - Method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
getDkMatrix(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
getDNAOneLetter(String) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
getDNATwoLetter(Character) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
getDoi() - Method in class org.biojava.nbio.structure.JournalArticle: Get the value of DOI field.
getDomain(String, AtomCache) - Method in interface org.biojava.nbio.structure.domain.PDPProvider: Get the structure for a particular PDP domain
getDomain(String, AtomCache) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider: Get the structure for a particular PDP domain
getDomainByCathId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return CATH domain for CATH domain ID.
getDomainByCathId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDomainByScopID(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getDomainByScopID(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getDomainByScopID(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
getDomainByScopID(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getDomainCounter() - Method in class org.biojava.nbio.structure.cath.CathDomain
getDomainDescriptionFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDomainId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getDomainId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getDomainId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getDomainListFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDomainName() - Method in class org.biojava.nbio.structure.cath.CathDomain
getDomainNames(String) - Method in interface org.biojava.nbio.structure.domain.DomainProvider: Get a list of constituent domain identifiers
getDomainNames(String) - Method in class org.biojava.nbio.structure.domain.PDBDomainProvider: Gets a list of domain representatives for a given PDB ID.
getDomainNames(String) - Method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
getDomainProvider() - Static method in class org.biojava.nbio.structure.domain.DomainProviderFactory
getDomainRangesFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getDomainRangesXML(SortedSet<String>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getDomains() - Method in class org.biojava.nbio.structure.domain.pdp.CutDomain
getDomains() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
getDomainsById(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase: Get a particular ECOD domain by the domain ID (e.g.
getDomainsById(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Get a particular ECOD domain by the domain ID (e.g.
getDomainsByNodeId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return all CATH domains for a particular CATH node.
getDomainsByNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDomainsForPdb(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return all CATH domains for a PDB ID.
getDomainsForPdb(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDomainsForPdb(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase: Get a list of all ECOD domains for a particular PDB ID
getDomainsForPdb(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: public EcodInstallation(String cacheLocation) { this( cacheLocation, DEFAULT_VERSION ); } /** Get a list of all ECOD domains for a particular PDB ID
getDomainsForPDB(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getDomainsForPDB(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getDomainsForPDB(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Get a list of ScopDomains that have been assigned to a PDB ID
getDomainsForPDB(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getDomainsFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getDomainsXML(SortedSet<Domain>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getDomallFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDonor1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getDonor2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getDoublePivot() - Method in class org.biojava.nbio.structure.jama.LUDecomposition: Return pivot permutation vector as a one-dimensional double array
getDuplicationHint() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
getDuplicationHint() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
getDVar() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getEcNums() - Method in class org.biojava.nbio.structure.EntityInfo
getEcodDatabase() - Static method in class org.biojava.nbio.structure.ecod.EcodFactory: Returns the (singleton) database for the current default version
getEcodDatabase(String) - Static method in class org.biojava.nbio.structure.ecod.EcodFactory
getEditorList() - Method in class org.biojava.nbio.structure.JournalArticle: Get the list of editors of the JournalArticle
getEDSR() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the edsr property.
getEDSResolution() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the edsResolution property.
getEDSResolutionLow() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the edsResolutionLow property.
getElement() - Method in interface org.biojava.nbio.structure.Atom: Get element of the atom, e.g.
getElement() - Method in class org.biojava.nbio.structure.AtomImpl: Get element of the atom, e.g.
getElement1() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair
getElement2() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair
getElementaryAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes: Return all elementary axes of symmetry of the structure, that is, the axes stored in the List as unique and from which all the symmetry axes are constructed.
getElementFromHillIndex(int) - Static method in enum org.biojava.nbio.structure.Element: Returns the Element that corresponds to the specified Hill Order.
getElementType() - Method in enum org.biojava.nbio.structure.Element: Returns the Element Type for this Element.
getElipsisRadii() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getEmptyChemComp() - Static method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp: Creates a new instance of the dummy empty ChemComp.
getEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
getEnd() - Method in class org.biojava.nbio.structure.ResidueRange
getEnergy() - Method in class org.biojava.nbio.structure.secstruc.HBond
getEngineered() - Method in class org.biojava.nbio.structure.EntityInfo
getEnsemble() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the parent Ensemble of the MultipleAlignment.
getEnsemble() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getEnt() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the ent property.
getEntities() - Method in class org.biojava.nbio.structure.io.sifts.SiftsXMLParser
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getEntityId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
getEntityInformation() - Method in interface org.biojava.nbio.structure.Structure: Get all the Compounds for this Structure.
getEntityInformation() - Method in class org.biojava.nbio.structure.StructureImpl: Get all the Compounds for this Structure.
getEntry() - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation: Gets the value of the entry property.
getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
getEnumValuesAsString(Class<T>) - Static method in class org.biojava.nbio.structure.align.util.CliTools: Constructs a comma-separated list of values for an enum.
getEnzClass() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getEqr() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: returns the number of euqivalent residues in this alignment
getEvalCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getEvCode() - Method in class org.biojava.nbio.structure.Site: gets the REMARK 800 EVIDENCE CODE for the site.
getExampleUnitCell() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
getExperimentalTechniques() - Method in class org.biojava.nbio.structure.PDBHeader: Return the Set of ExperimentalTechniques, usually the set is of size 1 except for hybrid experimental techniques when the Set will contain 2 or more values
getExpression_system_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getExpressionSystem() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemAtccNumber() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemCell() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemCellLine() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemCellularLocation() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemGene() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemOrgan() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemOrganelle() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemOtherDetails() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemPlasmid() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemStrain() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemTaxId() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemTissue() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemVariant() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemVector() - Method in class org.biojava.nbio.structure.EntityInfo
getExpressionSystemVectorType() - Method in class org.biojava.nbio.structure.EntityInfo
getExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
getExtensions() - Method in interface org.biojava.nbio.structure.io.StructureIOFile: Returns a list of extensions supported by this class
getExtensions() - Method in enum org.biojava.nbio.structure.StructureIO.StructureFiletype
getFailedLines() - Method in class org.biojava.nbio.structure.scop.Astral: Gets a map describing lines read in the file that weren't understood.
getFamilyId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getFatCatAligner() - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
getFetchBehavior() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Get the behavior for fetching files from the server
getFetchBehavior() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
getFetchBehavior() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Get the behavior for fetching files from the server
getFGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getFGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getFile1() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getFile2() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getFileExtension(File) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils
getFileFormat() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
getFilename(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Converts a PDB ID into a filename with the proper extension
getFilename(String) - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
getFilename(String) - Method in class org.biojava.nbio.structure.io.PDBFileReader
getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
getFileParsingParameters() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.PDBFileParser
getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
getFileParsingParameters() - Method in interface org.biojava.nbio.structure.io.StructureProvider: Get the parameters that should be used for file parsing
getFileParsingParams() - Method in class org.biojava.nbio.structure.align.util.AtomCache
getFilePrefix(File) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils
getFinalIndex(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block: Calculates and returns the last position of the specified structure in the alignment that is not null.
getFinalIndex(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getFinalResidue(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block: Calculates and returns the last residue of the specified structure in the alignment that is not null.
getFinalResidue(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getFirst(String) - Method in class org.biojava.nbio.structure.AtomPositionMap
getFirst() - Method in class org.biojava.nbio.structure.AtomPositionMap
getFirst() - Method in class org.biojava.nbio.structure.contact.Pair
getFirstAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
getFirstGroupAsa(ResidueNumber) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Gets the GroupAsa for the corresponding residue number of first chain
getFirstGroupAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Gets a map of ResidueNumbers to GroupAsas for all groups of first chain.
getFlippableSidechain() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the flippableSidechain property.
getFocusAfpList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getFocusAfpn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getFocusRes1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getFocusRes2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getFocusResn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getFoFcCorrelation() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the foFcCorrelation property.
getFold() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getFold() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getFoldId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getFolds() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer: Get valid symmetry order for this stoichiometry.
getFolds() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getFoldType() - Method in enum org.biojava.nbio.structure.xtal.TransformType
getFormat() - Method in class org.biojava.nbio.structure.cath.CathDomain
getFormula() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getFormula() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getFormula_weight() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getFormula_weight() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getFragCompat() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getFragLen() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getFragLen() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
getFragLen() - Method in class org.biojava.nbio.structure.align.model.AFP
getFragLenSq() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getFragment(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools: get a continue subset of Atoms based by the starting position and the length
getFragment() - Method in class org.biojava.nbio.structure.EntityInfo
getFragmentFromIdxList(Atom[], int[]) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools: get a subset of Atoms based by their positions
getFragmentId() - Method in class org.biojava.nbio.structure.cath.CathFragment
getFragmentLength() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getFragmentMiniDistance() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getFragmentNoClone(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools: get a continue subset of Atoms based by the starting position and the length does not clone the original atoms.
getFragmentPairs() - Method in class org.biojava.nbio.structure.align.StructurePairAligner: get the results of step 1 - the FragmentPairs used for seeding the alignment
getFragmentsByPdbId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
getFragmentsByPdbId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getFragScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getFrom() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
getFrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getFromHeteroAtomId(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromHeteroAtomId(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromHeteroAtomIds(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromHeteroAtomIds(List<String>) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromHeteroAtomIds(String...) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromPdbId(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromPdbId(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromPdbIds(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromPdbIds(List<String>) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromPdbIds(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromPdbIds(String...) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFullAtomSequence(List<Group>, Map<Integer, Integer>, boolean) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner: Returns the full sequence of the Atom records of a parent with X instead of HETATMSs.
getFullMatrix() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Returns a matrix that describes both rotation and translation.
getGagPolyproteins() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: get all PDB IDs of gag-polyproteins
getGamma() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
getGamma() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getGapCreate() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getGapExtCol() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getGapExtCol() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getGapExtend() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getGapExtend() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
getGapExtend() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
getGapExtension() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getGapExtension() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
getGapExtension() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getGapExtension() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getGapExtRow() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getGapExtRow() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getGapLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getGapOpen() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getGapOpen() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
getGapOpen() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getGapOpen() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
getGapOpen() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
getGapOpen() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getGapOpenCol() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getGapOpenCol() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getGapOpenRow() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getGapOpenRow() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getGaps() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: return the number of gaps in this alignment
getGene() - Method in class org.biojava.nbio.structure.EntityInfo
getGene_src_common_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_dev_stage() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_genus() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_species() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_strain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_tissue() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_tissue_fraction() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGenus() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner: Returns a transformation matrix transform polyhedra for Cn structures.
getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner: Returns a transformation matrix transform polyhedra for Cn structures.
getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner: Returns the geometric center of polyhedron.
getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner: Returns the geometric center of polyhedron.
getGlobalSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Returns list of global quaternary structure symmetry results
getGroup() - Method in class org.biojava.nbio.structure.asa.GroupAsa
getGroup() - Method in interface org.biojava.nbio.structure.Atom: Return the parent Group of the Atom.
getGroup() - Method in class org.biojava.nbio.structure.AtomImpl: Return the parent Group of the Atom.
getGroup() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
getGroup_PDB() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getGroupAsas() - Method in class org.biojava.nbio.structure.asa.AsaCalculator: Calculates ASA for all atoms and return them as a GroupAsa array (one element per residue in structure) containing ASAs per residue and per atom.
getGroupByPDB(ResidueNumber) - Method in interface org.biojava.nbio.structure.Chain: Get a group by its PDB residue numbering.
getGroupByPDB(ResidueNumber) - Method in class org.biojava.nbio.structure.ChainImpl: Get a group by its PDB residue numbering.
getGroupByPDBResidueNumber(Structure, ResidueNumber) - Static method in class org.biojava.nbio.structure.StructureTools: Get a group represented by a ResidueNumber.
getGroupContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface
getGroupDistancesWithinShell(Structure, Atom, Set<ResidueNumber>, double, boolean, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Finds Groups in structure that contain at least one Atom that is within radius Angstroms of centroid.
getGroupFromChemCompDictionary(String) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
getGroups() - Method in class org.biojava.nbio.structure.Site
getGroups(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Returns the List of Groups of the corresponding representative Atom array.
getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in interface org.biojava.nbio.structure.Chain: Get all groups that are located between two PDB residue numbers.
getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in interface org.biojava.nbio.structure.Chain: Get all groups that are located between two PDB residue numbers.
getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in class org.biojava.nbio.structure.ChainImpl: Deprecated.
getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.ChainImpl: Get all groups that are located between two PDB residue numbers.
getGroupsWithinShell(Structure, Atom, Set<ResidueNumber>, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
getGroupsWithinShell(Structure, Group, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Returns a Set of Groups in a structure within the distance specified of a given group.
getGroupTable() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
getH() - Method in class org.biojava.nbio.structure.jama.QRDecomposition: Return the Householder vectors
getHeaderVars() - Method in class org.biojava.nbio.structure.EntityInfo
getHeight() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
getHeight() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism: Returns the radius of a sphere, that is tangent to each of the octahedron's edges
getHelix(int) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
getHelixLayers() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getHelixLayers() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
getHelixRmsdThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getHelixRmsdToRiseRatio() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getHetero() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
getHetero() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getHetGroups() - Method in interface org.biojava.nbio.structure.Structure
getHetGroups() - Method in class org.biojava.nbio.structure.StructureImpl: Caution: we should probably remove this to avoid confusion.
getHGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getHGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getHieFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getHieURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
getHigherOrderRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
getHillOrder() - Method in enum org.biojava.nbio.structure.Element: Returns the Hill Order of this Element.
getHomologyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getHost_org_common_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getHost_org_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getHost_org_genus() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getHost_org_species() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getHost_org_strain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getHSDMTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate a phylogenetic tree of the MultipleAlignment using dissimilarity scores (DS), based in SDM Substitution Matrix (ideal for distantly related proteins, structure-derived) and the Neighbor Joining algorithm from forester.
getIclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
getIcode() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the icode property.
getiCode1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getiCode2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getId() - Method in class org.biojava.nbio.structure.align.model.AFP
getId() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getId() - Method in interface org.biojava.nbio.structure.Chain: Get the ID used by Hibernate.
getId() - Method in class org.biojava.nbio.structure.ChainImpl: Get the ID used by Hibernate.
getId() - Method in class org.biojava.nbio.structure.contact.StructureInterface
getId() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
getId() - Method in class org.biojava.nbio.structure.DBRef: Get the ID used by Hibernate.
getId() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
getId() - Method in class org.biojava.nbio.structure.EntityInfo: get the ID used by Hibernate
getId() - Method in class org.biojava.nbio.structure.HetatomImpl: the Hibernate database ID
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getId() - Method in class org.biojava.nbio.structure.PDBHeader: Get the ID used by Hibernate.
getId() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo: The identifier for this Biological Assembly, from 1 to n
getId() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Returns the identifier for this biological assembly transformation.
getId() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getId() - Method in class org.biojava.nbio.structure.rcsb.RCSBTaxonomy
getId() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
getId() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement: Returns the ID of this element.
getId() - Method in interface org.biojava.nbio.structure.Structure: Get the ID used by Hibernate
getId() - Method in class org.biojava.nbio.structure.StructureImpl: get the ID used by Hibernate
getId() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
getId() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets the standard numeric identifier for the space group.
getId() - Method in enum org.biojava.nbio.structure.xtal.TransformType
getIdbnsBegin() - Method in class org.biojava.nbio.structure.DBRef: Insertion code of initial residue of the segment, if PDB is the reference.
getIdbnsEnd() - Method in class org.biojava.nbio.structure.DBRef: Insertion code of the ending residue of the segment, if PDB is the reference.
getIdCode() - Method in class org.biojava.nbio.structure.DBRef: get the idCode for this entry
getIdCode() - Method in class org.biojava.nbio.structure.PDBHeader: The PDB code for this protein structure.
getIdenticalSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getIdentifier() - Method in class org.biojava.nbio.structure.align.client.StructureName: Get the original form of the identifier
getIdentifier() - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier
getIdentifier() - Method in class org.biojava.nbio.structure.cath.CathDomain
getIdentifier() - Method in class org.biojava.nbio.structure.domain.PDPDomain
getIdentifier() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getIdentifier() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
getIdentifier() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
getIdentifier() - Method in class org.biojava.nbio.structure.PassthroughIdentifier
getIdentifier() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getIdentifier() - Method in interface org.biojava.nbio.structure.Structure: Get a string representing this structure's contents.
getIdentifier() - Method in interface org.biojava.nbio.structure.StructureIdentifier: Get the String form of this identifier.
getIdentifier() - Method in class org.biojava.nbio.structure.StructureImpl: Get a string representing this structure's contents.
getIdentifier() - Method in class org.biojava.nbio.structure.SubstructureIdentifier: Get the String form of this identifier.
getIdentifier() - Method in class org.biojava.nbio.structure.URLIdentifier
getIdentity() - Method in class org.biojava.nbio.structure.align.model.AFPChain: The percent of residues that are sequence-identical in the alignment.
getIdx1() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: the positions of the structure equivalent positions in atom set 1
getIdx2() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: the positions of the structure equivalent atoms in atom set 2
getIdxlist() - Method in class org.biojava.nbio.structure.align.helper.JointFragments
getImagEigenvalues() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition: Return the imaginary parts of the eigenvalues
getInChI() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getInChIKey() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getIndex() - Method in class org.biojava.nbio.structure.align.helper.GapArray
getIndex() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getIndex() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement: Returns the index of the SSE for its type.
getInertiaTensor() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getInitialK() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getInitials() - Method in class org.biojava.nbio.structure.Author
getInputStream(URL, int) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: connect to DAS server and return result as an InputStream.
getInputStream(URL) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: connect to DAS server and return result as an InputStream.
getInputStream(URL, boolean, int) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: open a URL and return an InputStream to it if acceptGzipEncoding == true, use GZIPEncoding to compress communication
getInputStream(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Load or download the specified structure and return it as an InputStream for direct parsing.
getInsCode() - Method in class org.biojava.nbio.structure.ResidueNumber
getInsCode() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getInsCode() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getInsCode1() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getInsCode2() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron: Returns the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces
getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron: Returns the radius of an inscribed sphere, that is tangent to each of the octahedron's faces
getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism: Returns the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces
getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron: Returns the radius of an inscribed sphere, that is tangent to each of the tetrahedrons's faces
getInsertBegin() - Method in class org.biojava.nbio.structure.DBRef: Initial insertion code of the PDB sequence segment.
getInsertEnd() - Method in class org.biojava.nbio.structure.DBRef: Ending insertion code of the PDB sequence segment.
getInstalledDomainDescription() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getInstalledDomainList() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getInstalledDomall() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getInstalledNodeList() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getInstance(QuatSymmetryResults) - Static method in class org.biojava.nbio.structure.symmetry.core.AxisAligner: Returns an instance of AxisAligner for differnt type of QuatSymmetryResults (factory method)
getInt_Tables_number() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
getInteractingRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
getInterfacingResidues(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns the residues belonging to the interface, i.e.
getInternalChainID() - Method in interface org.biojava.nbio.structure.Chain: If available, returns the internal chain ID that is used in mmCIF files (asym_id), otherwise null
getInternalChainID() - Method in class org.biojava.nbio.structure.ChainImpl
getIntersection(DistanceBox<T>) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
getIoTime() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getIoTime() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the io time for this object, in milliseconds.
getIoTime() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getIoTime() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getIoverSigma() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the ioverSigma property.
getJclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
getJmolScript(Atom[]) - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Returns a Jmol script which will display the axis of rotation.
getJmolScript(Atom[], int) - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Returns a Jmol script which will display the axis of rotation.
getJoinRMSCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getJournalArticle() - Method in class org.biojava.nbio.structure.PDBHeader: Get the associated publication as defined by the JRNL records in a PDB file.
getJournalArticle() - Method in interface org.biojava.nbio.structure.Structure: Get the associated publication as defined by the JRNL records in a PDB file.
getJournalArticle() - Method in class org.biojava.nbio.structure.StructureImpl: get the associated publication as defined by the JRNL records in a PDB file.
getJournalName() - Method in class org.biojava.nbio.structure.JournalArticle
getKappa() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getKimuraTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate a phylogenetic tree of the MultipleAlignment using Kimura distances and the Neighbor Joining algorithm from forester.
getL() - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition: Return triangular factor.
getL() - Method in class org.biojava.nbio.structure.jama.LUDecomposition: Return lower triangular factor
getLabel_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getLabel_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getLabel_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getLabel_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getLabel_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getLabel_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getLabel_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getLabel_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getLabel_entity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getLabel_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getLabel_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getLargestSubunit() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getLast(String) - Method in class org.biojava.nbio.structure.AtomPositionMap
getLast() - Method in class org.biojava.nbio.structure.AtomPositionMap
getLayerLines() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getLcmp() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getLcmp() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getLegend(String) - Static method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getLength() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getLength(int, int, String) - Method in class org.biojava.nbio.structure.AtomPositionMap: Calculates the number of residues of the specified chain in a given range, inclusive.
getLength(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap: Calculates the number of atoms between two ResidueNumbers, inclusive.
getLength() - Method in interface org.biojava.nbio.structure.Bond: Gets the distance between the two atoms of this bond.
getLength() - Method in class org.biojava.nbio.structure.BondImpl: Gets the distance between the two atoms of this bond.
getLength() - Method in class org.biojava.nbio.structure.cath.CathDomain
getLength() - Method in class org.biojava.nbio.structure.cath.CathFragment
getLength() - Method in class org.biojava.nbio.structure.cath.CathSegment
getLength() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getLength() - Method in class org.biojava.nbio.structure.ResidueRangeAndLength
getLength() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement: Return the length (number of residues) in the SSE.
getLength() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism: Returns the radius of a circumscribed sphere, that goes through all vertices
getLength1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getLength2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getLength_a() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getLength_a_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getLength_b() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getLength_b_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getLength_c() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getLength_c_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getLengthDirectional(int, int, String) - Method in class org.biojava.nbio.structure.AtomPositionMap: Calculates the number of residues of the specified chain in a given range.
getLengthDirectional(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap: Calculates the number of atoms between two ResidueNumbers, inclusive.
getLfrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getLigands() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getLigands() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigands
getLigRSRnbrMean() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the ligRSRnbrMean property.
getLigRSRnbrStdev() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the ligRSRnbrStdev property.
getLigRSRnumnbrs() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the ligRSRnumnbrs property.
getLigRSRZ() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the ligRSRZ property.
getLikeSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getLineLoops() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
getLocalFile(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Searches for previously downloaded files
getLocalFileName(String) - Static method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider: Returns the file name that contains the definition for this ChemComp
getLocalSymmetries() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Returns a list of lists of local quaternary structure symmetry results
getLocalTimeLimit() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getLowerBound() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getLs_d_res_high() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_d_res_low() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_matrix_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_number_parameters() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_number_reflns_all() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_number_reflns_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_number_reflns_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_number_reflns_R_work() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_number_restraints() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_percent_reflns_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_percent_reflns_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_R_factor_all() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_R_factor_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_R_factor_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_R_factor_R_free_error() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_R_factor_R_free_error_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_R_factor_R_work() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_redundancy_reflns_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_wR_factor_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_wR_factor_R_work() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLto() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getM() - Method in class org.biojava.nbio.structure.align.model.AFP
getMacromolecularSize() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
getManual() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getMapProperty() - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
getMatchingAtomRes(Chain, List<Chain>) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
getMatMatrix() - Method in class org.biojava.nbio.structure.align.ce.CECalculator: Caution: this matrix is overwriten with very different data at several points in the alignment algorithm.
getMatMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced: Caution: this matrix is overwriten with very different data at several points in the alignment algorithm.
getMatrix() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix(int, int, int, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Get a submatrix.
getMatrix(int[], int[]) - Method in class org.biojava.nbio.structure.jama.Matrix: Get a submatrix.
getMatrix(int, int, int[]) - Method in class org.biojava.nbio.structure.jama.Matrix: Get a submatrix.
getMatrix(int[], int, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Get a submatrix.
getMatrix11() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix12() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix13() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix21() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix22() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix23() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix31() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix32() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix33() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrixFromAlgebraic(String) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getMatTransform() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
getMaxAtoms() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: The maximum numbers of atoms to load in a protein structure (prevents memory overflows)
getMaxDimension() - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Gets the maximum dimension of the unit cell.
getMaxGap() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getMaxGapFrag() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getMaxGapSize() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: the Max gap size parameter G .
getMaxGapSize() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams: CE specific parameter: set the Max gap size parameter G (during AFP extension).
getMaximumCovalentValence() - Method in enum org.biojava.nbio.structure.Element: Returns the maximum valence for this Element.
getMaximumExtend(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools: Returns the maximum extend of the structure in the x, y, or z direction.
getMaximumLocalCombinations() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMaximumLocalResults() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMaximumLocalSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMaximumValence() - Method in enum org.biojava.nbio.structure.Element: Returns the maximum valence for this Element.
getMaxIter() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getMaxNrIterationsForOptimization() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: Get the maximum nr of times the (slow) optimiziation of alignment should iterate.
getMaxOptRMSD() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: Returns the maximum RMSD cutoff to be applied during alignment optimization (default: 99 = unlimited)
getMaxOptRMSD() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams: (jCE specific): maximum RMSD that shall be calculated for the alignment.
getMaxPenalty() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getMaxrefine() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getMaxRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getMaxSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getMaxSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getMaxSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getMaxSymmOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getMaxTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getMaxTra() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters: get the maximum number of Twists that are allowed...
getMaxTra() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
getMaxTra() - Method in class org.biojava.nbio.structure.align.model.AFPChain: get the maximum nr of Twists that are allowed...
getMCScore(MultipleAlignment, double, double, double) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the MC score, specific for the MultipleAlignment algorithm.
getMean() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the mean property.
getMean() - Method in class org.biojava.nbio.structure.validation.BondOutlier: Gets the value of the mean property.
getMean() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the mean property.
getMean() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the mean property.
getMembers() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
getMergedClusters(double) - Method in class org.biojava.nbio.structure.symmetry.core.ClusterMerger: Combine clusters based on the given sequence identity
getMethod() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
getMethod() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getMethod() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Returns name of method used for symmetry perception.
getMethod_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getMethod_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron: Returns the radius of a sphere, that is tangent to each of the icosahedron's edges
getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron: Returns the radius of a sphere, that is tangent to each of the octahedron's edges
getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron: Returns the radius of a sphere, that is tangent to each of the tetrahedron's edges
getMinAlignedStructures() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getMinBlockLen() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getMinCoreLength() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getMinCPLength() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
getMinCPLength() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
getMindiff() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the mindiff property.
getMindiff() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the mindiff property.
getMinDistance() - Method in class org.biojava.nbio.structure.contact.GroupContact
getMinimumHelixAngle() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMinimumHelixRise() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMinimumSequenceLength() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMinimumSequenceLengthFraction() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMinimumValence() - Method in enum org.biojava.nbio.structure.Element: Returns the minimum valence for this Element.
getMinLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getMinMax(double[]) - Method in class org.biojava.nbio.structure.contact.BoundingBox: Returns an array of size 2 with min and max values of given double array
getMinRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getMinSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getMinSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getMinSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getMinTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getMirrors() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getMisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getMisLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getMisScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getMMcifConsumer() - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
getMod_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
getModDate() - Method in class org.biojava.nbio.structure.PDBHeader
getModel(int) - Method in interface org.biojava.nbio.structure.Structure: Retrieve all Chains belonging to a model .
getModel(int) - Method in class org.biojava.nbio.structure.StructureImpl: retrieve all Chains belonging to a model .
getModel() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the model property.
getModel_Cartn_x() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getModel_Cartn_y() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getModel_Cartn_z() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getModelledSubgroup() - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation: Gets the value of the modelledSubgroup property.
getModelNumber() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getMogAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the mogAngleOutlier property.
getMogBondOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the mogBondOutlier property.
getMogulIgnore() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the mogulIgnore property.
getMolecule() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getMoleculeIds() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Return the pair of identifiers identifying each of the 2 molecules of this interface in the asymmetry unit (usually the chain identifier if this interface is between 2 chains)
getMolecules() - Method in class org.biojava.nbio.structure.contact.StructureInterface
getMolId() - Method in class org.biojava.nbio.structure.EntityInfo: Return the molecule identifier, called entity_id in mmCIF dictionary.
getMomentsOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getMon_nstd_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getMon_nstd_parent_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getMTranspose() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getMultipleAlignment() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Returns the parent MultipleAlignment of the BlockSet.
getMultipleAlignment() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
getMultipleAlignment(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the MultipleAlignments at the specified index in the ensemble.
getMultipleAlignment(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getMultipleAlignment() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getMultipleAlignments() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the List of MultipleAlignments in the ensemble.
getMultipleAlignments() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getMultiplicity() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getMutation() - Method in class org.biojava.nbio.structure.EntityInfo
getN() - Method in interface org.biojava.nbio.structure.AminoAcid: Get N atom.
getN() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Get N atom.
getName() - Method in class org.biojava.nbio.structure.align.client.StructureName: Deprecated.
use StructureName.getIdentifier()
getName() - Method in interface org.biojava.nbio.structure.Atom: Get atom name, e.g.
getName() - Method in class org.biojava.nbio.structure.AtomImpl: Get atom name, e.g.
getName() - Method in class org.biojava.nbio.structure.cath.CathDomain
getName() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique
getName() - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
getName() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getName() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
getName() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getName() - Method in class org.biojava.nbio.structure.rcsb.RCSBMacromolecule
getName() - Method in class org.biojava.nbio.structure.rcsb.RCSBTaxonomy
getName() - Method in class org.biojava.nbio.structure.scop.ScopDescription
getName() - Method in interface org.biojava.nbio.structure.Structure: Get biological name of Structure.
getName() - Method in class org.biojava.nbio.structure.StructureImpl: Get biological name of Structure.
getName() - Method in class org.biojava.nbio.structure.validation.Program: Gets the value of the name property.
getName() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
getName1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getName1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getName1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getName2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getName2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getName2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getNames() - Method in class org.biojava.nbio.structure.scop.Astral
getnAtom() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getnAtom() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getNatomsEDS() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the natomsEDS property.
getNaturalPos() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getNavMap() - Method in class org.biojava.nbio.structure.AtomPositionMap
getNcbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
getNclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
getNcsOperators() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo: Get the NCS operators.
getNcuts() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
getNdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getNdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getNeighbors(Point3d) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
getNeighborsWithCache(Point3d) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
getNext() - Method in class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
getNext() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
getNMRStructures() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: get list of all current NMR structures
getNodeId() - Method in class org.biojava.nbio.structure.cath.CathNode
getNodeListFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getNonenantpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getNormAlignScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getNotObserved() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getNrAlignments() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getNrAtoms(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Count how many Atoms are contained within a Structure object.
getNrBioAssemblies() - Method in class org.biojava.nbio.structure.PDBHeader: Get the number of biological assemblies available in the PDB header
getNrBiolAssemblies(String) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider: Returns the number of available biological assemblies.
getNrBiolAssemblies(String) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
getNrBiolAssemblies() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getNrBiolAssemblies(String) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
getNrBiolAssemblies() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: Returns the number of available biological assemblies.
getNrBiolAssemblies(String) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
getNrBiolAssemblies() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getNrBiologicalAssemblies(String) - Static method in class org.biojava.nbio.structure.StructureIO
getNrCPU() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getNrEQR() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Get the number of structurally equivalent residues
getNrGroups(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Count how many groups are contained within a structure object.
getNrThreads() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getNseg() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
getnStart() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getNStart() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation: Returns the number of starts if this rotation represents a helical rotation
getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getNucleotides() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
getNum() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
getNum() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
getNumAtomContacts() - Method in class org.biojava.nbio.structure.contact.GroupContact
getNumericalBondOrder() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond: Converts this ChemCompBond's value_order attribute into an int using the conversion:
getNumFreeReflections() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the numFreeReflections property.
getNumHReduce() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the numHReduce property.
getNumHReduce() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the numHReduce property.
getNumIindices() - Method in class org.biojava.nbio.structure.contact.GridCell
getNumJindices() - Method in class org.biojava.nbio.structure.contact.GridCell
getNumLeft() - Method in class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
getNumLeft() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
getNumMillerIndices() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the numMillerIndices property.
getNumobs() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the numobs property.
getNumobs() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the numobs property.
getNumOperators() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets the number of symmetry operators corresponding to this SpaceGroup (counting the identity operator)
getNumRes() - Method in class org.biojava.nbio.structure.EntityInfo
getO() - Method in interface org.biojava.nbio.structure.AminoAcid: Get O atom.
getO() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Get O atom.
getO3Prime() - Method in class org.biojava.nbio.structure.NucleotideImpl: Returns the O3' atom if present, otherwise null
getO5Prime() - Method in class org.biojava.nbio.structure.NucleotideImpl: Returns the O5' atom if present, otherwise null
getObs() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the obs property.
getObs() - Method in class org.biojava.nbio.structure.validation.BondOutlier: Gets the value of the obs property.
getObsoleteBehavior() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns how this instance deals with obsolete entries.
getObsoleteBehavior() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
getObsoleteBehavior() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Returns how this instance deals with obsolete entries.
getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Location of obsolete files within the directory, as an array of paths.
getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.PDBFileReader
getObsval() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the obsval property.
getObsval() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the obsval property.
getOccupancy() - Method in interface org.biojava.nbio.structure.Atom: Get occupancy.
getOccupancy() - Method in class org.biojava.nbio.structure.AtomImpl
getOccupancy() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getOccupancy_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getOccupancy_max() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOccupancy_min() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOligomeric_count() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
getOligomeric_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
getOmega() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getOne_letter_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getOneLetterCode(ChemComp, ChemicalComponentDictionary) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
getOneLetterCode(ChemComp) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
getOper_expression() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
getOperator() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
getOptAln() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Tracks the Atom positions in the optimal alignment.
getOptAlnAsList(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Retrieves the optimum alignment from an AFPChain and returns it as a java collection.
getOptimization() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getOptimizationSteps() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getOptLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain: The length of each block
getOptLength() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getOptRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getOrbits() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getOrbits() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getOrbits() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getOrder() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
getOrder(List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
getOrder() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
getOrderDetectorMethod() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getOrderedPairs() - Method in class org.biojava.nbio.structure.quaternary.CartesianProduct: Generates the list of ordered pair between two sets.
getOrgan() - Method in class org.biojava.nbio.structure.EntityInfo
getOrganelle() - Method in class org.biojava.nbio.structure.EntityInfo
getOrganism_common_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
getOrganism_scientific() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
getOrganismCommon() - Method in class org.biojava.nbio.structure.EntityInfo
getOrganismScientific() - Method in class org.biojava.nbio.structure.EntityInfo
getOrganismTaxId() - Method in class org.biojava.nbio.structure.EntityInfo
getOrigGroup() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getOrigGroup() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getOriginalCenters() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getORmsdThr() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: Get the Original RMSD threshold from which the alignment optimization is started
getOrthologousSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getOther(Atom) - Method in interface org.biojava.nbio.structure.Bond: A utility method to get the other atom in a bond, given one of its atoms.
getOther(Atom) - Method in class org.biojava.nbio.structure.BondImpl: A utility method to get the other atom in a bond, given one of its atoms.
getOtherTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Deprecated.
getOutFile() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
getOutFile() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getOutFile() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getOverall_FOM_free_R_set() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOverall_FOM_work_R_set() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOverall_SU_B() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOverall_SU_ML() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOverall_SU_R_Cruickshank_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOverall_SU_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOwab() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the owab property.
getOxidationState() - Method in enum org.biojava.nbio.structure.Element: Returns a typical oxidation state for this Element.
getP() - Method in class org.biojava.nbio.structure.NucleotideImpl: Returns the P atom if present, otherwise null
getP1() - Method in class org.biojava.nbio.structure.align.model.AFP
getP2() - Method in class org.biojava.nbio.structure.align.model.AFP
getPair() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
getPair() - Method in class org.biojava.nbio.structure.contact.AtomContact
getPair() - Method in class org.biojava.nbio.structure.contact.GroupContact
getPairs() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
getPairwiseAlignment(SequenceAlignmentCluster) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getPara(int, int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
getParameters() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
getParameters() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
getParameters() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeMain
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
getParameters() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
getParameters() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
getParameters() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner: Return the parameters of this algorithm instance.
getParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
getParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
getParameters() - Method in interface org.biojava.nbio.structure.align.StructureAlignment: Return the paramers for this algorithm.
getParams() - Method in class org.biojava.nbio.structure.align.FarmJob
getParams() - Method in class org.biojava.nbio.structure.align.StructurePairAligner: get the parameters.
getParams() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getParent() - Method in interface org.biojava.nbio.structure.Chain: Deprecated.
use getStructure(Structure) instead.
getParent() - Method in class org.biojava.nbio.structure.ChainImpl: Deprecated.
use getStructure instead.
getParent() - Method in class org.biojava.nbio.structure.DBRef: Get the structure object that this DBRef relates to.
getParent(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary: Get the parent of a component.
getParentChains() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Finds the parent chains by looking up the references of first atom of each side of this interface
getParentCompounds() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Finds the parent compounds by looking up the references of first atom of each side of this interface
getParentId() - Method in class org.biojava.nbio.structure.cath.CathNode
getParentSunid() - Method in class org.biojava.nbio.structure.scop.ScopNode
getPartner() - Method in class org.biojava.nbio.structure.secstruc.HBond
getPartner1() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
getPartner2() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
getPath() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getPath() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
getPath() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getPath() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Get the path that is used to cache PDB files.
getPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Returns the path value.
getPathSize() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getPathSize() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getPaulingElectronegativity() - Method in enum org.biojava.nbio.structure.Element: Returns the Pauling electronegativity for this Element.
getPdb1() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getPdb1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getPdb2() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getPdb2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getPdb_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getPdb_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getPdb_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getPdb_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getPdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getPdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getPdb_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getPdb_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getPdbAln() - Method in class org.biojava.nbio.structure.align.model.AFPChain: used temporarily during XML serialization to track the PDB positions of the alignmnet
getPdbChainIdClusters() - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
getPdbChainIdClusters(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
getPDBCode() - Method in interface org.biojava.nbio.structure.Structure: Get PDB code of structure.
getPDBCode() - Method in class org.biojava.nbio.structure.StructureImpl: Get PDB code of structure.
getPDBCode1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getPDBCode2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getPdbEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getPdbFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getPdbFilePath() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getPdbFilePath() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
getPdbGroup() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getPdbGroup() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getPDBHeader() - Method in interface org.biojava.nbio.structure.Structure: Return the header information for this PDB file
getPDBHeader() - Method in class org.biojava.nbio.structure.StructureImpl: Return the header information for this PDB file
getPdbId() - Method in class org.biojava.nbio.structure.align.client.StructureName: Get the PDB ID for this name, if any.
getPdbId() - Method in class org.biojava.nbio.structure.cath.CathDomain: Deprecated.
This method is poorly named; use CathDomain.getThePdbId() or CathDomain.getPdbIdAndChain() instead
getPdbId() - Method in class org.biojava.nbio.structure.domain.PDPDomain
getPdbId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getPdbId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getPdbId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getPdbId() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getPdbId() - Method in class org.biojava.nbio.structure.rcsb.RCSBDescription
getPdbId() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigands
getPdbId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getPdbId() - Method in interface org.biojava.nbio.structure.Structure: Deprecated.
From BioJava 4.2, use Structure.getPDBCode() or getStructureIdentifier().toCanonical().getPdbId()
getPdbId() - Method in class org.biojava.nbio.structure.StructureImpl: Deprecated.
getPdbId() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
getPdbIdAndChain() - Method in class org.biojava.nbio.structure.cath.CathDomain: Returns a string of the form PDBID.CHAIN.
getPDBName() - Method in interface org.biojava.nbio.structure.Group: Get the PDB 3-letter name for this group.
getPDBName() - Method in class org.biojava.nbio.structure.HetatomImpl: Returns the PDBName.
getPdbPairs(String, int, String) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
getPdbResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getPdbResNum() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getPdbResNum() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getPdbResNum() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getPDBresnum1() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
getPDBresnum2() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
getPDBRevisionNumber() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the pdbRevisionNumber property.
getPDBserial() - Method in interface org.biojava.nbio.structure.Atom: Get PDB atom number.
getPDBserial() - Method in class org.biojava.nbio.structure.AtomImpl: Get PDB atom number.
getPdbSerial() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
getPdbStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getPdbx_align() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_align_begin() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getPdbx_alt_source_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_alt_source_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_ambiguous_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_aromatic_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_aromatic_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getPdbx_atcc() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_auth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getPdbx_auth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getPdbx_auth_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getPdbx_auth_seq_align_beg() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_auth_seq_align_end() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_auth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getPdbx_auth_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_beg_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_beg_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_blank_PDB_chainid_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
getPdbx_CASP_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
getPdbx_cell() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_cell_line() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_cellular_location() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_component_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_component_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_component_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_data_cutoff_high_absF() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_data_cutoff_high_rms_absF() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_data_cutoff_low_absF() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_db_accession() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getPdbx_db_accession() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_db_align_beg_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_db_align_end_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_description() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getPdbx_description() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_descriptor() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
getPdbx_diffrn_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_dist_value() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ec() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getPdbx_end_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_end_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_evidence_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getPdbx_formal_charge() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getPdbx_formal_charge() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_fragment() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getPdbx_fragment() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_full_space_group_name_H_M() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
getPdbx_gene_src_atcc() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_cell() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_cell_line() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_cellular_location() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_fragment() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_gene() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_ncbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_organ() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_organelle() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_plasmid() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_plasmid_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_scientific_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_variant() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_atcc() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_cell() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_cell_line() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_cellular_location() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_culture_collection() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_gene() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_ncbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_organ() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_organelle() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_scientific_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_strain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_tissue() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_tissue_fraction() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_variant() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_vector() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_vector_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_ideal_coordinates_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_ideal_coordinates_missing_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_initial_date() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_isotropic_thermal_model() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_keywords() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
getPdbx_leaving_atom_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_leaving_atom_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_leaving_atom_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ls_cross_valid_method() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_ls_sigma_F() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_ls_sigma_I() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_method_to_determine_struct() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_model_Cartn_x_ideal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_model_Cartn_y_ideal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_model_Cartn_z_ideal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_model_coordinates_db_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_model_coordinates_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_model_coordinates_missing_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_model_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
getPdbx_model_type_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
getPdbx_modified() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
getPdbx_modified_date() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_mutation() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getPdbx_ncbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_num_res() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getPdbx_num_residues() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getPdbx_number_of_molecules() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_organ() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_organelle() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_organism_scientific() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_overall_ESU_R() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_overall_ESU_R_Free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_overall_phase_error() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_overall_SU_R_Blow_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_overall_SU_R_free_Blow_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_overall_SU_R_free_Cruickshank_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_PDB_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_PDB_id_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_pdb_id_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getPdbx_pdb_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_PDB_model_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getPdbx_pdb_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_plasmid_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_plasmid_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_polymer_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_processing_site() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_ptnr1_label_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr1_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr1_standard_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr2_label_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr2_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr3_label_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr3_label_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr3_label_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr3_label_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr3_label_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr3_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_R_Free_selection_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_ref_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_refine_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_release_status() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_replaced_by() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_replaces() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_residue_numbering() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_secretion() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_seq_align_beg_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_seq_align_end_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_seq_db_accession_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_seq_db_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_seq_db_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_seq_one_letter_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getPdbx_seq_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_solvent_ion_probe_radii() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_solvent_shrinkage_radii() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_solvent_vdw_probe_radii() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_src_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_src_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_starting_model() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_stereo_config() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_stereo_config() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getPdbx_stereochem_target_val_spec_case() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_stereochemistry_target_values() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_subcomponent_list() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_synonyms() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_TLS_residual_ADP_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_unique_axis() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getPdbx_value_order() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_variant() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbxStructAssemblies() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
getPdbxStructAssemblies() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getPdbxStructAssemblies() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: Data access method for list describing all assemblies
getPdbxStructAssemblies() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getPdbxStructAssembly(int) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getPdbxStructAssembly(int) - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: get the data for a particular pdbxStructAssembly.
getPdbxStructAssembly(int) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getPdbxStructAssemblyGen(int) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getPdbxStructAssemblyGen(int) - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: get the data for a particular pdbxStructAssemblyGen.
getPdbxStructAssemblyGen(int) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getPdbxStructAssemblyGens() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
getPdbxStructAssemblyGens() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getPdbxStructAssemblyGens() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: Data access method for list describing all assemblies
getPdbxStructAssemblyGens() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getPdbxStructOperList() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getPdbxStructOperList() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: Get all the possible operators
getPdbxStructOperList() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getPdbxStructOperLists() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
getPDPDomain(String) - Method in interface org.biojava.nbio.structure.domain.PDPProvider: Get a StructureIdentifier representing the specified PDP domain.
getPDPDomain(String) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider: Get a StructureIdentifier representing the specified PDP domain.
getPDPDomainNamesForPDB(String) - Method in interface org.biojava.nbio.structure.domain.PDPProvider: Get a list of all PDP domains for a given PDB entry
getPDPDomainNamesForPDB(String) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider: Get a list of all PDP domains for a given PDB entry
getPdpprovider() - Method in class org.biojava.nbio.structure.align.util.AtomCache
getPercentFreeReflections() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the percentFreeReflections property.
getPercentRamaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the percentRamaOutliers property.
getPercentRotaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the percentRotaOutliers property.
getPercentRSRZOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the percentRSRZOutliers property.
getPercId() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
getPeriod() - Method in enum org.biojava.nbio.structure.Element: Returns the period in the periodic table of this Element.
getPermutation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getPermutation(int) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
getPermutation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getPermutationSize() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getPhi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc: Calculate the phi angle.
getPhi() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getPhi() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the phi property.
getPivot() - Method in class org.biojava.nbio.structure.jama.LUDecomposition: Return pivot permutation vector
getPlasmid_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPlasmid_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPmid() - Method in class org.biojava.nbio.structure.JournalArticle: Get the value of PMID field.
getPointGroup() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
getPolygonVertices(int, double, Point3d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.Prism: Returns the vertices of an n-fold polygon of given radius and center
getPolymers() - Method in class org.biojava.nbio.structure.rcsb.RCSBDescription
getPolymerType() - Method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType: Gets the associated PolymerType, which are less specific
getPolymerType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPos1() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getPos2() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getPosition(ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap: Gets the 0-based index of residueNumber to the matched atoms
getPositionInQueue(String, String, String, String) - Method in class org.biojava.nbio.structure.align.client.JFatCatClient
getPositionInQueue(String, String, String, String, int) - Method in class org.biojava.nbio.structure.align.client.JFatCatClient
getPredominantGroupType(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Get the predominant GroupType for a given Chain, following these rules: if the ratio of number of residues of a certain GroupType to total non-water residues is above the threshold 0.95, then that GroupType is returned if there is no GroupType that is above the threshold then the GroupType with most members is chosen, logging it
getPrimitiveMultiplicity() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getPrincipalAxes() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getPrincipalAxisIndex() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
getPrincipalMomentsOfInertia() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getProbability() - Method in class org.biojava.nbio.structure.align.model.AFPChain: The probability (FATCAT) or Z-score (CE) of the alignment.
getProgram() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
getProgram() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
getProgram() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
getProgram() - Method in class org.biojava.nbio.structure.validation.Programs: Gets the value of the program property.
getProgram_version() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
getProgram_version() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
getProgram_version() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
getPrograms() - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation: Gets the value of the programs property.
getProjectedDistance(Atom) - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Get the distance from a point to the axis of rotation
getProjectedPoint(Atom) - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Projects a given point onto the axis of rotation
getProperties() - Method in interface org.biojava.nbio.structure.Group: return properties.
getProperties() - Method in class org.biojava.nbio.structure.HetatomImpl: return properties.
getProperties() - Method in class org.biojava.nbio.structure.validation.Program: Gets the value of the properties property.
getProperty(String) - Method in interface org.biojava.nbio.structure.Group: get a single property .
getProperty(String) - Method in class org.biojava.nbio.structure.HetatomImpl: get a single property .
getProteinChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
getProteinChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
getProteinGraph() - Method in class org.biojava.nbio.structure.symmetry.core.SubunitGraph
getProteinSequenceForStructure(Structure, Map<Integer, Group>) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher: Generates a ProteinSequence corresponding to the sequence of struct, and maintains a mapping from the sequence back to the original groups.
getPseudoStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getPsi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc: Calculate the psi angle.
getPsi() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getPsi() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the psi property.
getPtnr1_auth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_auth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_auth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_label_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_label_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_label_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_label_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_symmetry() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_auth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_auth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_auth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_label_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_label_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_label_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_label_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_symmetry() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPublicationDate() - Method in class org.biojava.nbio.structure.JournalArticle
getPublisher() - Method in class org.biojava.nbio.structure.JournalArticle
getPx() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getQ() - Method in class org.biojava.nbio.structure.jama.QRDecomposition: Generate and return the (economy-sized) orthogonal factor
getQuat4d(int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
getQuat4d(int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
getQuaternaryStructure(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Method that converts the symmetric units of a structure into different chains, so that internal symmetry can be translated into quaternary.
getQuaternarySymmetry(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Given a symmetry result, it calculates the overall global symmetry, factoring out the alignment and detection steps of QuatSymmetryDetector algorithm.
getR() - Method in class org.biojava.nbio.structure.jama.QRDecomposition: Return the upper triangular factor
getRadius(Atom) - Static method in class org.biojava.nbio.structure.asa.AsaCalculator: Gets the van der Waals radius of the given atom following the values defined by Chothia (1976) J.Mol.Biol.105,1-14 NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates" slightly the heavy atoms to account for Hydrogens.
getRadius() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner: Returns the radius for drawing polyhedra
getRadius() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getRadius() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner: Returns the radius for drawing the minor rotation axis in the xy-plane
getRadiusOfGyration() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getRama() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the rama property.
getRandomSeed() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getRandomSleepTime() - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
getRandomUsername() - Static method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
getRange() - Method in class org.biojava.nbio.structure.ecod.EcodDomain: Get the range of this domain, in PDB residue numbers (mmCif's _pdbx_poly_seq_scheme.pdb_seq_num and pdb_ins_code).
getRange() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement: Returns the residue range of this SSE.
getRanges() - Method in class org.biojava.nbio.structure.AtomPositionMap: Returns a list of ResidueRanges corresponding to this entire AtomPositionMap.
getRanges() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getRanges() - Method in interface org.biojava.nbio.structure.Structure: Deprecated.
From BioJava 4.2, use getStructureIdentifier().toCanonical().getRanges()
getRanges() - Method in class org.biojava.nbio.structure.StructureImpl: Deprecated.
getRealEigenvalues() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition: Return the real parts of the eigenvalues
getRecordType() - Method in interface org.biojava.nbio.structure.AminoAcid: Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
getRecordType() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
getReducedCAStructure(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools: Deprecated.
Use the more generic BioAssemblyTools.getReducedStructure(Structure)
getReducedStructure(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools: reduce a structure to a single-atom representation (e.g.
getReducedStructure(Structure, String) - Static method in class org.biojava.nbio.structure.StructureTools: Deprecated.
Use StructureIdentifier.reduce(Structure) instead (v. 4.2.0)
getReducedStructure(Structure, int) - Static method in class org.biojava.nbio.structure.StructureTools: Deprecated.
Use StructureIdentifier.reduce(Structure) instead (v. 4.2.0)
getRef() - Method in class org.biojava.nbio.structure.JournalArticle: Get the value of REF field.
getRef_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getRefChainId() - Method in class org.biojava.nbio.structure.EntityInfo: Return the ref chain id value.
getRefineMethod() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getRefmacVersion() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the refmacVersion property.
getRefn() - Method in class org.biojava.nbio.structure.JournalArticle: Get the value of REFN field.
getRefRMSD(MultipleAlignment, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: /** Calculates the average RMSD from all structures to a reference s tructure, given a set of superimposed atoms.
getRefRMSD(List<Atom[]>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the average RMSD from all structures to a reference s tructure, given a set of superimposed atoms.
getRefTMScore(MultipleAlignment, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the average TMScore from all structures to a reference structure, given a set of superimposed atoms.
getRefTMScore(List<Atom[]>, List<Integer>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the average TMScore from all structures to a reference structure, given a set of superimposed atoms.
getRelativeAsaC() - Method in class org.biojava.nbio.structure.asa.GroupAsa: Returns the relative (complexed) ASA, i.e.
getRelativeAsaU() - Method in class org.biojava.nbio.structure.asa.GroupAsa: Returns the relative (uncomplexed) ASA, i.e.
getRelativePercentileClashscore() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the relativePercentileClashscore property.
getRelativePercentileDCCRfree() - Method in class org.biojava.nbio.structure.validation.Entry
getRelativePercentilePercentRamaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the relativePercentilePercentRamaOutliers property.
getRelativePercentilePercentRotaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the relativePercentilePercentRotaOutliers property.
getRelativePercentilePercentRSRZOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the relativePercentilePercentRSRZOutliers property.
getRelativePercentileRNAsuiteness() - Method in class org.biojava.nbio.structure.validation.Entry
getRepeatRelation(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes: Return the repeat superposition relation needed to obtain the axis of symmetry (which repeats and in which order have to be superimposed to obtain the axis).
getRepeatsID() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult: Return the symmetric repeats as structure identifiers, if the result is symmetric and it was refined, return null otherwise.
getRepeatTransform(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes: Return the transformation that needs to be applied to a determinate repeat so that all get superimposed to the same point.
getRepeatUnitCenters() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
getRepeatUnitIndices() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
getRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
getRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getReplaced(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary: if ChemComp is replacing another one, get the old version otherwise return the same ChemComp again.
getReplaced(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
getReplacement(String, boolean, boolean) - Static method in class org.biojava.nbio.structure.PDBStatus: Gets the PDB which superseded oldPdbId.
getReplacer(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary: if ChemComp is replaced by another one, get the newer version otherwise return the same ChemComp again.
getReplacer(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
getReplaces() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
getReplaces(String, boolean) - Static method in class org.biojava.nbio.structure.PDBStatus: Get the ID of the protein which was made obsolete by newPdbId.
getRepresentative() - Method in class org.biojava.nbio.structure.cath.CathNode
getRepresentative() - Method in class org.biojava.nbio.structure.EntityInfo: Get the representative Chain for this Compound.
getRepresentative() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
getRepresentativeAtomArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Gets a representative atom for each group that is part of the chain backbone.
getRepresentativeAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Gets a representative atom for each group that is part of the chain backbone.
getRepresentativeAtoms(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the representative atoms for the provided name.
getRepresentativeAtoms(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache
getRepresentativeAtomsInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools: Returns the set of intra-chain contacts for the given chain for C-alpha or C3' atoms (including non-standard aminoacids appearing as HETATM groups), i.e.
getRepresentativeAtomsOnly(List<Chain>) - Static method in class org.biojava.nbio.structure.io.CAConverter: Convert a List of chain objects to another List of chains, containing Representative atoms only.
getRepresentativeAtomsOnly(Chain) - Static method in class org.biojava.nbio.structure.io.CAConverter: Convert a Chain to a new Chain containing C-alpha atoms only.
getRepresentativeChain(String, String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
getRepresentativeDomains() - Method in interface org.biojava.nbio.structure.domain.DomainProvider: Get the full list of representative domains for the PDB.
getRepresentativeDomains() - Method in class org.biojava.nbio.structure.domain.PDBDomainProvider: Gets a list of all domain representatives
getRepresentativeDomains() - Method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
getRepresentatives(String, int) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
GetRepresentatives - Class in org.biojava.nbio.structure.rcsb: TODO Move this to Representatives.
GetRepresentatives() - Constructor for class org.biojava.nbio.structure.rcsb.GetRepresentatives
getRepresentatives(int) - Static method in class org.biojava.nbio.structure.rcsb.GetRepresentatives: Returns a representative set of PDB protein chains at the specified sequence identity cutoff.
getRepresentatives(Astral.AstralSet) - Static method in class org.biojava.nbio.structure.scop.Astral: Get a list of representatives' names for the specified ASTRAL cutoff.
getRepresentatives(String) - Static method in class org.biojava.nbio.structure.scop.Astral: Get a list of representatives' names for the specified ASTRAL cutoff.
getRepresentatives(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
getResidue(int) - Method in class org.biojava.nbio.structure.AugmentedResidueRange: Returns the ResidueNumber that is at position positionInRange in this ResidueRange.
getResidue(int, AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange: Returns the ResidueNumber that is at position positionInRange in this ResidueRange.
getResidueNumber() - Method in interface org.biojava.nbio.structure.Group: returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.
getResidueNumber() - Method in class org.biojava.nbio.structure.HetatomImpl: returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.
getResidueRanges() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getResidueRanges() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getResidueRanges() - Method in interface org.biojava.nbio.structure.Structure: Deprecated.
From BioJava 4.2, use getStructureIdentifier().toCanonical().getResidueRanges()
getResidueRanges() - Method in class org.biojava.nbio.structure.StructureImpl: Deprecated.
getResidueRanges() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
getResidues() - Method in class org.biojava.nbio.structure.io.FastaStructureParser: For each residue in the fasta file, return the ResidueNumber in the corresponding structure.
getResidues() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
getResidueType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getResidueTypeFromString(String) - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType
getResidueTypes() - Method in enum org.biojava.nbio.structure.GroupType: Get a set of ResidueTypes loosely equivalent to this GroupType.
getResname() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the resname property.
getResName1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getResName2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getResNames() - Method in class org.biojava.nbio.structure.EntityInfo
getResnum() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the resnum property.
getResnum1() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getResnum2() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getResolution() - Method in class org.biojava.nbio.structure.cath.CathDomain
getResolution() - Method in class org.biojava.nbio.structure.PDBHeader
getResourceManager(String) - Static method in class org.biojava.nbio.structure.align.util.ResourceManager
getResScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getResSeq1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getResSeq2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getRestypesNotcheckedForBondAngleGeometry() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the restypesNotcheckedForBondAngleGeometry property.
getResultFile() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getRev_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
getReverse() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getRevisionRecords() - Method in class org.biojava.nbio.structure.PDBHeader
getRfree() - Method in class org.biojava.nbio.structure.PDBHeader
getRibosomes() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
getRimResidues(double, double) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns the residues belonging to the interface rim, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is below the given bsaToAsaCutoff
getRise() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getRms() - Method in class org.biojava.nbio.structure.align.helper.JointFragments
getRMS(Atom[], Atom[], JointFragments) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner: get the RMS of the JointFragments pair frag
getRms() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getRMS(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.SVDSuperimposer: Calculate the RMS (root mean square) deviation of two sets of atoms.
getRmsd() - Method in class org.biojava.nbio.structure.align.model.AFP
getRMSD(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the RMSD of all-to-all structure comparisons (distances) of the given MultipleAlignment.
getRMSD(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the RMSD of all-to-all structure comparisons (distances), given a set of superimposed atoms.
getRmsd() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
getRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
getRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getRmsd() - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
getRmsdCenters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getRmsdCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters: The cutoff to be used during AFP detection
getRmsdCut() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
getRmsdIntra() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getRMSDMatrix(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate the RMSD matrix of a MultipleAlignment, that is, entry (i,j) of the matrix contains the RMSD between structures i and j.
getRmsdThr() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: RMSD Threshold
getRmsdThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getRmsdThrJoin() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: RMSD threshold for joining of AFPs
getRnaSuiteness() - Method in class org.biojava.nbio.structure.validation.Entry
getRndSeed() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getRootURL() - Method in class org.biojava.nbio.structure.scop.ScopMirror: Get the URL for the root download directory, or null if none is set.
getRot() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getRota() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the rota property.
getRotatedAtoms(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay: New structures are downloaded if they were not cached in the alignment and they are entirely transformed here with the superposition information in the Multiple Alignment.
getRotation() - Method in class org.biojava.nbio.structure.SVDSuperimposer: Get the Rotation matrix that is required to superimpose the two atom sets.
getRotation(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
getRotationAxis() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Get a unit vector along the rotation axis
getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Returns rotation group (point group) information representing rotational quaternary symmetry, see http://en.wikipedia.org/wiki/Rotation_group_SO(3)
getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getRotationMatrix() - Method in class org.biojava.nbio.structure.align.ce.CECalculator: Gets the rotation matrix from the last call to calc_rmsd.
getRotationMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced: Gets the rotation matrix from the last call to calc_rmsd.
getRotationMatrix() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1
getRotationMatrix() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Get the rotation matrix corresponding to this axis
getRotationMatrix(double) - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Get the rotation matrix corresponding to a rotation about this axis
getRotationMatrix(Matrix4d) - Static method in class org.biojava.nbio.structure.Calc: Convert Vecmath transformation into a JAMA rotation matrix.
getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
getRotationPos() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Get a position on the rotation axis.
getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getRotAxisAndAngle(Matrix3d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup: Given a rotation matrix calculates the rotation axis and angle for it.
getRotAxisAngle(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getRotAxisType(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup: Given a transformation matrix containing a rotation returns the type of rotation: 1 for identity, 2 for 2-fold rotation, 3 for 3-fold rotation, 4 for 4-fold rotation, 6 for 6-fold rotation, -1 for inversions, -2 for mirror planes, -3 for 3-fold improper rotation, -4 for 4-fold improper rotation and -6 for 6-fold improper rotation
getRotMax(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
getRow() - Method in class org.biojava.nbio.structure.align.helper.IndexPair
getRowDimension() - Method in class org.biojava.nbio.structure.jama.Matrix: Get row dimension.
getRowPackedCopy() - Method in class org.biojava.nbio.structure.jama.Matrix: Make a one-dimensional row packed copy of the internal array.
getRows() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getRows() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getRscc() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the rscc property.
getRsr() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the rsr property.
getRsrz() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the rsrz property.
getS() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition: Return the diagonal matrix of singular values
getSaid() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the said property.
getSaveOutputDir() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getScaleableMatrixPanel(Matrix) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
getScid() - Method in class org.biojava.nbio.structure.validation.SymmClash: Gets the value of the scid property.
getSCOP() - Static method in class org.biojava.nbio.structure.scop.ScopFactory: Get the current default instance for the default version
getSCOP(boolean) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
getSCOP(String) - Static method in class org.biojava.nbio.structure.scop.ScopFactory: requests a particular version of SCOP.
getSCOP(String, boolean) - Static method in class org.biojava.nbio.structure.scop.ScopFactory: Gets an instance of the specified scop version.
getScopDescription() - Method in class org.biojava.nbio.structure.scop.server.ScopDescriptions
getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getScopDescriptionBySunid(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Return the SCOP description for a node in the hierarchy by its "sunid" id.
getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getScopDescriptionFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopDescriptionsXML(List<ScopDescription>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopDescriptionXML(ScopDescription) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopDomain() - Method in class org.biojava.nbio.structure.scop.server.ScopDomains
getScopDomainFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getScopDomainsBySunid(Integer) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Get a SCOP domain by its sunid
getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getScopDomainsXML(List<ScopDomain>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopDomainXML(ScopDomain) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopDownloadURL() - Method in class org.biojava.nbio.structure.scop.ScopInstallation: Deprecated.
getScopId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getScopNode(int) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getScopNode(int) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getScopNode(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Access a particular ScopNode.
getScopNode(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getScopNode() - Method in class org.biojava.nbio.structure.scop.server.ScopNodes
getScopNodeFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopNodesXML(List<ScopNode>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopNodeXML(ScopNode) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopVersion() - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getScopVersion() - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getScopVersion() - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Returns the SCOP version
getScopVersion() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getScore() - Method in class org.biojava.nbio.structure.align.model.AFP
getScore(String) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
getScore(String) - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache: Get the value for a particular score.
getScore() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getScore() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: the alignment score
getScore() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getScore() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
getScore() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getScores() - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
getScores() - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache: Get a collection of all scores that have been set.
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers: Returns QuatSymmetryScores averaged over all rotations (except the first rotation, which is the unit operation E)
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup: Returns QuatSymmetryScores averaged over all rotations (except the first rotation, which is the unit operation E)
getScoreThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getScoringStrategy() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getScoringStrategy() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
getScrewTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Get the component of translation parallel to the axis of rotation
getSearchFile() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters: An input file to be used for the DB search
getSecond() - Method in class org.biojava.nbio.structure.contact.Pair
getSecondAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
getSecondGroupAsa(ResidueNumber) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Gets the GroupAsa for the corresponding residue number of second chain
getSecondGroupAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Gets a map of ResidueNumbers to GroupAsas for all groups of second chain.
getSecretion() - Method in class org.biojava.nbio.structure.EntityInfo
getSecStrucElements(Structure) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools: Obtain the List of secondary structure elements (SecStrucElement) of a Structure.
getSecStrucElements(List<Group>) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools: Obtain the List of secondary structure elements (SecStrucElement) of a List of Groups (assumed to be sequential, this is, connected in the original Structure).
getSecStrucInfo(Structure) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools: Obtain the List of secondary structure information (SecStrucInfo) of a Structure.
getSeedFragmentLength() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getSeedRmsdCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getSegId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
getSegmentAtPos(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
getSegmentId() - Method in class org.biojava.nbio.structure.cath.CathSegment
getSegments() - Method in class org.biojava.nbio.structure.cath.CathDomain
getSegments() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
getSegments() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
getSelfAlignment() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getSeq() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the seq property.
getSeq_align_beg() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getSeq_align_end() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getSeq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getSeq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getSeq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getSeqBegin() - Method in class org.biojava.nbio.structure.DBRef: Initial sequence number of the PDB sequence segment.
getSeqEnd() - Method in class org.biojava.nbio.structure.DBRef: Ending sequence number of the PDB sequence segment.
getSeqIdRange() - Method in class org.biojava.nbio.structure.ecod.EcodDomain: Get the range of this domain, in 1-based residue indices (mmCif's _pdbx_poly_seq_scheme.seq_id) Note that EcodDomain.getRange() is used when constructing the domain.
getSeqMisMatches() - Method in interface org.biojava.nbio.structure.Chain: Get annotated sequence mismatches for this chain.
getSeqMisMatches() - Method in class org.biojava.nbio.structure.ChainImpl
getSeqNum() - Method in class org.biojava.nbio.structure.ResidueNumber
getSeqNum() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getSeqNum() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getSeqresEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getSeqResGroup(int) - Method in interface org.biojava.nbio.structure.Chain: Return the Group at given position, from within groups in the SEQRES records of the chain, i.e.
getSeqResGroup(int) - Method in class org.biojava.nbio.structure.ChainImpl: Return the Group at given position, from within groups in the SEQRES records of the chain, i.e.
getSeqResGroups(GroupType) - Method in interface org.biojava.nbio.structure.Chain: Returns a List of all SEQRES groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
getSeqResGroups() - Method in interface org.biojava.nbio.structure.Chain: Returns a list of all groups in SEQRES records of the chain, i.e.
getSeqResGroups(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl: Returns a List of all SEQRES groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
getSeqResGroups() - Method in class org.biojava.nbio.structure.ChainImpl: Returns a list of all groups in SEQRES records of the chain, i.e.
getSeqResLength() - Method in interface org.biojava.nbio.structure.Chain: Returns the number of groups in the SEQRES records of the chain, i.e.
getSeqResLength() - Method in class org.biojava.nbio.structure.ChainImpl: Returns the number of groups in the SEQRES records of the chain, i.e.
getSeqResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getSeqResSequence() - Method in interface org.biojava.nbio.structure.Chain: Returns the PDB SEQRES sequence as a one-letter sequence string.
getSeqResSequence() - Method in class org.biojava.nbio.structure.ChainImpl: Returns the PDB SEQRES sequence as a one-letter sequence string.
getSeqResSequence() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getSeqresStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getSequence() - Method in class org.biojava.nbio.structure.cath.CathDomain
getSequence() - Method in class org.biojava.nbio.structure.cath.CathSegment
getSequenceAlignment(MultipleAlignment, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate the sequence alignment Strings for the whole alignment.
getSequenceAlignment(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate the sequence alignment Strings for the whole alignment.
getSequenceAlignmentClusters() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getSequenceAlignmentClusters(double) - Method in class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains: Get a non-redundent set of clusters for a given sequence cutoff
getSequenceAlignmentClusters() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
getSequenceAlignmentLength() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getSequenceClusterCount() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getSequenceClusterIds() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getSequenceClusterIds() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getSequenceCount() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getSequenceHeader() - Method in class org.biojava.nbio.structure.cath.CathDomain
getSequenceHeader() - Method in class org.biojava.nbio.structure.cath.CathSegment
getSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
getSequenceIdentityThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
getSequenceIdentityThresholds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getSequencePseudoSymmetryThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getSequences() - Method in class org.biojava.nbio.structure.io.FastaStructureParser: Gets the protein sequences read from the Fasta file.
getSequences() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
getSequenceString(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getSeqWeight() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
getSerialversionuid() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getSerNum() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getServer() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getServer() - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider
getServer() - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getServerName() - Static method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Return the String with the PDB server name, including the leading protocol String (http:// or ftp://).
getShift() - Method in class org.biojava.nbio.structure.align.ce.CECalculator: Gets the shift from the last call to calc_rmsd.
getShift() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced: Gets the shift from the last call to calc_rmsd.
getShift() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: returns the shift vector that has to be applied on structure to to shift on structure one
getShortName() - Method in enum org.biojava.nbio.structure.xtal.TransformType
getShortSymbol() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets the international short name (as used in PDB), e.g.
getShowDBresult() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getSiftsMapping(String) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
getSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Returns the similarity score for the alignment.
getSimilarity1() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Deprecated.
use getCoverage1() instead
getSimilarity2() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Deprecated.
use getCoverage2() instead
getSingularValues() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition: Return the one-dimensional array of singular values
getSite_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getSiteID() - Method in class org.biojava.nbio.structure.Site
getSites() - Method in interface org.biojava.nbio.structure.Structure
getSites() - Method in class org.biojava.nbio.structure.StructureImpl
getSize() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
getSmiles() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getSOILD() - Method in class org.biojava.nbio.structure.cath.CathDomain
getSolvent_model_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getSolvent_model_param_bsol() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getSolvent_model_param_ksol() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getSource() - Method in class org.biojava.nbio.structure.align.client.StructureName
getSource() - Method in class org.biojava.nbio.structure.cath.CathDomain
getSpace_group_name_H_M() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
getSpace_group_name_Hall() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
getSpaceGroup() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo: Get the SpaceGroup
getSpaceGroup(int) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser: Gets the space group for the given standard identifier.
getSpaceGroup(String) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser: Get the space group for the given international short name, using the PDB format, e.g.
getSparse() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getSpecies() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getSpeciesId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getSphereCount() - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
getSphereCount() - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
getSplitDirPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Location of split files within the directory, as an array of paths.
getSplitDirPath() - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
getSplitDirPath() - Method in class org.biojava.nbio.structure.io.PDBFileReader
getSplitpat1() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getSplitpat2() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getSrc_method() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getSsBondListFromBondList(List<Bond>) - Static method in class org.biojava.nbio.structure.io.SSBondImpl
getSSBonds() - Method in interface org.biojava.nbio.structure.Structure: Get the list of disulfide Bonds as they have been defined in the PDB files
getSSBonds() - Method in class org.biojava.nbio.structure.StructureImpl: Get the list of disulfide Bonds as they have been defined in the PDB files
getSSEThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getStart() - Method in class org.biojava.nbio.structure.cath.CathFragment
getStart() - Method in class org.biojava.nbio.structure.cath.CathSegment
getStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
getStart() - Method in class org.biojava.nbio.structure.ResidueRange
getStart_construct_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getStartIndex(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block: Calculates and returns the first position of the specified structure in the alignment that is not null.
getStartIndex(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getStartPage() - Method in class org.biojava.nbio.structure.JournalArticle
getStartResidue(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block: Calculates and returns the first residue of the specified structure in the alignment that is not null.
getStartResidue(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor: StartupParameters is a bean to store all the possible command line parameters.
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
getStatus() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
getStatus(String) - Static method in class org.biojava.nbio.structure.PDBStatus: Get the status of the PDB in question.
getStatus(String[]) - Static method in class org.biojava.nbio.structure.PDBStatus: Get the status of the a collection of PDBs in question in a single query.
getStdev() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the stdev property.
getStdev() - Method in class org.biojava.nbio.structure.validation.BondOutlier: Gets the value of the stdev property.
getStdev() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the stdev property.
getStdev() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the stdev property.
getStepSize() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters: how many pairs should be requested for alignment from server?
getStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getStop() - Method in class org.biojava.nbio.structure.cath.CathFragment
getStop() - Method in class org.biojava.nbio.structure.cath.CathSegment
getStrain() - Method in class org.biojava.nbio.structure.EntityInfo
getStrain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getStrain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
getString(String) - Method in class org.biojava.nbio.structure.align.util.ResourceManager
getStructAssemblies() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
getStructAssemblyGens() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
getStructOpers() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
getStructuralTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate a phylogenetic tree of the MultipleAlignment using RMSD distances and the Neighbor Joining algorithm from forester.
getStructure(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Request a Structure based on a name.
getStructure(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Get the structure corresponding to the given StructureIdentifier.
getStructure() - Method in interface org.biojava.nbio.structure.Chain: Returns the parent Structure of this chain.
getStructure() - Method in class org.biojava.nbio.structure.ChainImpl: Returns the parent Structure of this chain.
getStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
getStructure(URL) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
getStructure(File) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Handles the actual parsing of the file into a Structure object.
getStructure() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer: This method will return the parsed protein structure, once the parsing has been finished
getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
getStructure() - Method in class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder: Gets the structure.
getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.PDBFileReader
getStructure(String) - Method in interface org.biojava.nbio.structure.io.StructureIOFile: Open filename and return a Structure object.
getStructure(File) - Method in interface org.biojava.nbio.structure.io.StructureIOFile: Read file from File and returns a Structure object.
getStructure(String) - Static method in class org.biojava.nbio.structure.StructureIO: Loads a structure based on a name.
getStructure(String) - Static method in class org.biojava.nbio.structure.StructureTools: Short version of StructureTools.getStructure(String, PDBFileParser, AtomCache) which creates new parsers when needed
getStructure(String, PDBFileParser, AtomCache) - Static method in class org.biojava.nbio.structure.StructureTools: Flexibly get a structure from an input String.
getStructureById(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
getStructureById(String) - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
getStructureById(String) - Method in interface org.biojava.nbio.structure.io.StructureProvider: get the structure for a PDB ID
getStructureForCathDomain(StructureName) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns a Structure corresponding to the CATH identifier supplied in structureName, using the the CathDatabase at CathFactory.getCathDatabase().
getStructureForCathDomain(StructureName, CathDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns a Structure corresponding to the CATH identifier supplied in structureName, using the specified CathDatabase.
getStructureForDomain(ScopDomain) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForDomain(ScopDomain, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForDomain(ScopDomain, ScopDatabase, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForDomain(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForDomain(String, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Loads a structure directly by PDB ID
getStructureId() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getStructureId() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getStructureIdentifier(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the StructureIdentifier associated with the structure index from its parent Ensemble.
getStructureIdentifier(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getStructureIdentifier() - Method in interface org.biojava.nbio.structure.Structure: Get an identifier corresponding to this structure
getStructureIdentifier() - Method in class org.biojava.nbio.structure.StructureImpl
getStructureIdentifiers() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns a List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
getStructureIdentifiers() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getStructureIds() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getStructures() - Method in class org.biojava.nbio.structure.io.FastaStructureParser: Gets the protein structures mapped from the Fasta file.
getSubRanges(Structure, String) - Static method in class org.biojava.nbio.structure.StructureTools: Deprecated.
Use StructureIdentifier instead (4.2.0)
getSubstitutionMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
getSubstructureMatchingProteinSequence(ProteinSequence, Structure) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher: Get a substructure of wholeStructure containing only the Groups that are included in sequence.
getSubunitCount() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getSubunitRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Returns protein subunit information that was used to determine symmetry information
getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getSubunitTypeCount() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
getSunID() - Method in class org.biojava.nbio.structure.scop.ScopDescription
getSunid() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getSunid() - Method in class org.biojava.nbio.structure.scop.ScopNode
getSuperfamilyId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getSurfaceResidues(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns the residues belonging to the surface
getSurname() - Method in class org.biojava.nbio.structure.Author
getSwissprotId() - Method in interface org.biojava.nbio.structure.Chain: Gets the Swissprot id of this chain.
getSwissprotId() - Method in class org.biojava.nbio.structure.ChainImpl: get the Swissprot id of this chains .
getSym1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getSym2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getSymDeviation() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getSymmClash() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the symmClash property.
getSymmetry() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Returns the symmetry group.
getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getSymmetryAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes: Return all symmetry axes of of the structure: the set of axes that describe all parts of the structure.
getSymmetryClass(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.C2RotationSolver
getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.HelixSolver
getSymmetryOperations() - Method in interface org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver
getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.RotationSolver
getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.SystematicSolver
getSymmetryOrder(Map<Integer, Integer>, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Helper for AlignmentTools.getSymmetryOrder(Map, Map, int, float) with a true identity function (X->X).
getSymmetryOrder(Map<Integer, Integer>, Map<Integer, Integer>, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Tries to detect symmetry in an alignment.
getSymmetryOrder(AFPChain, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Guesses the order of symmetry in an alignment
getSymmGroup() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getSymmLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getSymmLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getSymmOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult: Return the symmetry order determined by the order detector if the symmetry is significant.
getSymmType() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getSymop() - Method in class org.biojava.nbio.structure.validation.SymmClash: Gets the value of the symop property.
getSynonyms() - Method in class org.biojava.nbio.structure.EntityInfo
getSynonyms() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getSynthetic() - Method in class org.biojava.nbio.structure.EntityInfo
getT() - Method in class org.biojava.nbio.structure.align.model.AFP
getTaxonomy() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getTempFactor() - Method in interface org.biojava.nbio.structure.Atom: Get temp factor.
getTempFactor() - Method in class org.biojava.nbio.structure.AtomImpl
getText(Group) - Method in class org.biojava.nbio.structure.io.GroupToSDF
getText() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
getText() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
getTGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getTGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getThePdbId() - Method in class org.biojava.nbio.structure.cath.CathDomain: Returns the PDB ID.
getThreads() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getThree_letter_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getTime() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getTimeout() - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
getTimeout() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getTissue() - Method in class org.biojava.nbio.structure.EntityInfo
getTissue() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getTissue_fraction() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getTitle() - Method in class org.biojava.nbio.structure.EntityInfo
getTitle() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
getTitle() - Method in class org.biojava.nbio.structure.JournalArticle: Get the value of title
getTitle() - Method in class org.biojava.nbio.structure.PDBHeader
getTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getTmIntra() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getTMScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Returns the tmScore of the alignment.
getTMScore(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPChainScorer
getTMScore(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.SVDSuperimposer: Calculate the TM-Score for the superposition.
getTMScoreAlternate(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.SVDSuperimposer: Calculate the TM-Score for the superposition.
getTo() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
getTo() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getTopologyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getTorsionPenalty() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getTotal() - Method in class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
getTotal() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
getTotalArea() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns the total area buried upon formation of this interface, defined as: 1/2[ (ASA1u-ASA1c) + (ASA2u-ASA2u) ] , with:
getTotalArea() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster: Return the average buried surface area for this interface cluster
getTotalLenIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getTotalLenOpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getTotalRmsdIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain: this is the init-RMSD, not the final RMSD after refinement.
getTotalRmsdOpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain: The RMSD of the final alignment.
getTraceRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getTraces() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getTraceTmScoreMin() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getTrans() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getTranscoefpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getTransfAlgebraic(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets a transformation algebraic string given its index.
getTransfAlgebraic() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getTransformation(Matrix, Matrix) - Static method in class org.biojava.nbio.structure.Calc: Convert JAMA rotation and translation to a Vecmath transformation matrix.
getTransformation(Matrix, Atom) - Static method in class org.biojava.nbio.structure.Calc: Convert JAMA rotation and translation to a Vecmath transformation matrix.
getTransformation() - Method in class org.biojava.nbio.structure.SVDSuperimposer
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getTransformation(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets a transformation by index expressed in crystal axes basis.
getTransformationMap() - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser: Returns a map of bioassembly transformations
getTransformationMatrix() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Return the transformation (both rotational and translational component) as a 4x4 transformation matrix.
getTransformationMatrix() - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
getTransformations() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Returns a transformation matrix for each structure giving the 3D superimposition information of the multiple structure alignment.
getTransformations() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
getTransformations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets all transformations except for the identity in crystal axes basis.
getTransformationsOrthonormal() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo: Gets all symmetry transformation operators corresponding to this structure's space group (including the identity, at index 0) expressed in the orthonormal basis.
getTransformedCoordinates() - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
getTransformId() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
getTransforms() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Return the 2 crystal transform operations performed on each of the molecules of this interface.
getTransforms() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo: Return the list of BiologicalAssemblyTransformations needed to generate the biological assembly.
getTransformType() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Returns the TransformType of this transformation: AU, crystal translation, fractional translation , 2 3 4 6-fold rotations, 2 3 4 6-fold screw rotations, -1 -3 -2 -4 -6 inversions/rotoinversions.
getTranslatedBbs(Vector3d) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox: Returns a new BoundingBoxes object containing the same bounds as this BoundingBoxes object translated by the given translation
getTranslation(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
getTranslation() - Method in class org.biojava.nbio.structure.SVDSuperimposer: Get the shift vector.
getTranslationVector(Matrix4d) - Static method in class org.biojava.nbio.structure.Calc: Extract the translational vector of a Vecmath transformation.
getTranslScrewComponent() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
getTranslScrewComponent(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.CrystalTransform: Given a transformation matrix containing a rotation and translation returns the screw component of the rotation.
getTransmembraneProteins() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: get all Transmembrane proteins
getTransNCS() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the transNCS property.
getTree(CathDomain) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return the CATH sub-tree for a particular domain.
getTree(CathDomain) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getTree(ScopDomain) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: get the SCOP sub-tree for a particular domain.
getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getTurn() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getTwi() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getTwinFraction() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the twinFraction property.
getTwinL() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the twinL property.
getTwinL2() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the twinL2 property.
getTwistedGroups() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
getTwoFoldsPerpendicular() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
getType() - Method in class org.biojava.nbio.structure.AminoAcidImpl
getType() - Method in class org.biojava.nbio.structure.EntityInfo
getType() - Method in interface org.biojava.nbio.structure.Group: Get Type of group, one of GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE
getType() - Method in class org.biojava.nbio.structure.HetatomImpl: Get Type of group, one of GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getType() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
getType() - Method in class org.biojava.nbio.structure.NucleotideImpl
getType() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getType() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getType() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
getType() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement: Returns the SecStrucType of this element.
getType() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
getType() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getType_symbol() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getType_symbol() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getU() - Method in class org.biojava.nbio.structure.jama.LUDecomposition: Return upper triangular factor
getU() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition: Return the left singular vectors
getUid() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getUnalignedGroups(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools: List of groups from the structure not included in ca (e.g.
getUnaryOperators() - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver: Returns a list of operators for this assembly.
getUniProtAccessionId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getUniprotEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getUniProtId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getUniProtId() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getUniProtId() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getUniProtPos() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getUniProtResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getUniprotStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getUniqueInterfaces() - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder: Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.
getUniqueInterfaces(double) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder: Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.
getUniqueSequenceList() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getUnitv() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getUnitVectors() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getUpdates() - Method in class org.biojava.nbio.structure.rcsb.RCSBUpdates
getUpperBound() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getUrl() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Get the top-level ECOD server URL.
getUrl() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
getURL() - Method in class org.biojava.nbio.structure.URLIdentifier
getUsed() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getUsedAtomNames() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getUserConfigHelp() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams: The help text for each of these parameters.
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
getUserConfigHelp() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getUserConfigParameterNames() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams: The labels to be displayed to the user for each parameter
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getUserConfigParameters() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams: get the list of parameters that the user can change through the user interface.
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
getUserConfigParameters() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getUserConfigTypes() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams: Get the data types of the parameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getUsername() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getUserOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getV() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition: Return the eigenvector matrix
getV() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition: Return the right singular vectors
getValenceElectronCount() - Method in enum org.biojava.nbio.structure.Element: Returns the number of valence electrons for this Element.
getValidFolds(List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer: Find valid symmetry orders for a given stoichiometry.
getValue() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
getValue() - Method in class org.biojava.nbio.structure.align.helper.GapArray
getValue_order() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getVariant() - Method in class org.biojava.nbio.structure.EntityInfo
getVDWRadius() - Method in enum org.biojava.nbio.structure.Element: Returns the van der Waals radius of this Element.
getVector() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getVector3dScrewTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
getVersion() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
getVersion() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeCPMain
getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeMain
getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
getVersion() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
getVersion() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
getVersion() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
getVersion() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getVersion() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
getVersion() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the version of the algorithm used to generate the MultipleAlignment objects.
getVersion() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getVersion() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner: Get the Version information for this Algorithm.
getVersion() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
getVersion() - Method in interface org.biojava.nbio.structure.align.StructureAlignment: Get the Version information for this Algorithm.
getVersion() - Method in class org.biojava.nbio.structure.cath.CathDomain
getVersion() - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase: Return the release version.
getVersion() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
getVersion() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Return the ECOD version, as parsed from the file.
getVersion() - Method in class org.biojava.nbio.structure.validation.Program: Gets the value of the version property.
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron: Returns the vertices of an n-fold polygon of given radius and center
getVertices() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism: Returns the vertices of an n-fold polygon of given radius and center
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism: Returns the vertices of an n-fold polygon of given radius and center
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron: Returns the vertices of an n-fold polygon of given radius and center
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getViewCount() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getViewMatrix(int) - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getViewName(int) - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
getVolume() - Method in class org.biojava.nbio.structure.JournalArticle
getVolume() - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Returns the volume of this unit cell.
getWeight() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getWeight() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getWidth() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism: Returns the radius of an inscribed sphere, that is tangent to each of the octahedron's faces
getWilsonBaniso() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the wilsonBaniso property.
getWilsonBestimate() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the wilsonBestimate property.
getWinSize() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: The window size to look at
getWinSize() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
getX() - Method in interface org.biojava.nbio.structure.Atom: Get coordinate X.
getX() - Method in class org.biojava.nbio.structure.AtomImpl: Get coordinate X.
getXGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getXGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getXMLcreationDate() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the xmLcreationDate property.
getXtriageInputColumns() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the xtriageInputColumns property.
getXYZEuler(Matrix) - Static method in class org.biojava.nbio.structure.Calc: Convert a rotation Matrix to Euler angles.
getY() - Method in interface org.biojava.nbio.structure.Atom: Get coordinate Y.
getY() - Method in class org.biojava.nbio.structure.AtomImpl: Get coordinate Y.
getZ() - Method in interface org.biojava.nbio.structure.Atom: Get coordinate Z.
getZ() - Method in class org.biojava.nbio.structure.AtomImpl: Get coordinate Z.
getZ() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo: Deprecated.
As of 4.0, use SpaceGroup.getMultiplicity() and Structure.size()
getZ() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the z property.
getZ() - Method in class org.biojava.nbio.structure.validation.BondOutlier: Gets the value of the z property.
getZ_PDB() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getZscore() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the zscore property.
getZscore() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the zscore property.
getZYZEuler(Matrix) - Static method in class org.biojava.nbio.structure.Calc: Gets euler angles for a matrix given in ZYZ convention.
GLOBAL_ALIGN1 - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
GLOBAL_ALIGN2 - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
Gotoh - Class in org.biojava.nbio.structure.align.pairwise: a class to perform Gotoh algorithm
Gotoh(Alignable) - Constructor for class org.biojava.nbio.structure.align.pairwise.Gotoh
GraphComponentOrderDetector - Class in org.biojava.nbio.structure.symmetry.internal: The GraphOrderDetector transforms the self-alignment into a Graph and extracts its maximally connected Components.
GraphComponentOrderDetector() - Constructor for class org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector
GraphComponentRefiner - Class in org.biojava.nbio.structure.symmetry.internal: The GraphRefiner transforms the self-alignment into a Graph and extracts its maximally connected Components.
GraphComponentRefiner() - Constructor for class org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner
grayOutCEOrig(Atom[], int, int, CECalculator, Matrix, int, double[], double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Grays out the main diagonal of a duplicated distance matrix.
grayOutPreviousAlignment(AFPChain, Atom[], int, int, CECalculator, Matrix, int, double[], double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Grid - Class in org.biojava.nbio.structure.contact: A grid to be used for calculating atom contacts through geometric hashing algorithm.
Grid(double) - Constructor for class org.biojava.nbio.structure.contact.Grid: Creates a Grid, the cutoff is in Angstroms and can be specified to a precision of 0.01A
GridCell - Class in org.biojava.nbio.structure.contact: A grid cell to be used in contact calculation via geometric hashing algorithm.
GridCell() - Constructor for class org.biojava.nbio.structure.contact.GridCell
Group - Interface in org.biojava.nbio.structure: This is the data structure for a single Group of atoms.
GroupAsa - Class in org.biojava.nbio.structure.asa: A class to store the results of ASA calculations, it can hold ASA values per atom present in Group
GroupAsa(Group) - Constructor for class org.biojava.nbio.structure.asa.GroupAsa
GroupContact - Class in org.biojava.nbio.structure.contact: A pair of residues that are in contact
GroupContact() - Constructor for class org.biojava.nbio.structure.contact.GroupContact
GroupContactSet - Class in org.biojava.nbio.structure.contact: A set of residue-residue contacts.
GroupContactSet() - Constructor for class org.biojava.nbio.structure.contact.GroupContactSet
GroupContactSet(AtomContactSet) - Constructor for class org.biojava.nbio.structure.contact.GroupContactSet: Constructs a GroupContactSet by collapsing the given AtomContactSet into residue-residue (group-group) contacts.
GroupIterator - Class in org.biojava.nbio.structure: An iterator over all groups of a structure.
GroupIterator(Structure) - Constructor for class org.biojava.nbio.structure.GroupIterator: Constructs a GroupIterator object.
GroupToSDF - Class in org.biojava.nbio.structure.io
GroupToSDF() - Constructor for class org.biojava.nbio.structure.io.GroupToSDF
GroupType - Enum in org.biojava.nbio.structure: This contains basic categories for Group types.
GTSlikeScore(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
guessFiletype(String) - Static method in class org.biojava.nbio.structure.StructureIO: Attempts to guess the type of a structure file based on the extension
guessOrderFromAngle(double, int) - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Returns the rotation order o that gives the lowest value of |2PI / o - theta, given that the value is strictly lower than threshold, for orders o=1,...,maxOrder.
guessPDBID(String) - Static method in class org.biojava.nbio.structure.URLIdentifier: Recognizes PDB IDs that occur at the beginning of name followed by some delimiter.
guessScopDomain(String, ScopDatabase) - Static method in class org.biojava.nbio.structure.align.client.StructureName: Guess a scop domain.
guessSequentialAlignment(Map<Integer, Integer>, boolean) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Takes a potentially non-sequential alignment and guesses a sequential version of it.
GuiWrapper - Class in org.biojava.nbio.structure.align.ce: A class to wrap some of the strucutre.gui classes using Reflection
GuiWrapper() - Constructor for class org.biojava.nbio.structure.align.ce.GuiWrapper

H

has3D() - Method in interface org.biojava.nbio.structure.Group: Return true or false, depending if this group has 3D coordinates or not.
has3D() - Method in class org.biojava.nbio.structure.HetatomImpl: returns true or false, depending if this group has 3D coordinates or not.
hasAltLoc() - Method in interface org.biojava.nbio.structure.Group: Test if this group has alternate locations.
hasAltLoc() - Method in class org.biojava.nbio.structure.HetatomImpl
hasAminoAtoms() - Method in interface org.biojava.nbio.structure.Group: Calculate if this group has all atoms required for an amino acid backbone.
hasAminoAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl: Calculate if this group has all atoms required for an amino acid backbone.
hasAtom(String) - Method in interface org.biojava.nbio.structure.Group: Tell whether a particular atom exists within this group.
hasAtom(String) - Method in class org.biojava.nbio.structure.HetatomImpl: Tell whether a particular atom exists within this group.
hasBiolAssembly(String) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider: Does the PDB ID have biological assembly information?
hasBiolAssembly(String) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
hasBiolAssembly() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
hasBiolAssembly(String) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
hasBiolAssembly() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: Does the PDB ID have biological assembly information?
hasBiolAssembly(String) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
hasBiolAssembly() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
hasBiologicalAssembly(String) - Static method in class org.biojava.nbio.structure.StructureIO: Does the provider PDB ID have a biological assembly?
hasChain(String) - Method in interface org.biojava.nbio.structure.Structure: Check if a chain with the id chainId is contained in this structure.
hasChain(String) - Method in class org.biojava.nbio.structure.StructureImpl: Check if a chain with the id chainId is contained in this structure.
hasContact(Atom, Atom) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
hasContact(AtomIdentifier, AtomIdentifier) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
hasContact(Group, Group) - Method in class org.biojava.nbio.structure.contact.GroupContactSet: Tell whether the given group pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers
hasContact(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.contact.GroupContactSet: Tell whether the given pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers
hasContact(ResidueIdentifier, ResidueIdentifier) - Method in class org.biojava.nbio.structure.contact.GroupContactSet: Tell whether the given pair is a contact in this GroupContactSet, in a chain-identifier independent way: contacts happening between different copies of the same Compound(Entity) will be considered equal as long as they have the same residue numbers.
hasContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContactSet: Returns true if at least 1 contact from this set is within the given distance.
hashCode() - Method in class org.biojava.nbio.structure.align.client.PdbPair
hashCode() - Method in class org.biojava.nbio.structure.align.client.StructureName
hashCode() - Method in class org.biojava.nbio.structure.align.model.AFPChain
hashCode() - Method in class org.biojava.nbio.structure.Author
hashCode() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
hashCode() - Method in class org.biojava.nbio.structure.contact.Pair
hashCode() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
hashCode() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
hashCode() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
hashCode() - Method in class org.biojava.nbio.structure.io.SSBondImpl
hashCode() - Method in class org.biojava.nbio.structure.ResidueNumber
hashCode() - Method in class org.biojava.nbio.structure.ResidueRange
hashCode() - Method in class org.biojava.nbio.structure.ResidueRangeAndLength
hashCode() - Method in class org.biojava.nbio.structure.scop.ScopDescription
hashCode() - Method in class org.biojava.nbio.structure.Site
hashCode() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
hashCode() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
hasJournalArticle() - Method in class org.biojava.nbio.structure.PDBHeader: Return whether or not the entry has an associated journal article or publication.
hasJournalArticle() - Method in interface org.biojava.nbio.structure.Structure: Return whether or not the entry has an associated journal article or publication.
hasJournalArticle() - Method in class org.biojava.nbio.structure.StructureImpl: Return whether or not the entry has an associated journal article or publication.
hasMore() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
hasNext() - Method in class org.biojava.nbio.structure.AtomIterator: Is there a next atom ?
hasNext() - Method in class org.biojava.nbio.structure.GroupIterator: is there a group after the current one in the structure?
hasNext() - Method in class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
hasParent() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
hasPrecalculatedResult(String, String, String, String) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
hasPrecalculatedResult(String, String, String, String, int) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
hasProteinSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Returns true if structure contains protein subunits.
HasResultXMLConverter - Class in org.biojava.nbio.structure.align.xml
HasResultXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.HasResultXMLConverter
HBond - Class in org.biojava.nbio.structure.secstruc: Container that represents a hidrogen bond.
HBond() - Constructor for class org.biojava.nbio.structure.secstruc.HBond
HBond(HBond) - Constructor for class org.biojava.nbio.structure.secstruc.HBond
HBONDHIGHENERGY - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc: higher limit for H-bond energy
HBONDLOWENERGY - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc: Minimal H-bond energy in cal/mol
HelicalRepeatUnit - Class in org.biojava.nbio.structure.symmetry.core
HelicalRepeatUnit(Subunits) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
Helix - Class in org.biojava.nbio.structure.symmetry.core
Helix() - Constructor for class org.biojava.nbio.structure.symmetry.core.Helix
HelixAxisAligner - Class in org.biojava.nbio.structure.symmetry.core
HelixAxisAligner(QuatSymmetryResults) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
HelixExtender - Class in org.biojava.nbio.structure.symmetry.core
HelixExtender(Subunits, Helix) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixExtender
HelixLayers - Class in org.biojava.nbio.structure.symmetry.core
HelixLayers() - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixLayers
HelixSolver - Class in org.biojava.nbio.structure.symmetry.core
HelixSolver(Subunits, int, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixSolver
HetatomImpl - Class in org.biojava.nbio.structure: Generic Implementation of a Group interface.
HetatomImpl() - Constructor for class org.biojava.nbio.structure.HetatomImpl: Construct a Hetatom instance.
HetatomImpl.PerformanceBehavior - Enum in org.biojava.nbio.structure: Behaviors for how to balance memory vs.
hieFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
HTTPConnectionTools - Class in org.biojava.nbio.structure.align.util: a class that takes care about opening HttpURLConnections and sets the proper timeouts
HTTPConnectionTools() - Constructor for class org.biojava.nbio.structure.align.util.HTTPConnectionTools
hypot(double, double) - Static method in class org.biojava.nbio.structure.jama.Maths: sqrt(a^2 + b^2) without under/overflow.

I

icode - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
IcosahedralSampler - Class in org.biojava.nbio.structure.symmetry.geometry
Icosahedron - Class in org.biojava.nbio.structure.symmetry.geometry
Icosahedron() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
Identifier - Class in org.biojava.nbio.structure: Deprecated.
Use StructureName instead. Deprecated in v. 4.2.0
Identifier() - Constructor for class org.biojava.nbio.structure.Identifier: Deprecated.
identity(int, int) - Static method in class org.biojava.nbio.structure.jama.Matrix: Generate identity matrix
IDENTITY - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder
IDENTITY - Static variable in class org.biojava.nbio.structure.xtal.CrystalTransform
IDENTITY_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.CompoundFinder: Identity value for 2 chains to be considered part of same entity
IdentityMap() - Constructor for class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
identityMatch(Atom[], String, int, int, String) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster: Match a sequence to this cluster at 100% identity.
IdxComparator - Class in org.biojava.nbio.structure.align.helper
IdxComparator() - Constructor for class org.biojava.nbio.structure.align.helper.IdxComparator
index - Variable in class org.biojava.nbio.structure.align.helper.GapArray
indexOf(String, String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
IndexPair - Class in org.biojava.nbio.structure.align.helper
IndexPair() - Constructor for class org.biojava.nbio.structure.align.helper.IndexPair
IndexPair(short, short) - Constructor for class org.biojava.nbio.structure.align.helper.IndexPair
initializeBreakFlag(boolean[][]) - Method in interface org.biojava.nbio.structure.align.ce.MatrixListener
initializeCellTranslations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
initPaths() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Should be called whenever any of the path variables change.
initSumOfDistances(int, int, int, int, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
initSumOfDistances(int, int, int, int, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
interrupt() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch: stops what is currently happening and does not continue
inverse() - Method in class org.biojava.nbio.structure.jama.Matrix: Matrix inverse or pseudoinverse
invert(Atom) - Static method in class org.biojava.nbio.structure.Calc
invertAlignment(AFPChain) - Method in class org.biojava.nbio.structure.align.ce.CeCPMain: Swaps the order of structures in an AFPChain
ioverSigma - Variable in class org.biojava.nbio.structure.validation.Entry
IS_DOMAIN_ASSEMBLY - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser: Deprecated way of indicating there is an assembly.
IS_REPRESENTATIVE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser: Indicates a manual representative
isAlignSeqRes() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.
isAutoFetch() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
isAutoFetch() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
Use AtomCache.getFetchBehavior()
isAutoFetch() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Deprecated.
Use LocalPDBDirectory.getFetchBehavior()
isBend() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
isBetaStrand() - Method in enum org.biojava.nbio.structure.secstruc.SecStrucType: A Beta-Strand is an extended set of sequential Bridges that, together with other Beta-Strands, is part of a Beta-Sheet.
isBioAssembly() - Method in class org.biojava.nbio.structure.align.client.StructureName
isBiologicalAssembly() - Method in interface org.biojava.nbio.structure.Structure: Get flag that indicates if this structure is a biological assembly
isBiologicalAssembly() - Method in class org.biojava.nbio.structure.StructureImpl: Gets flag that indicates if this structure is a biological assembly
isCacheEnabled() - Method in class org.biojava.nbio.structure.domain.SerializableCache
isCathID() - Method in class org.biojava.nbio.structure.align.client.StructureName
isCellReasonable() - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Checks whether the dimensions of this crystal cell are reasonable for protein crystallography: if all 3 dimensions are below 10.0 the cell is considered unrealistic and false returned
isChainPureNonPolymer(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Returns true if the given chain is composed of non-polymeric groups only
isChainWaterOnly(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Returns true if the given chain is composed of water molecules only
isChalcogen() - Method in enum org.biojava.nbio.structure.Element: Returns true if Element is a chalcogen (O, S, Se, Te, Po).
isCompatible(ResidueGroup) - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup: Determine if two Residuegroups (maximally connected components of the alignment Graph) are compatible, based in the following criterion:
isComplete() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
isConnected(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc: Test if two amino acids are connected, i.e.
isCrystallographic() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique
isCrystallographic(Set<ExperimentalTechnique>) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique: Given a Set of ExperimentalTechniques returns true if at least one is crystallographic
isCrystallographic() - Method in interface org.biojava.nbio.structure.Structure: Test if this structure is a crystallographic structure, i.e.
isCrystallographic() - Method in class org.biojava.nbio.structure.StructureImpl: Whether this Structure is a crystallographic structure or not.
isDebug() - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Deprecated.
isDefined() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
isDoAngleCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
isDoDensityCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
isDoDistanceCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
isDomainSplit() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
isDoRMSCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
isDownloadAll() - Method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider: By default this provider will download only some of the ChemComp files.
isEcodDomain() - Method in class org.biojava.nbio.structure.align.client.StructureName
isEmpty() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp: Indicates whether this compound was created with
isEnantiomorphic() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
isEquivalent(CrystalTransform) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Returns true if the given CrystalTransform is equivalent to this one.
isErrorXML(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser: returns true if the alignment XML contains an error message
isFetchCurrent() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
Use FileParsingParameters#getObsoleteBehavior() instead (4.0.0)
isFetchCurrent() - Method in class org.biojava.nbio.structure.io.PDBFileReader: Deprecated.
Use FileParsingParameters#getObsoleteBehavior()
isFetchFileEvenIfObsolete() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
Use FileParsingParameters#getObsoleteBehavior() instead (4.0.0)
isFetchFileEvenIfObsolete() - Method in class org.biojava.nbio.structure.io.PDBFileReader: Deprecated.
Use FileParsingParameters#getObsoleteBehavior()
isFile() - Method in class org.biojava.nbio.structure.align.client.StructureName: Indicates that the identifier was determined to correspond to a file.
isFlexible() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
isFractionalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Tells whether this transformation contains a fractional translational component (whatever its rotational component).
isFullRank() - Method in class org.biojava.nbio.structure.jama.QRDecomposition: Is the matrix full rank?
isGaps() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
isGuiModuleInstalled() - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
isHalogen() - Method in enum org.biojava.nbio.structure.Element: Returns true if Element is a halogen (F, Cl, Br, I, At).
isHeaderOnly() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: Parse only the PDB file header out of the files
isHeavyAtom() - Method in enum org.biojava.nbio.structure.Element: Returns true is the Element is an not Hydrogen (or an isotope of Hydrogen).
isHelixType() - Method in enum org.biojava.nbio.structure.secstruc.SecStrucType: Helix type can be 3-10 helix, pi-helix or alpha-helix.
isHeteroAtom() - Method in enum org.biojava.nbio.structure.Element: Returns true if Element is not Hydrogen and not Carbon.
isHomomeric() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns true if the 2 molecules of this interface are the same entity (i.e.
isHydrogen() - Method in enum org.biojava.nbio.structure.Element: Returns true if this Element is Hydrogen.
isIdentity() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Tells whether this transformation is the identity: no rotation and no translation
isInfinite() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns true if the transformation applied to the second molecule of this interface has an infinite character (pure translation or screw rotation) and both molecules of the interface have the same asymmetric unit identifier (chain id): in such cases the interface would lead to infinite fiber-like (linear or helical) assemblies
isInfinite() - Method in enum org.biojava.nbio.structure.xtal.TransformType: Tells whether the transform type produces infinite assemblies if interface happens between identical chains
isIsologous() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Tell whether the interface is isologous, i.e.
isJoinFast() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
isJoinPlo() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
isLocal() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Return true
isLocalSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
isMatch(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList: Return true is the sequence and residues numbers of the passed in array of atoms matches those of this unique sequence list
isMetal() - Method in enum org.biojava.nbio.structure.Element: Returns true if ElementType is a metal.
isMetal() - Method in enum org.biojava.nbio.structure.ElementType: Returns true if ElementType is a metal.
isMetalloid() - Method in enum org.biojava.nbio.structure.Element: Returns true if ElementType is a metalloid.
isMetalloid() - Method in enum org.biojava.nbio.structure.ElementType: Returns true if ElementType is a metalloid.
isNmr() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique
isNmr(Set<ExperimentalTechnique>) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique: Given a Set of ExperimentalTechniques returns true if at least one is NMR
isNmr() - Method in interface org.biojava.nbio.structure.Structure: Test if this structure is an NMR structure.
isNmr() - Method in class org.biojava.nbio.structure.StructureImpl: Whether this Structure is a NMR structure or not.
isNonMetal() - Method in enum org.biojava.nbio.structure.Element: Returns true if ElementType is a non-metal.
isNonMetal() - Method in enum org.biojava.nbio.structure.ElementType: Returns true if ElementType is a non-metal.
isNonsingular() - Method in class org.biojava.nbio.structure.jama.LUDecomposition: Is the matrix nonsingular?
isNoOverlap() - Method in class org.biojava.nbio.structure.contact.Grid: Tells whether (after having added atoms to grid) the i and j grids are not overlapping.
isNucleicAcid(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Tell whether given chain is DNA or RNA
isNucleotide(String) - Static method in class org.biojava.nbio.structure.StructureTools: Test if the three-letter code of an ATOM entry corresponds to a nucleotide or to an aminoacid.
isOnTheFly() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
isOutputPDB() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters: When writing the results to a file, don;t write as XML but write aligned PDB file
isParseBioAssembly() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: Should the biological assembly info (REMARK 350) be parsed from the PDB file?
isParseCAOnly() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: The flag if only the C-alpha atoms of the structure should be parsed.
isParseSecStruc() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: Is secondary structure assignment being parsed from the file? default is null
isPdbDirSplit() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters: Deprecated.
Always returns true (4.0.0)
isPdbId() - Method in class org.biojava.nbio.structure.align.client.StructureName
isPDPDomain() - Method in class org.biojava.nbio.structure.align.client.StructureName
isPreferredResult() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
isPrint - Static variable in class org.biojava.nbio.structure.align.ce.CECalculator
isPrint - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
isPrintCE() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters: Display the output string in CE style
isPrintFatCat() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
isPrintXML() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
isProtein(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Tell whether given chain is a protein chain
isPseudoStoichiometric() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
isPseudoStoichiometric() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
isPseudoSymmetric() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
isPublished() - Method in class org.biojava.nbio.structure.JournalArticle
isPureCrystalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Tells whether this transformation is a pure crystal lattice translation, i.e.
isPureTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Tells whether this transformation is a pure translation: either a pure crystal (lattice) translation or a fractional (within unit cell) translation: space groups Ixxx, Cxxx, Fxxx have operators with fractional translations within the unit cell.
isReachable() - Method in class org.biojava.nbio.structure.scop.ScopMirror
isRefined() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
isRefined(MultipleAlignment) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Returns true a symmetry multiple alignment has been refined, false otherwise.
isReplaced(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
isReplaced(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
isReplacer(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
isReplacer(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
isRotation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Tells whether this transformation is a rotation disregarding the translational component, i.e.
isRunBackground() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters: Flag if a job that only runs one parallell job should be run in its own thread or in the main thread.
isScopName() - Method in class org.biojava.nbio.structure.align.client.StructureName
isScrew() - Method in enum org.biojava.nbio.structure.xtal.TransformType: Tells whether the transform type is a screw or glide plane
isSequentialAlignment() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Get whether this alignment has the normal topology, ie the residues aligned in each block increase sequentially over the original protein.
isSequentialAlignment(AFPChain, boolean) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Checks that the alignment given by afpChain is sequential.
isShortAlign() - Method in class org.biojava.nbio.structure.align.model.AFPChain
isShow3d() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
isShowAFPRanges() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
isShowAFPRanges() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
isShowMenu() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
isSignificant() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult: Conditions checked are: score above the threshold, order higher than 1 and refinement succeeded.
isSignificant(MultipleAlignment, double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Returns true if the symmetry alignment is significant, false otherwise.
isSignificantResult() - Method in class org.biojava.nbio.structure.align.model.AFPChain
isSPD() - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition: Is the matrix symmetric and positive definite?
isStandard() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
isStandardChemComp(ChemComp) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
isStrictSCOP() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
since 4.2
isSymRelated() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Tells whether the interface corresponds to one mediated by crystallographic symmetry, i.e.
isTryAllCPs() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
isUnaryExpression(String) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools: Checks if the passed in expression is a unary operator expression Example: (1,2,3) or (1-60) are unary operator expressions (1-60)(61-88) is a binary operator expression, representing a cartesian product of the two parenthesised lists
isUpdateRemediatedFiles() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
isUpdateRemediatedFiles() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: Deprecated.
Properties which impact downloading and caching behavior have been moved to the StructureIOFile implementations. See LocalPDBDirectory#getFetchBehavior(LocalPDBDirectory.FetchBehavior)
isURL() - Method in class org.biojava.nbio.structure.align.client.StructureName
isUseInternalChainId() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: Should we use internal (asym_id) or public facing (author) chain ids
isUseMmCif() - Method in class org.biojava.nbio.structure.align.util.AtomCache
isVerbose() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters: Flag if the job should be run in verbose mode.
isVerbose() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
isWaitForAlignments() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
isWater() - Method in interface org.biojava.nbio.structure.Group: Determines if this group is water.
isWater() - Method in class org.biojava.nbio.structure.HetatomImpl
iterator() - Method in class org.biojava.nbio.structure.AugmentedResidueRange: Returns a new Iterator over every ResidueNumber in this ResidueRange.
iterator() - Method in class org.biojava.nbio.structure.contact.AtomContactSet
iterator() - Method in class org.biojava.nbio.structure.contact.GroupContactSet
iterator() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
iterator() - Method in interface org.biojava.nbio.structure.Group: get an Atom Iterator.
iterator() - Method in class org.biojava.nbio.structure.HetatomImpl: return an AtomIterator.
iterator() - Method in class org.biojava.nbio.structure.math.SymbolTable: Return an Iterator for the keys in the table.
iterator(AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange: Returns a new Iterator over every ResidueNumber in this ResidueRange.
iterator(AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRangeAndLength: Returns a new Iterator over every ResidueNumber in this ResidueRange.

J

JFatCatClient - Class in org.biojava.nbio.structure.align.client
JFatCatClient() - Constructor for class org.biojava.nbio.structure.align.client.JFatCatClient
JobKillException - Exception in org.biojava.nbio.structure.align.client
JobKillException(String) - Constructor for exception org.biojava.nbio.structure.align.client.JobKillException
JointFragments - Class in org.biojava.nbio.structure.align.helper: A utility class that defines which set of atoms are considered to be on equivalent positions.
JointFragments() - Constructor for class org.biojava.nbio.structure.align.helper.JointFragments
jointFragments(JointFragments[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
JournalArticle - Class in org.biojava.nbio.structure: PDB-specific
JournalArticle() - Constructor for class org.biojava.nbio.structure.JournalArticle

K

key - Variable in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements
keys() - Method in class org.biojava.nbio.structure.math.SymbolTable: Return an Iterable for the keys in the table.
keySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

L

Ladder - Class in org.biojava.nbio.structure.secstruc: A Ladder is a set of one or more consecutive bridges of identical type.
Ladder() - Constructor for class org.biojava.nbio.structure.secstruc.Ladder
LAST_REMEDIATION_DATE - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory: Date of the latest PDB file remediation
LATEST_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathFactory
LATEST_VERSION - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
length() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Returns the total number of aligned positions (columns) in the Block.
length() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
length() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Returns the total number of aligned residues (columns) in the alignment: the sum of all Block lengths.
length() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
length() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the total number of aligned residues (columns) in the multiple alignment: the sum of all BlockSet lengths.
length() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
ligRSRnbrMean - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
ligRSRnbrStdev - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
ligRSRnumnbrs - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
ligRSRZ - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
lineSplit - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
lineSplit - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
linkChains2Compound(Structure) - Method in class org.biojava.nbio.structure.io.PDBFileParser: After the parsing of a PDB file the Chain and EntityInfo objects need to be linked to each other.
LinkRecord(String, String, String, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
ListStringWrapper - Class in org.biojava.nbio.structure.scop.server
ListStringWrapper() - Constructor for class org.biojava.nbio.structure.scop.server.ListStringWrapper
load() - Static method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping: Loads the SIFTS mapping.
load(boolean) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping: Loads the SIFTS mapping.
loadFromDirectAccess() - Method in class demo.DemoMMCIFReader: An example demonstrating how to directly use the mmCif file parsing classes.
loadIdentifier(String, AtomCache) - Static method in class org.biojava.nbio.structure.Identifier: Deprecated.
Create a new StructureName instead.
loadPDB(String) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
loadSimple() - Method in class demo.DemoMMCIFReader: A basic example how to load an mmCif file and get a Structure object
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.align.client.StructureName
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.cath.CathDomain
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.domain.PDPDomain
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.PassthroughIdentifier: Passthrough identifiers don't know how to load a structure
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.scop.ScopDomain
loadStructure(AtomCache) - Method in interface org.biojava.nbio.structure.StructureIdentifier: Loads a structure encompassing the structure identified.
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.SubstructureIdentifier: Loads the complete structure based on SubstructureIdentifier.getPdbId().
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.URLIdentifier: Load the structure from the URL
loadStructureFromCache() - Method in class demo.DemoLoadStructure
loadStructureFromCifByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
loadStructureFromPdbByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
loadStructureIO() - Method in class demo.DemoLoadStructure
LocalPDBDirectory - Class in org.biojava.nbio.structure.io: Superclass for classes which download and interact with the PDB's FTP server, specifically PDBFileReader and MMCIFFileReader.
LocalPDBDirectory(String) - Constructor for class org.biojava.nbio.structure.io.LocalPDBDirectory: Subclasses should provide default and single-string constructors.
LocalPDBDirectory() - Constructor for class org.biojava.nbio.structure.io.LocalPDBDirectory
LocalPDBDirectory.FetchBehavior - Enum in org.biojava.nbio.structure.io: Controls when the class should fetch files from the ftp server
LocalPDBDirectory.ObsoleteBehavior - Enum in org.biojava.nbio.structure.io: Behaviors for when an obsolete structure is requested.
LocalProteinDomainParser - Class in org.biojava.nbio.structure.domain: Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures.
LocalScopDatabase - Interface in org.biojava.nbio.structure.scop: Classes which implement ScopDatabase in a way which allows them to serve queries without accessing the internet should implement this interface instead.
logger - Static variable in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
logger - Static variable in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
logStatus(String) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener
logStatus(String) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener
LOOP_START - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
lu() - Method in class org.biojava.nbio.structure.jama.Matrix: LU Decomposition
LUDecomposition - Class in org.biojava.nbio.structure.jama: LU Decomposition.
LUDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.LUDecomposition: LU Decomposition provides a data structure to access L, U and piv.

M

main(String[]) - Static method in class demo.ChemCompDistribution
main(String[]) - Static method in class demo.DemoAsa
main(String[]) - Static method in class demo.DemoAtomCache
main(String[]) - Static method in class demo.DemoBerkeleyScop
main(String[]) - Static method in class demo.DemoCATH
main(String[]) - Static method in class demo.DemoCE
main(String[]) - Static method in class demo.DemoCeSymm
main(String[]) - Static method in class demo.DemoChangeChemCompProvider
main(String[]) - Static method in class demo.DemoCommandLineStartup
main(String[]) - Static method in class demo.DemoContacts
main(String[]) - Static method in class demo.DemoCrystalInterfaces
main(String[]) - Static method in class demo.DemoDomainsplit
main(String[]) - Static method in class demo.DemoFATCAT
main(String[]) - Static method in class demo.DemoLoadSecStruc
main(String[]) - Static method in class demo.DemoLoadStructure
main(String[]) - Static method in class demo.DemoMMCIFReader
main(String[]) - Static method in class demo.DemoMultipleMC
main(String[]) - Static method in class demo.DemoSCOP
main(String[]) - Static method in class demo.DemoSecStrucCalc
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeMain: Example Parameters: -pdbFilePath /tmp -autoFetch -printCE -pdb1 1cnv -pdb2 3cna
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
main(String[]) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
main(String[]) - Static method in class org.biojava.nbio.structure.align.FarmJob
main(String[]) - Static method in class org.biojava.nbio.structure.align.fatcat.FatCat: See demo/FatCatDemo.java for an example how to run.
main(String[]) - Static method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
main(String[]) - Static method in class org.biojava.nbio.structure.align.StructurePairAligner: example usage of this class
main(String[]) - Static method in class org.biojava.nbio.structure.Calc
main(String[]) - Static method in class org.biojava.nbio.structure.domain.PDBDomainProvider
main(String[]) - Static method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
main(String[]) - Static method in class org.biojava.nbio.structure.domain.RemotePDPProvider
main(String[]) - Static method in class org.biojava.nbio.structure.ecod.EcodInstallation
main(String[]) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Prints out the XML representation of an AFPChain from a file containing exactly two FASTA sequences.
main(String[]) - Static method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
main(String[]) - Static method in class org.biojava.nbio.structure.io.MMCIFFileReader
main(String[]) - Static method in class org.biojava.nbio.structure.io.PDBFileReader
main(String[]) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
main(String[]) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils
main(String[]) - Static method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
main(String[]) - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
main(String[]) - Static method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
main(String[]) - Static method in class org.biojava.nbio.structure.symmetry.analysis.ScanSymmetry
makeBonds() - Method in class org.biojava.nbio.structure.io.BondMaker: Creates bond objects and corresponding references in Atom objects: peptide bonds: inferred from sequence and distances nucleotide bonds: inferred from sequence and distances intra-group (residue) bonds: read from the chemical component dictionary, via ChemCompProvider
mandatoryArgs - Static variable in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
mapSeqresRecords(Chain, Chain) - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner: Map the seqRes groups to the atomRes chain.
marshal(List<String>) - Method in class org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter
mat - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
mat - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
matches(Group) - Method in interface org.biojava.nbio.structure.AtomPositionMap.GroupMatcher
matchSequenceToStructure(ProteinSequence, Structure) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher: Given a sequence and the corresponding Structure, get the ResidueNumber for each residue in the sequence.
Maths - Class in org.biojava.nbio.structure.jama
Maths() - Constructor for class org.biojava.nbio.structure.jama.Maths
Matrix - Class in org.biojava.nbio.structure.jama: Jama = Java Matrix class.
Matrix(int, int) - Constructor for class org.biojava.nbio.structure.jama.Matrix: Construct an m-by-n matrix of zeros.
Matrix(int, int, double) - Constructor for class org.biojava.nbio.structure.jama.Matrix: Construct an m-by-n constant matrix.
Matrix(double[][]) - Constructor for class org.biojava.nbio.structure.jama.Matrix: Construct a matrix from a 2-D array.
Matrix(double[][], int, int) - Constructor for class org.biojava.nbio.structure.jama.Matrix: Construct a matrix quickly without checking arguments.
Matrix(double[], int) - Constructor for class org.biojava.nbio.structure.jama.Matrix: Construct a matrix from a one-dimensional packed array
matrixFromEuler(double, double, double) - Static method in class org.biojava.nbio.structure.Calc: This conversion uses NASA standard aeroplane conventions as described on page: http://www.euclideanspace.com/maths/geometry/rotations/euler/index.htm Coordinate System: right hand Positive angle: right hand Order of euler angles: heading first, then attitude, then bank.
matrixInOptimizer(double[][]) - Method in interface org.biojava.nbio.structure.align.ce.MatrixListener
MatrixListener - Interface in org.biojava.nbio.structure.align.ce
max() - Method in class org.biojava.nbio.structure.math.SymbolTable: Return the largest key in the table.
MAX_ATOMS - Static variable in class org.biojava.nbio.structure.io.FileParsingParameters: The maximum number of atoms we will add to a structure, this protects from memory overflows in the few really big protein structures.
MAX_CUTS - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
MAX_PEPTIDE_BOND_LENGTH - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc: max distance CA atoms in peptide bond (backbone discontinuity)
MAXCONT - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
MAXDOM - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
maxGapSize - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
maxGapSize - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
MAXLEN - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
maxNrIterationsForOptimization - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
maxOptRMSD - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
maxOptRMSD - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
MAXSIZE - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
MC_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
mean - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
mean - Variable in class org.biojava.nbio.structure.validation.BondOutlier
mean - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier
mean - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier
mid - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange: midpoint of the alignment
min() - Method in class org.biojava.nbio.structure.math.SymbolTable: Return the smallest key in the table.
MIN_DOMAIN_LENGTH - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
MIN_VALID_CELL_SIZE - Static variable in class org.biojava.nbio.structure.xtal.CrystalCell
minCPLength - Variable in class org.biojava.nbio.structure.align.ce.CECPParameters
minCPLength - Variable in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
mindiff - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier
mindiff - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier
MINDIST - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc: min distance between two residues
minus(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: C = A - B
minusEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: A = A - B
MMCIF_DEFAULT_VALUE - Static variable in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: The character to be printed out as a default value in mmCIF files, e.g.
MMCIF_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
MMCIF_MISSING_VALUE - Static variable in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: The character to be printed out in cases where a value is not assigned in mmCIF files
MMCIF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.MMCIFFileReader
MMCIF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.MMCIFFileReader
MMCIF_TOP_HEADER - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser: The header appearing at the beginning of a mmCIF file.
MmCifBiolAssemblyProvider - Class in org.biojava.nbio.structure.quaternary.io
MmCifBiolAssemblyProvider() - Constructor for class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
MMcifConsumer - Interface in org.biojava.nbio.structure.io.mmcif: An interface for the events triggered by a MMcifParser.
MMCIFFileReader - Class in org.biojava.nbio.structure.io: How to parse an mmCif file:
MMCIFFileReader() - Constructor for class org.biojava.nbio.structure.io.MMCIFFileReader: Constructs a new MMCIFFileReader, initializing the extensions member variable.
MMCIFFileReader(String) - Constructor for class org.biojava.nbio.structure.io.MMCIFFileReader: Constructs a new PDBFileReader, initializing the extensions member variable.
MMCIFFileTools - Class in org.biojava.nbio.structure.io.mmcif: Some tools for mmCIF file writing.
MMCIFFileTools() - Constructor for class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
MMcifParser - Interface in org.biojava.nbio.structure.io.mmcif: Interface that needs to be implemented by an MMcifParser
MmCifPDBBiolAssemblyProvider - Class in org.biojava.nbio.structure.quaternary.io: A provider for information about biological units for PDB files that is based on reading local MMcif files.
MmCifPDBBiolAssemblyProvider() - Constructor for class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
mmcifProviderClassName - Static variable in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
model - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
ModelledSubgroup - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
ModelledSubgroup() - Constructor for class org.biojava.nbio.structure.validation.ModelledSubgroup
modelledSubgroup - Variable in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
mogAngleOutlier - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
MogAngleOutlier - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
MogAngleOutlier() - Constructor for class org.biojava.nbio.structure.validation.MogAngleOutlier
mogBondOutlier - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
MogBondOutlier - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
MogBondOutlier() - Constructor for class org.biojava.nbio.structure.validation.MogBondOutlier
mogulIgnore - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
MomentsOfInertia - Class in org.biojava.nbio.structure.symmetry.geometry
MomentsOfInertia() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia: Creates a new instance of MomentsOfInertia
MomentsOfInertia.SymmetryClass - Enum in org.biojava.nbio.structure.symmetry.geometry
multiIterator(AtomPositionMap, ResidueRange...) - Static method in class org.biojava.nbio.structure.ResidueRange: Returns a new Iterator over every ResidueNumber in the list of ResidueRanges.
multiIterator(AtomPositionMap, List<? extends ResidueRange>) - Static method in class org.biojava.nbio.structure.ResidueRange: Returns a new Iterator over every ResidueNumber in the list of ResidueRanges.
MultipleAlignment - Interface in org.biojava.nbio.structure.align.multiple: A MultipleAlignment is a Data Structure to store the core information of a multiple structure alignment, as a return type.
MultipleAlignmentDisplay - Class in org.biojava.nbio.structure.align.multiple.util: Utility functions to generalize the visualization of MultipleAlignments in molecular viewers.
MultipleAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay
MultipleAlignmentEnsemble - Interface in org.biojava.nbio.structure.align.multiple: A MultipleAlignmentEnsemble is a collection of MultipleAlignments that share the same structures (Atoms) and creation properties (algorithm, version, creation time, etc.).
MultipleAlignmentEnsembleImpl - Class in org.biojava.nbio.structure.align.multiple: A general implementation of a MultipleAlignmentEnsemble.
MultipleAlignmentEnsembleImpl() - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl: Default Constructor.
MultipleAlignmentEnsembleImpl(List<StructureIdentifier>) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl: Constructor using structure identifiers.
MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl: Copy constructor.
MultipleAlignmentEnsembleImpl(AFPChain, Atom[], Atom[], boolean) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl: Constructor from an AFPChain instance.
MultipleAlignmentImpl - Class in org.biojava.nbio.structure.align.multiple: A general implementation of a MultipleAlignment.
MultipleAlignmentImpl() - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl: Default Constructor.
MultipleAlignmentImpl(MultipleAlignmentEnsemble) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl: Constructor linking to an existing ensemble.
MultipleAlignmentImpl(MultipleAlignmentImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl: Copy constructor.
MultipleAlignmentScorer - Class in org.biojava.nbio.structure.align.multiple.util: Utility class for calculating common scores of MultipleAlignments.
MultipleAlignmentScorer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
MultipleAlignmentTools - Class in org.biojava.nbio.structure.align.multiple.util: Utility functions for working with MultipleAlignment.
MultipleAlignmentTools() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
MultipleAlignmentWriter - Class in org.biojava.nbio.structure.align.multiple.util: This class contains functions for the conversion of MultipleAlignment to various String outputs.
MultipleAlignmentWriter() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter
MultipleAlignmentXMLConverter - Class in org.biojava.nbio.structure.align.xml: Helper methods to convert all the hierarchy levels of a MultipleAlignment into an XML format.
MultipleAlignmentXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
MultipleAlignmentXMLParser - Class in org.biojava.nbio.structure.align.xml: Parse an XML file representing a MultipleAlignmentEnsemble, so that the original alignment can be recovered.
MultipleAlignmentXMLParser() - Constructor for class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
MultipleMcMain - Class in org.biojava.nbio.structure.align.multiple.mc: Main class of the Java implementation of the Combinatorial Extension - Monte Carlo (CEMC) Algorithm, as it was originally described by C.Guda, E.D.Scheeff, P.E.
MultipleMcMain(StructureAlignment) - Constructor for class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain: Default constructor.
MultipleMcOptimizer - Class in org.biojava.nbio.structure.align.multiple.mc: This class takes a MultipleAlignment seed previously generated and runs a Monte Carlo optimization in order to improve the overall score and highlight common structural motifs.
MultipleMcOptimizer(MultipleAlignment, MultipleMcParameters, int) - Constructor for class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer: Constructor.
MultipleMcParameters - Class in org.biojava.nbio.structure.align.multiple.mc: Contains the parameters to be sent to the MC optimization.
MultipleMcParameters() - Constructor for class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters: Constructor with DEFAULT values of the parameters.
MultipleStructureAligner - Interface in org.biojava.nbio.structure.align: Interface for the Multiple Structure Alignment Algorithms.
MultipleSuperimposer - Interface in org.biojava.nbio.structure.align.multiple.util: Interface for Multiple Alignment superposition algorithms.
MultiThreadedDBSearch - Class in org.biojava.nbio.structure.align: Performs a multi threaded database search for an input protein structure
MultiThreadedDBSearch(String, Structure, String, StructureAlignment, int, boolean) - Constructor for class org.biojava.nbio.structure.align.MultiThreadedDBSearch
mutate(Structure, String, String, String) - Method in class org.biojava.nbio.structure.Mutator: creates a new structure which is identical with the original one.
mutateResidue(AminoAcid, String) - Method in class org.biojava.nbio.structure.Mutator: create a new residue which is of the new type.
Mutator - Class in org.biojava.nbio.structure: A class that can change one amino acid to another.
Mutator() - Constructor for class org.biojava.nbio.structure.Mutator

N

n - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange: last allowed n-term
N_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name for the backbone amide nitrogen
name - Variable in class org.biojava.nbio.structure.align.client.StructureName
name - Variable in enum org.biojava.nbio.structure.secstruc.BridgeType
name - Variable in enum org.biojava.nbio.structure.secstruc.SecStrucType
name - Variable in class org.biojava.nbio.structure.validation.Program
natomsEDS - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
nBestTrace - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
nBestTrace - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
nBestTraces - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
nBestTraces - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
newAtomSite(AtomSite) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newAtomSite(AtomSite) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer: A new AtomSite record has been read.
newAtomSite(AtomSite) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newAuditAuthor(AuditAuthor) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newAuditAuthor(AuditAuthor) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer: AuditAuthor contains the info from the PDB-AUTHOR records.
newAuditAuthor(AuditAuthor) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newCell(Cell) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newCell(Cell) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newCell(Cell) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newChemCompAtom(ChemCompAtom) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newChemCompAtom(ChemCompAtom) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newChemCompAtom(ChemCompAtom) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newChemCompBond(ChemCompBond) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newChemCompDescriptor(ChemCompDescriptor) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newChemCompDescriptor(ChemCompDescriptor) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newChemCompDescriptor(ChemCompDescriptor) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newDatabasePDBremark(DatabasePDBremark) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newDatabasePDBremark(DatabasePDBremark) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newDatabasePDBremark(DatabasePDBremark) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newDatabasePDBrev(DatabasePDBrev) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newDatabasePDBrev(DatabasePDBrev) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newDatabasePDBrev(DatabasePDBrev) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newDatabasePDBrevRecord(DatabasePdbrevRecord) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newDatabasePDBrevRecord(DatabasePdbrevRecord) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newDatabasePDBrevRecord(DatabasePdbrevRecord) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newEntity(Entity) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newEntity(Entity) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newEntity(Entity) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newEntityPolySeq(EntityPolySeq) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newEntityPolySeq(EntityPolySeq) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newEntityPolySeq(EntityPolySeq) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer: The EntityPolySeq object provide the amino acid sequence objects for the Entities.
newEntitySrcGen(EntitySrcGen) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newEntitySrcGen(EntitySrcGen) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newEntitySrcGen(EntitySrcGen) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer: Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated.
newEntitySrcNat(EntitySrcNat) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newEntitySrcNat(EntitySrcNat) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newEntitySrcNat(EntitySrcNat) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newEntitySrcSyn(EntitySrcSyn) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newEntitySrcSyn(EntitySrcSyn) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newEntitySrcSyn(EntitySrcSyn) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newExptl(Exptl) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newExptl(Exptl) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newExptl(Exptl) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newGenericData(String, List<String>, List<String>) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newGenericData(String, List<String>, List<String>) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer: This method is called if no particular handler for the provided cif category has been implemented so far.
newGenericData(String, List<String>, List<String>) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newline - Static variable in class org.biojava.nbio.structure.align.AbstractStructureAlignment
newline - Static variable in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
newline - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat
newline - Static variable in class org.biojava.nbio.structure.align.model.AFPChain
newline - Static variable in class org.biojava.nbio.structure.align.model.AfpChainWriter
NEWLINE - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
newline - Static variable in class org.biojava.nbio.structure.PDBHeader
NEWLINE - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
newPdbxChemCompDescriptor(PdbxChemCompDescriptor) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxChemCompDescriptor(PdbxChemCompDescriptor) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxChemCompDescriptor(PdbxChemCompDescriptor) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxChemCompIndentifier(PdbxChemCompIdentifier) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxChemCompIndentifier(PdbxChemCompIdentifier) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxChemCompIndentifier(PdbxChemCompIdentifier) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxEntityNonPoly(PdbxEntityNonPoly) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxEntityNonPoly(PdbxEntityNonPoly) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxEntityNonPoly(PdbxEntityNonPoly) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxNonPolyScheme(PdbxNonPolyScheme) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxNonPolyScheme(PdbxNonPolyScheme) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxNonPolyScheme(PdbxNonPolyScheme) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxPolySeqScheme(PdbxPolySeqScheme) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxPolySeqScheme(PdbxPolySeqScheme) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxPolySeqScheme(PdbxPolySeqScheme) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxStrucAssembly(PdbxStructAssembly) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxStrucAssembly(PdbxStructAssembly) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxStrucAssembly(PdbxStructAssembly) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxStrucAssemblyGen(PdbxStructAssemblyGen) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxStrucAssemblyGen(PdbxStructAssemblyGen) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxStrucAssemblyGen(PdbxStructAssemblyGen) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxStructOperList(PdbxStructOperList) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxStructOperList(PdbxStructOperList) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxStructOperList(PdbxStructOperList) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newRefine(Refine) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newRefine(Refine) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newRefine(Refine) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructAsym(StructAsym) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructAsym(StructAsym) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructAsym(StructAsym) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructConn(StructConn) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructConn(StructConn) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructConn(StructConn) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructKeywords(StructKeywords) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructKeywords(StructKeywords) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructKeywords(StructKeywords) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructNcsOper(StructNcsOper) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructNcsOper(StructNcsOper) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructNcsOper(StructNcsOper) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructRef(StructRef) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructRef(StructRef) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructRef(StructRef) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructRefSeq(StructRefSeq) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructRefSeq(StructRefSeq) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructRefSeq(StructRefSeq) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer: create a DBRef record from the StrucRefSeq record:
newStructRefSeqDif(StructRefSeqDif) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructRefSeqDif(StructRefSeqDif) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructRefSeqDif(StructRefSeqDif) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructSite(StructSite) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructSite(StructSite) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructSite(StructSite) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructSiteGen(StructSiteGen) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructSiteGen(StructSiteGen) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructSiteGen(StructSiteGen) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newSymmetry(Symmetry) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newSymmetry(Symmetry) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newSymmetry(Symmetry) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
next() - Method in class org.biojava.nbio.structure.AtomIterator: Return next atom.
next() - Method in class org.biojava.nbio.structure.GroupIterator: get next Group.
nextStep(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
nextStep(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
nIter - Static variable in class org.biojava.nbio.structure.align.ce.CECalculator
nIter - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
nnz() - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix: return the number of nonzero entries (not the most efficient implementation)
nnz() - Method in class org.biojava.nbio.structure.math.SparseVector
nodeListFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
norm() - Method in class org.biojava.nbio.structure.math.SparseVector: Calculates the 2-norm
norm1() - Method in class org.biojava.nbio.structure.jama.Matrix: One norm
norm2() - Method in class org.biojava.nbio.structure.jama.Matrix: Two norm
norm2() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition: Two norm
normF() - Method in class org.biojava.nbio.structure.jama.Matrix: Frobenius norm
normInf() - Method in class org.biojava.nbio.structure.jama.Matrix: Infinity norm
NOT_DOMAIN_ASSEMBLY - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser: String for single-domain assemblies
NOT_REPRESENTATIVE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser: Indicates not a manual representative
notifyShutdown() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Send a signal to the cache that the system is shutting down.
NR_BIOL_APPEND - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
NR_BIOL_APPEND - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
nrModels() - Method in interface org.biojava.nbio.structure.Structure: Return the number of models .
nrModels() - Method in class org.biojava.nbio.structure.StructureImpl: return number of models.
nTrace - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
nTrace - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
nTraces - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
nTraces - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
NUC_CARBON_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
NUC_NITROGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
NUCLEOTIDE_REPRESENTATIVE - Static variable in class org.biojava.nbio.structure.StructureTools: The atom used as representative for nucleotides, equivalent to StructureTools.CA_ATOM_NAME for proteins
NucleotideImpl - Class in org.biojava.nbio.structure: A nucleotide group is almost the same as a Hetatm group.
NucleotideImpl() - Constructor for class org.biojava.nbio.structure.NucleotideImpl
nullifyComments() - Method in class org.biojava.nbio.structure.scop.ScopInstallation: Removes all of the comments (dir.com file) in order to free memory.
numFreeReflections - Variable in class org.biojava.nbio.structure.validation.Entry
numHReduce - Variable in class org.biojava.nbio.structure.validation.Entry
numHReduce - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
numMillerIndices - Variable in class org.biojava.nbio.structure.validation.Entry
numobs - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier
numobs - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier

O

O2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone O2' in RNA
O3_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone O3' in RNA
O4_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone O4' in RNA
O5_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone O4' in RNA
O_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name for the backbone carbonyl oxygen
ObjectFactory - Class in org.biojava.nbio.structure.validation: This object contains factory methods for each Java content interface and Java element interface generated in the org.biojava.nbio.structure.validation package.
ObjectFactory() - Constructor for class org.biojava.nbio.structure.validation.ObjectFactory: Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: org.biojava.nbio.structure.validation
obs - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
obs - Variable in class org.biojava.nbio.structure.validation.BondOutlier
obsval - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier
obsval - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier
Octahedron - Class in org.biojava.nbio.structure.symmetry.geometry
Octahedron() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Octahedron
OP1_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone O4' in RNA
OP2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone O4' in RNA
openHttpURLConnection(URL, int) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: open HttpURLConnection.
openHttpURLConnection(URL) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: open HttpURLConnection.
OperatorResolver - Class in org.biojava.nbio.structure.quaternary: A class to resolve the operators for transformations
OperatorResolver() - Constructor for class org.biojava.nbio.structure.quaternary.OperatorResolver
OptimalCECPMain - Class in org.biojava.nbio.structure.align.ce: A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.
OptimalCECPMain() - Constructor for class org.biojava.nbio.structure.align.ce.OptimalCECPMain
OptimalCECPParameters - Class in org.biojava.nbio.structure.align.ce: Contains the parameters that can be sent to CE
OptimalCECPParameters() - Constructor for class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
optimize() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer: Optimization method based in a Monte-Carlo approach.
optimize() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmOptimizer: Optimization method based in a Monte-Carlo approach.
optimizeAln(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer: optimize the alignment by dynamic programming
optimizeResult(int[], int, int[][]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer
order() - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup: The order of symmetry of the group is the number of connected residues.
OrderDetector - Interface in org.biojava.nbio.structure.symmetry.internal: A method to decide the order of symmetry (number of subunits) given a structure self-alignment, calculated by CE-Symm.
OrderedPair<T> - Class in org.biojava.nbio.structure.quaternary: An ordered pair represents a component of a cartesian product.
org.biojava.nbio.structure - package org.biojava.nbio.structure: Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.align - package org.biojava.nbio.structure.align: Classes for the alignment of structures.
org.biojava.nbio.structure.align.ce - package org.biojava.nbio.structure.align.ce: Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.align.client - package org.biojava.nbio.structure.align.client: This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.nbio.structure.align.events - package org.biojava.nbio.structure.align.events
org.biojava.nbio.structure.align.fatcat - package org.biojava.nbio.structure.align.fatcat: Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
org.biojava.nbio.structure.align.fatcat.calc - package org.biojava.nbio.structure.align.fatcat.calc
org.biojava.nbio.structure.align.helper - package org.biojava.nbio.structure.align.helper: Helper classes for structural alignment.
org.biojava.nbio.structure.align.model - package org.biojava.nbio.structure.align.model
org.biojava.nbio.structure.align.multiple - package org.biojava.nbio.structure.align.multiple
org.biojava.nbio.structure.align.multiple.mc - package org.biojava.nbio.structure.align.multiple.mc
org.biojava.nbio.structure.align.multiple.util - package org.biojava.nbio.structure.align.multiple.util
org.biojava.nbio.structure.align.pairwise - package org.biojava.nbio.structure.align.pairwise: Classes for the pairwise alignment of structures.
org.biojava.nbio.structure.align.seq - package org.biojava.nbio.structure.align.seq
org.biojava.nbio.structure.align.util - package org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.align.xml - package org.biojava.nbio.structure.align.xml: Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
org.biojava.nbio.structure.asa - package org.biojava.nbio.structure.asa
org.biojava.nbio.structure.cath - package org.biojava.nbio.structure.cath
org.biojava.nbio.structure.contact - package org.biojava.nbio.structure.contact
org.biojava.nbio.structure.domain - package org.biojava.nbio.structure.domain
org.biojava.nbio.structure.domain.pdp - package org.biojava.nbio.structure.domain.pdp
org.biojava.nbio.structure.ecod - package org.biojava.nbio.structure.ecod
org.biojava.nbio.structure.io - package org.biojava.nbio.structure.io: Input and Output of Structures
org.biojava.nbio.structure.io.mmcif - package org.biojava.nbio.structure.io.mmcif: Input and Output of mmcif files.
org.biojava.nbio.structure.io.mmcif.chem - package org.biojava.nbio.structure.io.mmcif.chem
org.biojava.nbio.structure.io.mmcif.model - package org.biojava.nbio.structure.io.mmcif.model: Datamodel objects used for processing mmcif files.
org.biojava.nbio.structure.io.mmtf - package org.biojava.nbio.structure.io.mmtf
org.biojava.nbio.structure.io.sifts - package org.biojava.nbio.structure.io.sifts
org.biojava.nbio.structure.io.util - package org.biojava.nbio.structure.io.util
org.biojava.nbio.structure.jama - package org.biojava.nbio.structure.jama: Matrix package for from JAMA
org.biojava.nbio.structure.math - package org.biojava.nbio.structure.math
org.biojava.nbio.structure.quaternary - package org.biojava.nbio.structure.quaternary
org.biojava.nbio.structure.quaternary.io - package org.biojava.nbio.structure.quaternary.io
org.biojava.nbio.structure.rcsb - package org.biojava.nbio.structure.rcsb
org.biojava.nbio.structure.scop - package org.biojava.nbio.structure.scop: Parsers and API for SCOP, Structural Classification of Proteins.
org.biojava.nbio.structure.scop.server - package org.biojava.nbio.structure.scop.server
org.biojava.nbio.structure.secstruc - package org.biojava.nbio.structure.secstruc
org.biojava.nbio.structure.symmetry.analysis - package org.biojava.nbio.structure.symmetry.analysis
org.biojava.nbio.structure.symmetry.core - package org.biojava.nbio.structure.symmetry.core
org.biojava.nbio.structure.symmetry.geometry - package org.biojava.nbio.structure.symmetry.geometry
org.biojava.nbio.structure.symmetry.internal - package org.biojava.nbio.structure.symmetry.internal
org.biojava.nbio.structure.symmetry.misc - package org.biojava.nbio.structure.symmetry.misc
org.biojava.nbio.structure.symmetry.utils - package org.biojava.nbio.structure.symmetry.utils
org.biojava.nbio.structure.validation - package org.biojava.nbio.structure.validation
org.biojava.nbio.structure.xtal - package org.biojava.nbio.structure.xtal
org.biojava.nbio.structure.xtal.io - package org.biojava.nbio.structure.xtal.io
oRmsdThr - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
overlaps(BoundingBox, double) - Method in class org.biojava.nbio.structure.contact.BoundingBox: Returns true if this bounding box overlaps given one, i.e.
overlaps(Subunits) - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
owab - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
OXIGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

P

P_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone phosphate in RNA
Pair<T> - Class in org.biojava.nbio.structure.contact: A Pair of objects.
Pair(T, T) - Constructor for class org.biojava.nbio.structure.contact.Pair: Creates a Pair from the specified elements.
PairwiseAlignment - Class in org.biojava.nbio.structure.symmetry.core
PairwiseAlignment(SequenceAlignmentCluster, SequenceAlignmentCluster) - Constructor for class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
params - Variable in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
params - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
params - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
params - Variable in class org.biojava.nbio.structure.align.ce.CeMain
params - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
params - Variable in class org.biojava.nbio.structure.align.util.AtomCache
parent - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
parse(BufferedReader) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser: Start the actual parsing.
parse(InputStream) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser: Start the actual parsing.
parse(InputStream) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
parse(BufferedReader) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
parse(String) - Static method in class org.biojava.nbio.structure.ResidueRange: Parse the residue range from a string.
parse(String, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength: Parses a residue range.
parse(String) - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
parseBinaryOperatorExpression(String) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
parseBlock(Node, BlockSet) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseBlockSet(Node, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseEnsemble(Node) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseFile(String, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser: Parse a DSSP output file and return the secondary structure annotation as a List of SecStrucState objects.
parseHeader(Node, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseMatrix4d(Node) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseMultiple(String) - Static method in class org.biojava.nbio.structure.ResidueRange
parseMultiple(List<String>) - Static method in class org.biojava.nbio.structure.ResidueRange
parseMultiple(List<String>, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength
parseMultiple(String, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength
parseMultipleAlignment(Node, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseMultiXML(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
parseOperatorExpressionString(String) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver: Parses the operator expression and save the operators as a list of unary or binary operators (i.e.
parsePDBFile(InputStream) - Method in class org.biojava.nbio.structure.io.PDBFileParser: Parse a PDB file and return a datastructure implementing PDBStructure interface.
parsePDBFile(BufferedReader) - Method in class org.biojava.nbio.structure.io.PDBFileParser: Parse a PDB file and return a datastructure implementing PDBStructure interface.
parseScoresCache(Node, ScoresCache) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseSpaceGroup(String) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup: Get the space group for the given international short name, using the PDB format, e.g.
parseSpaceGroupsXML(InputStream) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser: Load all SpaceGroup information from the file spacegroups.xml
parseString(String, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser: Parse a DSSP format String and return the secondary structure annotation as a List of SecStrucState objects.
parseStructures(Node, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseSymopLib(InputStream) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser: A parser for the symop.lib file provided by CCP4.
parseUnaryOperatorExpression(String) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
ParseUsingBioJava - Class in org.biojava.nbio.structure.io.mmtf
ParseUsingBioJava() - Constructor for class org.biojava.nbio.structure.io.mmtf.ParseUsingBioJava
parseXMLfile(String) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser: Creates a list of MultipleAlignment ensembles from an XML file.
parseXmlFile(InputStream) - Method in class org.biojava.nbio.structure.io.sifts.SiftsXMLParser
PassthroughIdentifier - Class in org.biojava.nbio.structure: A stub StructureIdentifier, representing the full structure in all cases.
PassthroughIdentifier(String) - Constructor for class org.biojava.nbio.structure.PassthroughIdentifier
PDB_AUTHOR_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo: Secondary strucuture assigned by the PDB author
PDB_CACHE_DIR - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
PDB_DIR - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
PDB_FILE_SERVER_PROPERTY - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
pdb_flag - Variable in class org.biojava.nbio.structure.HetatomImpl: stores if 3d coordinates are available.
PDB_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
pdb_name - Variable in class org.biojava.nbio.structure.HetatomImpl: 3 letter name of amino acid in pdb file.
PDB_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.PDBFileReader
pdb_REMARK_350_Handler(String) - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser: Parses REMARK 350 line.
PDB_SERVER_PROPERTY - Static variable in class org.biojava.nbio.structure.PDBStatus
PDB_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.PDBFileReader
PDBBioAssemblyParser - Class in org.biojava.nbio.structure.io: Parses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unit
PDBBioAssemblyParser() - Constructor for class org.biojava.nbio.structure.io.PDBBioAssemblyParser
PDBBioUnitDataProvider - Class in org.biojava.nbio.structure.quaternary.io: A BioUnitDataProvider that extracts the necessary info from PDB files
PDBBioUnitDataProvider() - Constructor for class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
PDBCrystallographicInfo - Class in org.biojava.nbio.structure: A class to hold crystallographic information about a PDB structure.
PDBCrystallographicInfo() - Constructor for class org.biojava.nbio.structure.PDBCrystallographicInfo
PDBDomainProvider - Class in org.biojava.nbio.structure.domain: Class to fetch domains through the RCSB's REST API.
PDBDomainProvider() - Constructor for class org.biojava.nbio.structure.domain.PDBDomainProvider
PDBDomainProvider(String, int) - Constructor for class org.biojava.nbio.structure.domain.PDBDomainProvider
PDBFileParser - Class in org.biojava.nbio.structure.io: This class implements the actual PDB file parsing.
PDBFileParser() - Constructor for class org.biojava.nbio.structure.io.PDBFileParser
PDBFileReader - Class in org.biojava.nbio.structure.io: The wrapper class for parsing a PDB file.
PDBFileReader() - Constructor for class org.biojava.nbio.structure.io.PDBFileReader: Constructs a new PDBFileReader, initializing the extensions member variable.
PDBFileReader(String) - Constructor for class org.biojava.nbio.structure.io.PDBFileReader: Constructs a new PDBFileReader, initializing the extensions member variable.
PDBHeader - Class in org.biojava.nbio.structure: A class that contains PDB Header information.
PDBHeader() - Constructor for class org.biojava.nbio.structure.PDBHeader
pdbId - Variable in class org.biojava.nbio.structure.align.client.StructureName
PDBID_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier: URL parameter specifying the PDB ID
PdbIdLists - Class in org.biojava.nbio.structure.rcsb: Utility classes for retrieving lists of PDB IDs.
PdbIdLists() - Constructor for class org.biojava.nbio.structure.rcsb.PdbIdLists
PdbPair - Class in org.biojava.nbio.structure.align.client: A pair for structure alignment
PdbPair(String, String) - Constructor for class org.biojava.nbio.structure.align.client.PdbPair
PdbPair(StructureName, StructureName) - Constructor for class org.biojava.nbio.structure.align.client.PdbPair
PdbPairsMessage - Class in org.biojava.nbio.structure.align.xml
PdbPairsMessage() - Constructor for class org.biojava.nbio.structure.align.xml.PdbPairsMessage
PdbPairXMLConverter - Class in org.biojava.nbio.structure.align.xml
PdbPairXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
PDBParseException - Exception in org.biojava.nbio.structure.io: An exception during the parsing of a PDB file.
PDBParseException(String) - Constructor for exception org.biojava.nbio.structure.io.PDBParseException: Constructs a PDBParseException object.
PDBParseException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.io.PDBParseException: Constructs a PDBParseException object.
PDBParseException(Throwable) - Constructor for exception org.biojava.nbio.structure.io.PDBParseException: Constructs a PDBParseException object.
pdbProviderClassName - Static variable in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
PDBRecord - Interface in org.biojava.nbio.structure: An interface implemented by all classes that represent PDB records
pdbRevisionNumber - Variable in class org.biojava.nbio.structure.validation.Entry
PDBStatus - Class in org.biojava.nbio.structure: Methods for getting the status of a PDB file (current, obsolete, etc) and for accessing different versions of the structure.
PDBStatus() - Constructor for class org.biojava.nbio.structure.PDBStatus
PDBStatus.Status - Enum in org.biojava.nbio.structure: Represents the status of PDB IDs.
PDBTemporaryStorageUtils - Class in org.biojava.nbio.structure.io.util: Internal use only.
PDBTemporaryStorageUtils() - Constructor for class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils
PDBTemporaryStorageUtils.LinkRecord - Class in org.biojava.nbio.structure.io.util: Temporary data storage for LINK records.
PdbxChemCompDescriptor - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxChemCompDescriptor() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
PdbxChemCompIdentifier - Class in org.biojava.nbio.structure.io.mmcif.model: _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier
PdbxChemCompIdentifier() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
PdbxEntityNonPoly - Class in org.biojava.nbio.structure.io.mmcif.model: A bean for the Pdbx_entity_nonpoly category.
PdbxEntityNonPoly() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
PdbxNonPolyScheme - Class in org.biojava.nbio.structure.io.mmcif.model: A bean for the PDBX_NONPOLY_SCHEME category, which provides residue level nomenclature mapping for non-polymer entities.
PdbxNonPolyScheme() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
PdbxPolySeqScheme - Class in org.biojava.nbio.structure.io.mmcif.model: A bean for the PDBX_POLY_SEQ_SCHEME category, which provides residue level nomenclature mapping for polymer entities.
PdbxPolySeqScheme() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
PdbxStructAssembly - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxStructAssembly() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
PdbxStructAssemblyGen - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxStructAssemblyGen() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
PdbxStructAssemblyGenXMLContainer - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxStructAssemblyGenXMLContainer() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
PdbxStructAssemblyXMLContainer - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxStructAssemblyXMLContainer() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
PdbxStructOperList - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxStructOperList() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
PdbxStructOperListXMLContainer - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxStructOperListXMLContainer() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
PDP_DOMAIN_IDENTIFIER - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
PDP_NAME_PATTERN - Static variable in class org.biojava.nbio.structure.domain.PDPDomain
PDPDistanceMatrix - Class in org.biojava.nbio.structure.domain.pdp
PDPDistanceMatrix() - Constructor for class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
PDPDomain - Class in org.biojava.nbio.structure.domain
PDPDomain(String, List<ResidueRange>) - Constructor for class org.biojava.nbio.structure.domain.PDPDomain
PDPParameters - Class in org.biojava.nbio.structure.domain.pdp
PDPParameters() - Constructor for class org.biojava.nbio.structure.domain.pdp.PDPParameters
pdpprovider - Variable in class org.biojava.nbio.structure.align.util.AtomCache
PDPProvider - Interface in org.biojava.nbio.structure.domain: Decomposes a structure into representative PDP domains.
percentFreeReflections - Variable in class org.biojava.nbio.structure.validation.Entry
percentRamaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
percentRotaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
percentRSRZOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
performanceBehavior - Static variable in class org.biojava.nbio.structure.HetatomImpl
PermutationGenerator - Class in org.biojava.nbio.structure.symmetry.utils
PermutationGenerator(int) - Constructor for class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
PermutationGroup - Class in org.biojava.nbio.structure.symmetry.core
PermutationGroup() - Constructor for class org.biojava.nbio.structure.symmetry.core.PermutationGroup
phi - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
PHOSPHOROUS_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
ping(String, int) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils: Pings a HTTP URL.
plus(Structure, Matrix) - Static method in class org.biojava.nbio.structure.Calc: calculate structure + Matrix coodinates ...
plus(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: C = A + B
plus(SparseSquareMatrix) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix: return C = A + B
plus(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseVector: Calcualtes return a + b
plusEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: A = A + B
Polyhedron - Interface in org.biojava.nbio.structure.symmetry.geometry
PolymerType - Enum in org.biojava.nbio.structure.io.mmcif.chem: Enumerates the classification of polymers.
polymerType - Variable in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType: The associated PolymerType
polymerTypeFromString(String) - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType
POLYNUCLEOTIDE_ONLY - Static variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType: Convenience Set of polymer types classified as DNA.
PositionInQueueXMLConverter - Class in org.biojava.nbio.structure.align.xml
PositionInQueueXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.PositionInQueueXMLConverter
postProcess(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
postProcessAlignment(AFPChain, Atom[], Atom[], CECalculator) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain: Circular permutation specific code to be run after the standard CE alignment
postProcessAlignment(AFPChain, Atom[], Atom[], CECalculator, CECPParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain: Circular permutation specific code to be run after the standard CE alignment
postQuery(String) - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: post am XML query (PDB XML query format) to the RESTful RCSB web service
prefetchStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Download a structure, but don't parse it yet or store it in memory.
prepareGroupsForDisplay(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
prepareStructure(int, int, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder
prepareURLConnection(String, int) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils: Prepare URLConnection with customised timeouts.
print(int, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Print the matrix to stdout.
print(PrintWriter, int, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Print the matrix to the output stream.
print(NumberFormat, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Print the matrix to stdout.
print(PrintWriter, NumberFormat, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Print the matrix to the output stream.
printAboutMe() - Static method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
printDomainsForPDB() - Method in class demo.DemoSCOP
printDSSP() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc: Generate a DSSP file format ouput String of this SS prediction.
printDSSPline(int) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
printFASTA() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc: Generate a FASTA sequence with the SS annotation letters in the aminoacid sequence order.
printFull() - Method in class org.biojava.nbio.structure.ResidueNumber
printHelixSummary() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc: Generate a summary of this SS prediction with information about the three types of helix turns in different row sequences.
printHelp() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
printHelp() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
printHelp() - Method in interface org.biojava.nbio.structure.align.ce.UserArgumentProcessor: Print help about the arguments
printHelp() - Method in class org.biojava.nbio.structure.align.FarmJob
printTimeStamps - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
printXMLalignment(PrettyXMLWriter, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
printXMLblock(PrettyXMLWriter, Block) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
printXMLblockSet(PrettyXMLWriter, BlockSet) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
printXMLensemble(PrettyXMLWriter, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
printXMLEQRInferPositions(PrettyXMLWriter, AFPChain, int, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
printXMLHeader(PrettyXMLWriter, AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
printXMLheader(PrettyXMLWriter, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
printXMLmatrix4d(PrettyXMLWriter, Matrix4d) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
printXMLscoresCache(PrettyXMLWriter, ScoresCache) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
Prism - Class in org.biojava.nbio.structure.symmetry.geometry
Prism(int) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Prism
PROBABILITY - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
process(String[]) - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
process(String[]) - Method in interface org.biojava.nbio.structure.align.ce.UserArgumentProcessor: Process user arguments that have been provided from the command line
process() - Method in class org.biojava.nbio.structure.io.FastaStructureParser: Parses the fasta file and loads it into memory.
Program - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
Program() - Constructor for class org.biojava.nbio.structure.validation.Program
program - Variable in class org.biojava.nbio.structure.validation.Programs
Programs - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
Programs() - Constructor for class org.biojava.nbio.structure.validation.Programs
programs - Variable in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
properties - Variable in class org.biojava.nbio.structure.validation.Program
PROTEIN_ONLY - Static variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType: Convenience Set of polymer types classified as protein.
ProteinChainExtractor - Class in org.biojava.nbio.structure.symmetry.core: Extracts information about all the chains in a structure, including chain Ids, sequences, and atoms.
ProteinChainExtractor(Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
ProteinComplexSignature - Class in org.biojava.nbio.structure.symmetry.misc
ProteinComplexSignature(String, List<String>, BlastClustReader) - Constructor for class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
ProteinSequenceClusterer - Class in org.biojava.nbio.structure.symmetry.core: Represents a set of non-identical protein sequences.
ProteinSequenceClusterer(Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
ProteinSequenceClusterer(Structure, Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
psi - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
purgeTempFiles(String) - Static method in class org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider: Cleanup chemical component (.cif.gz) files downloaded to tmpdir.
put(int, int, double) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix: set A[i][j] = value
put(int, double) - Method in class org.biojava.nbio.structure.math.SparseVector: Setter method (should it be renamed to set?)
put(Key, Value) - Method in class org.biojava.nbio.structure.math.SymbolTable: Put key-value pair into the symbol table.
putScore(String, Double) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
putScore(String, Double) - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache: Add a score to the list of scores.

Q

Q - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc

constant for electrostatic energy

qr() - Method in class org.biojava.nbio.structure.jama.Matrix

QR Decomposition

QRDecomposition - Class in org.biojava.nbio.structure.jama

QR Decomposition.

QRDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.QRDecomposition

QR Decomposition, computed by Householder reflections.

QuatSuperpositionScorer - Class in org.biojava.nbio.structure.symmetry.core

QuatSuperpositionScorer() - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer

QuatSymmetryDetector - Class in org.biojava.nbio.structure.symmetry.core

Detects global and local quaternary protein structure symmetry in a structure.

QuatSymmetryDetector(Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector

QuatSymmetryParameters - Class in org.biojava.nbio.structure.symmetry.core

QuatSymmetryParameters() - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

QuatSymmetryResults - Class in org.biojava.nbio.structure.symmetry.core

Holds the results of quaternary symmetry perception.

QuatSymmetryResults(Subunits, RotationGroup, String) - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

QuatSymmetryResults(Subunits, HelixLayers, String) - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

QuatSymmetryScores - Class in org.biojava.nbio.structure.symmetry.core

QuatSymmetryScores() - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

QuatSymmetrySolver - Interface in org.biojava.nbio.structure.symmetry.core

R

rama - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

random(int, int) - Static method in class org.biojava.nbio.structure.jama.Matrix

Generate matrix with random elements

randomPick(Collection<Number>) - Static method in class org.biojava.nbio.structure.align.util.CollectionTools

RANGE_REGEX - Static variable in class org.biojava.nbio.structure.ResidueRange

rank() - Method in class org.biojava.nbio.structure.jama.Matrix

Matrix rank

rank() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition

Effective numerical matrix rank

RATIO_GAPS_FOR_MISMATCH - Static variable in class org.biojava.nbio.structure.io.CompoundFinder

Above this ratio of mismatching residue types for same residue numbers we consider the 2 chains to have mismatching residue numbers and warn about it

RATIO_RESIDUES_TO_TOTAL - Static variable in class org.biojava.nbio.structure.StructureTools

Below this ratio of aminoacid/nucleotide residues to the sequence total, we use simple majority of aminoacid/nucleotide residues to decide the character of the chain (protein/nucleotide)

RawBioUnitDataProvider - Interface in org.biojava.nbio.structure.quaternary.io

Defines the methods that have to be implemented by a class that provides the data that is necessary to recreate the correct biological assembly of a protein.

RCSBDescription - Class in org.biojava.nbio.structure.rcsb

Corresponds to the wrapper element in an RCSB describeMol XML file.

RCSBDescription() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBDescription

RCSBDescriptionFactory - Class in org.biojava.nbio.structure.rcsb

Fetches information from RCSB's RESTful Web Service Interface.

RCSBDescriptionFactory() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory

RCSBLigand - Class in org.biojava.nbio.structure.rcsb

Corresponds to a ligand in a ligandInfo XML file.

RCSBLigand() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBLigand

RCSBLigands - Class in org.biojava.nbio.structure.rcsb

Corresponds to the wrapper element "ligandInfo" in an RCSB ligandInfo XML file.

RCSBLigands() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBLigands

RCSBLigandsFactory - Class in org.biojava.nbio.structure.rcsb

Fetches information from RCSB's RESTful Web Service Interface.

RCSBLigandsFactory() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory

RCSBMacromolecule - Class in org.biojava.nbio.structure.rcsb

Corresponds to a macromolecule in an RCSB describeMol XML file.

RCSBMacromolecule() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBMacromolecule

RCSBPolymer - Class in org.biojava.nbio.structure.rcsb

Corresponds to a polymer in a describeMol XML file.

RCSBPolymer() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBPolymer

RCSBTaxonomy - Class in org.biojava.nbio.structure.rcsb

Corresponds to a taxonomy in a describeMol XML file.

RCSBTaxonomy(String, int) - Constructor for class org.biojava.nbio.structure.rcsb.RCSBTaxonomy

RCSBUpdates - Class in org.biojava.nbio.structure.rcsb

RCSBUpdates() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBUpdates

read(BufferedReader) - Static method in class org.biojava.nbio.structure.jama.Matrix

Read a matrix from a stream.

ReadUtils - Class in org.biojava.nbio.structure.rcsb

Package-level static utilities for parsing XML.

ReadUtils() - Constructor for class org.biojava.nbio.structure.rcsb.ReadUtils

rebuildAFPChain(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser

replace the PDB res nums with atom positions:

rebuildQuaternaryStructure(Structure, List<BiologicalAssemblyTransformation>) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder

RectangularPrism - Class in org.biojava.nbio.structure.symmetry.geometry

RectangularPrism(double, double, double) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism

reduce(Structure) - Method in class org.biojava.nbio.structure.align.client.StructureName

reduce(Structure) - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier

reduce(Structure) - Method in class org.biojava.nbio.structure.cath.CathDomain

reduce(Structure) - Method in class org.biojava.nbio.structure.domain.PDPDomain

reduce(Structure) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

reduce(Structure) - Method in class org.biojava.nbio.structure.PassthroughIdentifier

reduce(Structure) - Method in class org.biojava.nbio.structure.scop.ScopDomain

reduce(Structure) - Method in interface org.biojava.nbio.structure.StructureIdentifier

Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.

reduce(Structure) - Method in class org.biojava.nbio.structure.SubstructureIdentifier

Takes a complete structure as input and reduces it to residues present in the specified ranges

reduce(Structure) - Method in class org.biojava.nbio.structure.URLIdentifier

ReducedChemCompProvider - Class in org.biojava.nbio.structure.io.mmcif

Unlike the DownloadChemCompProvider, this ChemCompProvider does not download any chem comp definitions.

ReducedChemCompProvider() - Constructor for class org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider

reduceFragments(List<FragmentPair>, FragmentPair, Matrix) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner

In helices often many similar fragments can be found.

reduceInitialFragments() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

if this is set to false, the time spent to joint the initial fragments (step 2) is increased.

REF_RMSD - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

ReferenceSuperimposer - Class in org.biojava.nbio.structure.align.multiple.util

Superimposes each structure in a MultipleAlignment onto a reference structure.

ReferenceSuperimposer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer

Default Constructor.

ReferenceSuperimposer(int) - Constructor for class org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer

Constructor using a specified structure as reference.

refine(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

Refinement procedure based on superposition and dynamic programming.

Refine - Class in org.biojava.nbio.structure.io.mmcif.model

Refine() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Refine

refine(AFPChain, Atom[], int) - Method in class org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner

refine(AFPChain, Atom[], int) - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner

refine(AFPChain, Atom[], int) - Method in interface org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner

Returns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.

RefinerFailedException - Exception in org.biojava.nbio.structure.symmetry.internal

Refinement of the self-alignment failed.

RefinerFailedException() - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

RefinerFailedException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

RefinerFailedException(String) - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

RefinerFailedException(Throwable) - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

refineSymmetry(AFPChain, Atom[], Atom[], int) - Static method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner

Refines a CE-Symm alignment so that it is perfectly symmetric.

refineSymmetry(Map<Integer, Integer>, int) - Static method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner

Refines a CE-Symm alignment so that it is perfectly symmetric.

refmacVersion - Variable in class org.biojava.nbio.structure.validation.Entry

REFTM_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

relativePercentileClashscore - Variable in class org.biojava.nbio.structure.validation.Entry

relativePercentileDCCRfree - Variable in class org.biojava.nbio.structure.validation.Entry

relativePercentilePercentRamaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry

relativePercentilePercentRotaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry

relativePercentilePercentRSRZOutliers - Variable in class org.biojava.nbio.structure.validation.Entry

relativePercentileRNAsuiteness - Variable in class org.biojava.nbio.structure.validation.Entry

reloadFromFile() - Method in class org.biojava.nbio.structure.domain.SerializableCache

remark800toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.Site

Appends the REMARK 800 section pertaining to the site onto the end of the StringBuffer provided.

remark800toPDB() - Method in class org.biojava.nbio.structure.Site

Provides REMARK 800 section pertaining to the site as a string.

RemoteBioUnitDataProvider - Class in org.biojava.nbio.structure.quaternary.io

RemoteBioUnitDataProvider() - Constructor for class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider

RemoteDomainProvider - Class in org.biojava.nbio.structure.domain

A DomainProvider that uses a mixture of SCOP and PDP domains.

RemoteDomainProvider() - Constructor for class org.biojava.nbio.structure.domain.RemoteDomainProvider

RemoteDomainProvider(boolean) - Constructor for class org.biojava.nbio.structure.domain.RemoteDomainProvider

initialize this provider with caching enabled

RemotePDPProvider - Class in org.biojava.nbio.structure.domain

A class that provided PDP assignments that are loaded from a remote web server

RemotePDPProvider() - Constructor for class org.biojava.nbio.structure.domain.RemotePDPProvider

RemotePDPProvider(boolean) - Constructor for class org.biojava.nbio.structure.domain.RemotePDPProvider

remoteProviderClassName - Static variable in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory

RemoteRawBioUnitDataProvider - Class in org.biojava.nbio.structure.quaternary.io

A BioUnitDataProvider that fetches the symmetry operations via remote calls to servers from RCSB PDB

RemoteRawBioUnitDataProvider() - Constructor for class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider

RemoteScopInstallation - Class in org.biojava.nbio.structure.scop

A class that fetches information about SCOP from a remote data-source.

RemoteScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.RemoteScopInstallation

remove() - Method in class org.biojava.nbio.structure.AtomIterator

does nothing.

remove() - Method in class org.biojava.nbio.structure.GroupIterator

does nothing .

removeAlgorithm(String) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory

Removes the specified algorithm from the list of options

removeGaps(ProteinSequence) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher

Removes all gaps ('-') from a protein sequence

removeGaps(T[][]) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher

Creates a new list consisting of all columns of gapped where no row contained a null value.

removeInterfacesBelowArea() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Removes from this interface list all interfaces with areas below the default cutoff area

removeInterfacesBelowArea(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Removes from this interface list all interfaces with areas below the given cutoff area

removeMMcifConsumer(MMcifConsumer) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser

remove a single consumer from the parser

removeMMcifConsumer(MMcifConsumer) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

removeModels(Structure) - Static method in class org.biojava.nbio.structure.StructureTools

Remove all models from a Structure and keep only the first

removeRotation(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

replaceOptAln(int[][][], AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

It replaces an optimal alignment of an AFPChain and calculates all the new alignment scores and variables.

replaceOptAln(AFPChain, Atom[], Atom[], Map<Integer, Integer>) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Takes an AFPChain and replaces the optimal alignment based on an alignment map

replaceOptAln(AFPChain, Atom[], Atom[], int, int[], int[][][]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

RepresentativeXMLConverter - Class in org.biojava.nbio.structure.align.xml

RepresentativeXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.RepresentativeXMLConverter

requestingAlignmentsFromServer(int) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener

requestingAlignmentsFromServer(int) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener

reset() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

reset() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

reset() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams

Set the parameters to the default.

reset() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

reset() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

reset() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

reset() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

reset() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

reset() - Method in class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator

reset() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator

resetModels() - Method in interface org.biojava.nbio.structure.Structure

Resets all models of this Structure

resetModels() - Method in class org.biojava.nbio.structure.StructureImpl

Resets all models of this Structure

ResidueGroup - Class in org.biojava.nbio.structure.symmetry.internal

A ResidueGroup is a set of residues that are part of a maximally connected component of the self-Alignment Graph in symmetry analysis.

ResidueGroup(Set<Integer>) - Constructor for class org.biojava.nbio.structure.symmetry.internal.ResidueGroup

Create a ResidueGroup object from a maximally connected component.

residueNumber - Variable in class org.biojava.nbio.structure.HetatomImpl

ResidueNumber - Class in org.biojava.nbio.structure

Everything that is needed to uniquely describe a residue position

ResidueNumber() - Constructor for class org.biojava.nbio.structure.ResidueNumber

ResidueNumber(ResidueNumber) - Constructor for class org.biojava.nbio.structure.ResidueNumber

ResidueNumber(String, Integer, Character) - Constructor for class org.biojava.nbio.structure.ResidueNumber

ResidueRange - Class in org.biojava.nbio.structure

A chain, a start residue, and an end residue.

ResidueRange(String, String, String) - Constructor for class org.biojava.nbio.structure.ResidueRange

ResidueRange(String, ResidueNumber, ResidueNumber) - Constructor for class org.biojava.nbio.structure.ResidueRange

ResidueRangeAndLength - Class in org.biojava.nbio.structure

A chain, a start residue, and an end residue.

ResidueRangeAndLength(String, ResidueNumber, ResidueNumber, int) - Constructor for class org.biojava.nbio.structure.ResidueRangeAndLength

ResidueRangeAndLength(String, String, String, int) - Constructor for class org.biojava.nbio.structure.ResidueRangeAndLength

RESIDUES_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier

URL parameter specifying residue ranges to include, e.g.

ResidueType - Enum in org.biojava.nbio.structure.io.mmcif.chem

Enumerates the possible classifications of residues.

resizeArray(Object, int) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner

Reallocates an array with a new size, and copies the contents of the old array to the new array.

resizeArray(Object, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Reallocates an array with a new size, and copies the contents of the old array to the new array.

resname - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

resnum - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

ResourceManager - Class in org.biojava.nbio.structure.align.util

A class that manages the Strings that are defined in the spice.properties file.

ResourceManager() - Constructor for class org.biojava.nbio.structure.align.util.ResourceManager

restypesNotcheckedForBondAngleGeometry - Variable in class org.biojava.nbio.structure.validation.Entry

RG - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

RG1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

rms_dk_diag(double[], double[], int, int, int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools

Given distance matrix diagonals dk1, dk2, get the rmsd of a fpair.

RMSD - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

rmsd(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

rmsdMin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

rmsdThr - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

rmsdThrJoin - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

RNA_ONLY - Static variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType

Convenience Set of polymer types classified as RNA.

rnaSuiteness - Variable in class org.biojava.nbio.structure.validation.Entry

rota - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

rotate(Atom[], double) - Method in class org.biojava.nbio.structure.align.util.RotationAxis

rotate(Atom, double[][]) - Static method in class org.biojava.nbio.structure.Calc

Rotate a single Atom aroud a rotation matrix.

rotate(Structure, double[][]) - Static method in class org.biojava.nbio.structure.Calc

Rotate a structure.

rotate(Group, double[][]) - Static method in class org.biojava.nbio.structure.Calc

Rotate a Group.

rotate(Atom, Matrix) - Static method in class org.biojava.nbio.structure.Calc

Rotate an Atom around a Matrix object.

rotate(Group, Matrix) - Static method in class org.biojava.nbio.structure.Calc

Rotate a group object.

rotate(Structure, Matrix) - Static method in class org.biojava.nbio.structure.Calc

Rotate a structure object.

rotate(Atom[], Matrix) - Static method in class org.biojava.nbio.structure.Calc

Rotation - Class in org.biojava.nbio.structure.symmetry.core

Rotation() - Constructor for class org.biojava.nbio.structure.symmetry.core.Rotation

RotationAxis - Class in org.biojava.nbio.structure.align.util

Calculates the rotation axis for an alignment

RotationAxis(AFPChain) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis

Calculate the rotation axis for the first block of an AFPChain

RotationAxis(Atom, Atom, double) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis

Create a rotation axis from a vector, a point, and an angle.

RotationAxis(Matrix, Atom) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis

Determine the location of the rotation axis based on a rotation matrix and a translation vector

RotationAxis(Matrix4d) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis

Create a rotation axis from a Matrix4d containing a rotational component and a translational component.

RotationAxisAligner - Class in org.biojava.nbio.structure.symmetry.core

RotationAxisAligner(QuatSymmetryResults) - Constructor for class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner

RotationGroup - Class in org.biojava.nbio.structure.symmetry.core

RotationGroup() - Constructor for class org.biojava.nbio.structure.symmetry.core.RotationGroup

RotationSolver - Class in org.biojava.nbio.structure.symmetry.core

RotationSolver(Subunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.RotationSolver

rotMatrixToString(Matrix4d) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

rscc - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

rsr - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

rsrz - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

run() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable

run() - Method in class org.biojava.nbio.structure.align.FarmJob

run() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

run() - Method in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider

Do the actual loading of the dictionary in a thread.

run() - Method in class org.biojava.nbio.structure.symmetry.analysis.ScanSymmetry

runOptimization(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer

run the optimization

S

s_min - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues

said - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

SandboxStyleStructureProvider - Class in org.biojava.nbio.structure.io

The "Sandbox" style of organizing files is to have a directory structure like below, i.e.

SandboxStyleStructureProvider() - Constructor for class org.biojava.nbio.structure.io.SandboxStyleStructureProvider

scalarProduct(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Scalar product (dot product).

scale(Atom, double) - Static method in class org.biojava.nbio.structure.Calc

Multiply elements of a by s

scale(double) - Method in class org.biojava.nbio.structure.math.SparseVector

Calculates alpha * a

scaleAdd(double, Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Perform linear transformation s*X+B, and store the result in b

scaleEquals(Atom, double) - Static method in class org.biojava.nbio.structure.Calc

Multiply elements of a by s (in place)

ScanSymmetry - Class in org.biojava.nbio.structure.symmetry.analysis

ScanSymmetry() - Constructor for class org.biojava.nbio.structure.symmetry.analysis.ScanSymmetry

scid - Variable in class org.biojava.nbio.structure.validation.SymmClash

SCOP_DOWNLOAD - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation

SCOP_DOWNLOAD_ALTERNATE - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation

ScopCategory - Enum in org.biojava.nbio.structure.scop

The various categories provided by SCOP.

ScopDatabase - Interface in org.biojava.nbio.structure.scop

General API how to interact with SCOP

ScopDescription - Class in org.biojava.nbio.structure.scop

Contains data from dir.des.scop.txt_1.75

ScopDescription() - Constructor for class org.biojava.nbio.structure.scop.ScopDescription

ScopDescriptions - Class in org.biojava.nbio.structure.scop.server

ScopDescriptions() - Constructor for class org.biojava.nbio.structure.scop.server.ScopDescriptions

ScopDomain - Class in org.biojava.nbio.structure.scop

Container for the information for a domain.

ScopDomain() - Constructor for class org.biojava.nbio.structure.scop.ScopDomain

ScopDomains - Class in org.biojava.nbio.structure.scop.server

ScopDomains() - Constructor for class org.biojava.nbio.structure.scop.server.ScopDomains

ScopFactory - Class in org.biojava.nbio.structure.scop

Controls the global ScopDatabase being used.

ScopFactory() - Constructor for class org.biojava.nbio.structure.scop.ScopFactory

ScopInstallation - Class in org.biojava.nbio.structure.scop

This class provides access to the SCOP protein structure classification.

ScopInstallation(String) - Constructor for class org.biojava.nbio.structure.scop.ScopInstallation

Create a new SCOP installation.

ScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.ScopInstallation

Create a new SCOP installation, downloading the file to "the right place".

ScopIOException - Exception in org.biojava.nbio.structure.scop

Indicates that an I/O error occurred with SCOP lazy initialization.

ScopIOException() - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException

ScopIOException(String) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException

ScopIOException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException

ScopIOException(Throwable) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException

ScopMirror - Class in org.biojava.nbio.structure.scop

Helper class to store paths to the four SCOP files The string "%s" is replaced with the version number.

ScopMirror(String, String, String, String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror

Specify all keys individually

ScopMirror(String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror

Specify a common root URL which is concatenated with individual filenames

ScopMirror(String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror

ScopMirror() - Constructor for class org.biojava.nbio.structure.scop.ScopMirror

Use default MRC location

ScopNode - Class in org.biojava.nbio.structure.scop

ScopNode() - Constructor for class org.biojava.nbio.structure.scop.ScopNode

ScopNodes - Class in org.biojava.nbio.structure.scop.server

ScopNodes() - Constructor for class org.biojava.nbio.structure.scop.server.ScopNodes

scopVersion - Variable in class org.biojava.nbio.structure.scop.ScopInstallation

ScoresCache - Interface in org.biojava.nbio.structure.align.multiple

Interface for classes which implement a temporary cache for various numeric scores, e.g.

scoringStrategy - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

scoringStrategy - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

SEC_STRUC - Static variable in interface org.biojava.nbio.structure.Group

Group property key for secondary structure annotation

SecStrucCalc - Class in org.biojava.nbio.structure.secstruc

Calculate and assign the secondary structure (SS) to the Groups of a Structure object.

SecStrucCalc() - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucCalc

SecStrucElement - Class in org.biojava.nbio.structure.secstruc

A secondary structure element (SSE) is an object representing a block of sequential residues that share the same secondary structure type.

SecStrucElement(SecStrucType, ResidueNumber, ResidueNumber, int, int, String) - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucElement

Create a new SSE object.

SecStrucInfo - Class in org.biojava.nbio.structure.secstruc

Container for the secondary structure information of a single residue.

SecStrucInfo(Group, String, SecStrucType) - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucInfo

SecStrucState - Class in org.biojava.nbio.structure.secstruc

This class extends the basic container for secondary structure annotation, including all the information used in the DSSP algorithm.

SecStrucState(Group, String, SecStrucType) - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucState

SecStrucTools - Class in org.biojava.nbio.structure.secstruc

This class contains methods for obtaining and converting secondary structure information from BioJava Structures.

SecStrucTools() - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucTools

SecStrucType - Enum in org.biojava.nbio.structure.secstruc

This enum contains all of the secondary structure types found in the DSSP output.

Segment - Class in org.biojava.nbio.structure.domain.pdp

Segment() - Constructor for class org.biojava.nbio.structure.domain.pdp.Segment

SegmentComparator - Class in org.biojava.nbio.structure.domain.pdp

SegmentComparator() - Constructor for class org.biojava.nbio.structure.domain.pdp.SegmentComparator

sendAFPChainToServer(String, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient

sendMultiAFPChainToServer(String, String, String) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient

sendMultiAFPChainToServer(String, String, String, String) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient

sendResultsToServer(List<String>) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable

sentResultsToServer(int, String) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener

sentResultsToServer(int, String) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener

seq - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

SeqMisMatch - Interface in org.biojava.nbio.structure

Created by andreas on 9/11/15.

SeqMisMatchImpl - Class in org.biojava.nbio.structure

Created by andreas on 9/11/15.

SeqMisMatchImpl() - Constructor for class org.biojava.nbio.structure.SeqMisMatchImpl

SeqRes2AtomAligner - Class in org.biojava.nbio.structure.io

Aligns the SEQRES residues to the ATOM residues.

SeqRes2AtomAligner() - Constructor for class org.biojava.nbio.structure.io.SeqRes2AtomAligner

SEQRESRECORD - Static variable in interface org.biojava.nbio.structure.AminoAcid

Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.

SequenceAlignmentCluster - Class in org.biojava.nbio.structure.symmetry.core

Represents a cluster of equivalent sequences

SequenceAlignmentCluster(QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster

SequenceFunctionOrderDetector - Class in org.biojava.nbio.structure.symmetry.internal

Calls Spencer's method for determining order.

SequenceFunctionOrderDetector() - Constructor for class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector

SequenceFunctionOrderDetector(int, float) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector

SequenceFunctionRefiner - Class in org.biojava.nbio.structure.symmetry.internal

Creates a refined alignment with the CE-Symm alternative self-alignment.

SequenceFunctionRefiner() - Constructor for class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner

seqWeight - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

SerializableCache<K,V> - Class in org.biojava.nbio.structure.domain

A class that provides all that is necessary to create a Serializable Cache

SerializableCache(String) - Constructor for class org.biojava.nbio.structure.domain.SerializableCache

set cacheFileName to null to disable caching

serialize(File) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

serializedCache - Variable in class org.biojava.nbio.structure.domain.SerializableCache

serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathDomain

serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathFragment

serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathNode

serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathSegment

serialVersionUID - Static variable in exception org.biojava.nbio.structure.io.PDBParseException

serialVersionUID - Static variable in exception org.biojava.nbio.structure.StructureException

SERVER_LOCATION - Static variable in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider

SERVICELOCATION - Static variable in class org.biojava.nbio.structure.rcsb.PdbIdLists

set(int, int, double) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a single element.

set(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP

set(Point3d[], Point3d[], double[]) - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP

setA(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setAbsoluteMinimumSequenceLength(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setAbsolutePercentialRNAsuiteness(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

setAbsolutePercentileClashscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the absolutePercentileClashscore property.

setAbsolutePercentileDCCRfree(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

setAbsolutePercentilePercentRamaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the absolutePercentilePercentRamaOutliers property.

setAbsolutePercentilePercentRotaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the absolutePercentilePercentRotaOutliers property.

setAbsolutePercentilePercentRSRZOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the absolutePercentilePercentRSRZOutliers property.

setAbsorpt_coefficient_mu(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setAbsorpt_correction_T_max(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setAbsorpt_correction_T_min(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setAbsorpt_correction_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setAbsorpt_process_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setAccept1(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setAccept2(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setAcceptedAtomNames(String[]) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

By default the parser will read in all atoms (unless using the CAonly switch).

setAcentricOutliers(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the acentricOutliers property.

setAddress(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor

setAfpAftIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpBefIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainList(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainTwiBin(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainTwiList(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainTwiNum(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpDisCut(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setAfpDisCut0(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setAfpIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpSet(List<AFP>) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Set the set of AFPs for this alignment.

setAlgorithm(StructureAlignment) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Caution has to be made when changing the algorithmName of an AFPChain, since downstream analysis methods (scores, display, etc) behave differently if the alignment is flexible (created with FatCat).

setAlgorithmName(String) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.

setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setAligMat(AligMatEl[][]) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setAligMat(int, int, AligMatEl) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setAligMat(AligMatEl[][]) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setAlign_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setAlign_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setAlign_se1(int[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setAlign_se1(int[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setAlign_se2(int[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setAlign_se2(int[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setAlignment(int[][][]) - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment

setAlignment1(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList

setAlignment2(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList

setAlignmentFractionThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setAlignmentLengthFraction(double) - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment

setAlignments(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

we only keep the first alternative...

setAlignPairs(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setAlignRes(List<List<Integer>>) - Method in interface org.biojava.nbio.structure.align.multiple.Block

Set the double List containing the aligned residues for each structure.

setAlignRes(List<List<Integer>>) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

setAlignScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlignScoreUpdate(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlignSeqRes(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Define if the SEQRES in the structure should be aligned with the ATOM records if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.

setAlnbeg1(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnbeg2(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnLength(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnseq1(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnseq2(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnsymb(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlpha(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setAlt_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setAltAligNumber(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setAltcode(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the altcode property.

setAltLoc(Character) - Method in interface org.biojava.nbio.structure.Atom

Set alternate Location.

setAltLoc(Character) - Method in class org.biojava.nbio.structure.AtomImpl

Set alternate Location.

setAltShortSymbol(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setAminoType(Character) - Method in interface org.biojava.nbio.structure.AminoAcid

Set the name of the AA, in single letter code .

setAminoType(Character) - Method in class org.biojava.nbio.structure.AminoAcidImpl

Set the name of the AA, in single letter code .

setAngle_alpha(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setAngle_alpha_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setAngle_beta(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setAngle_beta_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setAngle_gamma(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setAngle_gamma_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setAngleDiff(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setAngleThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setAniso_B(String[][]) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setArchitectureId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setArchitectureName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setAsaC(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa

setAsas(double[], double[], int, int, int) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setAsaU(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa

setAssembly_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen

setAssemblyId(Long) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setAssignments(Map<String, String>) - Method in class org.biojava.nbio.structure.domain.AssignmentXMLSerializer

setAsym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setAsym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setAsym_id_list(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen

setAsymUnit(Structure) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider

setAsymUnit(Structure) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider

setAsymUnit(Structure) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider

setAsymUnit(Structure) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider

setAsymUnit(Structure) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider

setAtcc(String) - Method in class org.biojava.nbio.structure.EntityInfo

setAtom(String) - Method in class org.biojava.nbio.structure.validation.Clash

Sets the value of the atom property.

setAtom(String) - Method in class org.biojava.nbio.structure.validation.SymmClash

Sets the value of the atom property.

setAtom0(String) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the atom0 property.

setAtom0(String) - Method in class org.biojava.nbio.structure.validation.BondOutlier

Sets the value of the atom0 property.

setAtom1(String) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the atom1 property.

setAtom1(String) - Method in class org.biojava.nbio.structure.validation.BondOutlier

Sets the value of the atom1 property.

setAtom2(String) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the atom2 property.

setAtom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setAtom_id_1(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setAtom_id_2(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setAtomArrays(List<Atom[]>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Sets the List of Atom arrays.

setAtomArrays(List<Atom[]>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setAtomAsaCs(List<Double>) - Method in class org.biojava.nbio.structure.asa.GroupAsa

setAtomAsaUs(List<Double>) - Method in class org.biojava.nbio.structure.asa.GroupAsa

setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

setAtomCache(AtomCache) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider

Set an AtomCache to use when fetching asymmetric units.

setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider

setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider

setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider

setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider

setAtomCache(AtomCache) - Static method in class org.biojava.nbio.structure.StructureIO

setAtomCaThreshold(int) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.

setAtomGroups(List<Group>) - Method in interface org.biojava.nbio.structure.Chain

Set all Groups with observed density in the chain, i.e.

setAtomGroups(List<Group>) - Method in class org.biojava.nbio.structure.ChainImpl

Set all Groups with observed density in the chain, i.e.

setAtomInfo(String, int, char, float, float, float, float, float, String, int) - Method in class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder

setAtoms(List<Atom>) - Method in interface org.biojava.nbio.structure.Group

Set the atoms of this group.

setAtoms(List<Atom>) - Method in class org.biojava.nbio.structure.HetatomImpl

Set the atoms of this group.

setAtoms(List<ChemCompAtom>) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setAtoms(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setAtoms(String) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the atoms property.

setAtoms(String) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the atoms property.

setAttemptedValidationSteps(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the attemptedValidationSteps property.

setAuth_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setAuth_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setAuth_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setAuth_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setAuth_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setAuth_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setAuth_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setAuth_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setAuth_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setAuth_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setAuth_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setAuth_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setAuthorList(List<Author>) - Method in class org.biojava.nbio.structure.JournalArticle

setAuthors(String) - Method in class org.biojava.nbio.structure.PDBHeader

setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Deprecated.
Use AtomCache.getFetchBehavior()

setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

Deprecated.
Use UserConfiguration.getFetchBehavior()

setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Deprecated.
Use #setFetchBehavior()

setAverageScore(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

setAvgoccu(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the avgoccu property.

setAxes(SymmetryAxes) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setAxisAngle(AxisAngle4d) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setAxisTypes(int[]) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setB(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setB_iso_max(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setB_iso_mean(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setB_iso_min(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setB_iso_or_equiv(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setB_iso_or_equiv_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setBadRmsd(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setBbs(Structure, Matrix4d[], boolean) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox

setBend(boolean) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setBeta(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setBinaryOperators(List<OrderedPair<String>>) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver

setBioAssemblies(Map<Integer, BioAssemblyInfo>) - Method in class org.biojava.nbio.structure.PDBHeader

setBioAssembly(Map<Integer, BioAssemblyData>) - Method in class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder

setBiol_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setBiologicalAssembly(boolean) - Method in interface org.biojava.nbio.structure.Structure

Set a flag to indicate if this structure is a biological assembly

setBiologicalAssembly(boolean) - Method in class org.biojava.nbio.structure.StructureImpl

Sets a flag to indicate if this structure is a biological assembly

setBiologicalUnit(String) - Method in class org.biojava.nbio.structure.EntityInfo

setBioUnitDataProvider(Class<? extends BioUnitDataProvider>) - Static method in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory

Set the type of provider to be created

setBioUnitDataProvider(String) - Static method in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory

Sets the data provider to the specified class name.

setBlock2Afp(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockGap(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockNum(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockNumClu(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockNumIni(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockNumSpt(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockResList(int[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockResSize(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockRmsd(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockRotationMatrix(Matrix[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlocks(List<Block>) - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Set the List of alignment Blocks of the BlockSet.

setBlocks(List<Block>) - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

setBlockScore(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockSet(BlockSet) - Method in interface org.biojava.nbio.structure.align.multiple.Block

Set the back-reference to its parent BlockSet.

setBlockSet(BlockSet) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

setBlockSets(List<BlockSet>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Sets the List of BlockSet List of the specified alignment.

setBlockSets(List<BlockSet>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

setBlockShiftVector(Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockSize(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBonds(List<Bond>) - Method in interface org.biojava.nbio.structure.Atom

Sets the bonds

setBonds(List<Bond>) - Method in class org.biojava.nbio.structure.AtomImpl

Sets the bonds

setBonds(List<ChemCompBond>) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setBravLattice(BravaisLattice) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setBridge1(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setBridge2(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setBulkSolventB(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the bulkSolventB property.

setBulkSolventK(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the bulkSolventK property.

setC(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setC1(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

setCa1(Atom[]) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setCa1Length(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setCa2Length(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setCache(AtomCache) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setCacheFilePath(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setCacheFilePath(String) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setCacheFilePath(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setCacheLocation(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setCacheLocation(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Set an alternate download location for files

setCacheLocation(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

setCachePath(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

set the location at which utility data should be cached.

setCalculationTime(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setCalculationTime(Long) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the running time spent to calculate this alignment.

setCalculationTime(Long) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setCalculationTime(long) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setCartn_x(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setCartn_x_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setCartn_y(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setCartn_y_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setCartn_z(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setCartn_z_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setCATH(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setCath(CathDatabase) - Static method in class org.biojava.nbio.structure.cath.CathFactory

Sets the default (singleton) CathDatabase.

setCathDownloadUrl(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setCathVersion(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setCCP4Version(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the ccp4Version property.

setCell(String) - Method in class org.biojava.nbio.structure.EntityInfo

setCell_setting(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry

setCellLine(String) - Method in class org.biojava.nbio.structure.EntityInfo

setCellularLocation(String) - Method in class org.biojava.nbio.structure.EntityInfo

setCenter1(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setCenter2(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setCentered(boolean) - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP

setCentricOutliers(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the centricOutliers property.

setChain(Chain) - Method in interface org.biojava.nbio.structure.Group

Sets the back-reference to its parent Chain.

setChain(Chain) - Method in class org.biojava.nbio.structure.HetatomImpl

Sets the back-reference to its parent Chain.

setChain(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the chain property.

setChain1(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setChain2(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setChainID(String) - Method in interface org.biojava.nbio.structure.Chain

Sets the name of this chain (Chain id in PDB file ).

setChainID(String) - Method in class org.biojava.nbio.structure.ChainImpl

Sets the name of this chain (Chain id in PDB file ).

setChainId(String) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

setChainId(String) - Method in class org.biojava.nbio.structure.DBRef

The chain ID of the corresponding chain.

setChainId(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setChainId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setChainId(String) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Sets the chain identified this transformation should be applied to.

setChainId(String) - Method in class org.biojava.nbio.structure.ResidueNumber

setChainID1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setChainID2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setChainInfo(String, int) - Method in class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder

setChainLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setChainRmsd(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

The RMSD of the chain of AFPs.

setChains(List<Chain>) - Method in class org.biojava.nbio.structure.EntityInfo

Set the chains for this Compound

setChains(List<Chain>) - Method in interface org.biojava.nbio.structure.Structure

Set the chains of a structure, if this is a NMR structure, this will only set model 0.

setChains(int, List<Chain>) - Method in interface org.biojava.nbio.structure.Structure

Set the chains for a model

setChains(List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the chains of a structure, if this is a NMR structure, this will only set model 0.

setChains(int, List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the chains for a model

setCharge(short) - Method in interface org.biojava.nbio.structure.Atom

Set the charge of this atom

setCharge(short) - Method in class org.biojava.nbio.structure.AtomImpl

setCharge(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.Group

Set the Chemical Component that closer describes this group.

setChemComp(ChemComp) - Method in class org.biojava.nbio.structure.HetatomImpl

setChemCompProvider(ChemCompProvider) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory

The new ChemCompProvider will be set in the static variable, so this provider will be used from now on until it is changed again.

setChildren(List<Integer>) - Method in class org.biojava.nbio.structure.scop.ScopNode

setCid(BigInteger) - Method in class org.biojava.nbio.structure.validation.Clash

Sets the value of the cid property.

setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

Set the radius of a circumscribed sphere, that goes through all vertices

setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

Set the radius of a circumscribed sphere, that goes through all vertices

setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

Set the radius of a circumscribed sphere, that goes through all vertices

setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Set the radius of a circumscribed sphere, that goes through all vertices

setClashmag(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Clash

Sets the value of the clashmag property.

setClashmag(BigDecimal) - Method in class org.biojava.nbio.structure.validation.SymmClash

Sets the value of the clashmag property.

setClashscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the clashscore property.

setClassId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setClassId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setClassification(String) - Method in class org.biojava.nbio.structure.PDBHeader

setClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setCluster(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

set the number of the cluster this alignment belongs to.

setCluster(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setCluster(StructureInterfaceCluster) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setCode(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper

setCol(short) - Method in class org.biojava.nbio.structure.align.helper.IndexPair

setComment(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setCommon_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor

setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier

setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly

setCompositionId(String) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

setCompound(EntityInfo) - Method in interface org.biojava.nbio.structure.Chain

Sets the Compound

setCompound(EntityInfo) - Method in class org.biojava.nbio.structure.ChainImpl

Sets the Compound

setCompounds(List<EntityInfo>) - Method in interface org.biojava.nbio.structure.Structure

Set the Compounds

setCompounds(List<EntityInfo>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the Compounds

setConn(Double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setConn_type_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setConnections(List<Map<String, Integer>>) - Method in interface org.biojava.nbio.structure.Structure

Deprecated.
use Atom.addBond(Bond) instead

setConnections(List<Map<String, Integer>>) - Method in class org.biojava.nbio.structure.StructureImpl

sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file:

setContacts(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setContacts(AtomContactSet) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setContacts(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setContig(int) - Method in class org.biojava.nbio.structure.align.helper.AligMatEl

setConvergenceSteps(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setCoords(double[]) - Method in interface org.biojava.nbio.structure.Atom

Set the coordinates.

setCoords(double[]) - Method in class org.biojava.nbio.structure.AtomImpl

Set the coordinates.

setCorrelation_coeff_Fo_to_Fc(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setCorrelation_coeff_Fo_to_Fc_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setCovered(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setCPPoint(Integer) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

setCreate_co(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setCreateAtomBonds(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should we create bonds between atoms when parsing a file.

setCreateAtomCharges(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should we create charges on atoms when parsing a file?

setCrystalCell(CrystalCell) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Set the crystal cell

setCrystallographicInfo(PDBCrystallographicInfo) - Method in class org.biojava.nbio.structure.PDBHeader

setCrystallographicInfo(PDBCrystallographicInfo) - Method in interface org.biojava.nbio.structure.Structure

Set crystallographic information for this structure

setCrystallographicInfo(PDBCrystallographicInfo) - Method in class org.biojava.nbio.structure.StructureImpl

Sets crystallographic information for this structure

setCrystals_number(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setCustomChain1(String) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

sets a chain in a custom, user provided file

setCustomFile1(String) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

set the file path for a custom, user provided file, not a standard PDB file.

setCut_sites(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.CutSites

setData(List<String>) - Method in class org.biojava.nbio.structure.scop.server.ListStringWrapper

setData(TreeSet<String>) - Method in class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper

setData(TreeMap<Integer, SpaceGroup>) - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

setDataAnisotropy(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the dataAnisotropy property.

setDatabase(String) - Method in class org.biojava.nbio.structure.DBRef

Specifies the database value.

setDataCompleteness(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the dataCompleteness property.

setDate(Date) - Method in class org.biojava.nbio.structure.cath.CathDomain

setDate(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

setDate_original(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

setDb_align_beg(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setDb_align_end(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setDb_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setDb_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setDb_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setDbAccession(String) - Method in class org.biojava.nbio.structure.DBRef

Sequence database accession code.

setDbIdCode(String) - Method in class org.biojava.nbio.structure.DBRef

Sequence database identification code.

setDBRefs(List<DBRef>) - Method in interface org.biojava.nbio.structure.Structure

Set the list of database references for this structure

setDBRefs(List<DBRef>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the list of database references for this structure

setDbSeqBegin(int) - Method in class org.biojava.nbio.structure.DBRef

Initial sequence number of the database seqment.

setDbSeqEnd(int) - Method in class org.biojava.nbio.structure.DBRef

The begin of the sequence position in the database

setDCCR(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the dccr property.

setDCCRefinementProgram(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the dccRefinementProgram property.

setDCCRfree(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the dccRfree property.

setDebug(boolean) - Method in class org.biojava.nbio.structure.align.StructurePairAligner

Deprecated.

setDefault() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

setDensityCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDepDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader

setDescription(String) - Method in class org.biojava.nbio.structure.cath.CathNode

setDescription(String) - Method in class org.biojava.nbio.structure.EntityInfo

setDescription(String) - Method in class org.biojava.nbio.structure.PDBHeader

setDescription(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setDescription(String) - Method in class org.biojava.nbio.structure.Site

sets the REMARK 800 description of the site

setDescription2(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Set the textual description for protein 2.

setDescriptor(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

setDescriptors(List<ChemCompDescriptor>) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setDetails(String) - Method in class org.biojava.nbio.structure.EntityInfo

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setDetails(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setDetails(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setDiagonalDistance(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDiagonalDistance2(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDirection(int) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setDisCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setDisCut(double) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setDisFilter(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setDisSmooth(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setDist(int[][]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

setDist(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Clash

Sets the value of the dist property.

setDist(BigDecimal) - Method in class org.biojava.nbio.structure.validation.SymmClash

Sets the value of the dist property.

setDist1(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setDist1(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setDist2(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setDist2(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setDisTable1(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setDisTable2(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContact

setDistanceCutoff(Double) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setDistanceCutoff(Double) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setDistanceIncrement(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setDistanceMatrix(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain

A matrix with ca1length rows and ca2length columns.

setDistanceMatrix(Matrix) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

The distance matrix this alignment is based on

setDoAngleCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDoDensityCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDoDistanceCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDoi(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of doi

setDomainCounter(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setDomainId(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setDomainId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setDomainName(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setDomainProvider(DomainProvider) - Static method in class org.biojava.nbio.structure.domain.DomainProviderFactory

setDomainSplit(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setDonor1(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setDonor2(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setDoRMSCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDownloadAll(boolean) - Method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider

By default this provider will download only some of the ChemComp files.

setDuplicationHint(CECPParameters.DuplicationHint) - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

setDuplicationHint(CECPParameters.DuplicationHint) - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

setDVar(Double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setEcNums(List<String>) - Method in class org.biojava.nbio.structure.EntityInfo

setEcodDatabase(String) - Static method in class org.biojava.nbio.structure.ecod.EcodFactory

Updates the default version

setEditorList(List<Author>) - Method in class org.biojava.nbio.structure.JournalArticle

setEDSR(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the edsr property.

setEDSResolution(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the edsResolution property.

setEDSResolutionLow(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the edsResolutionLow property.

setElement(Element) - Method in interface org.biojava.nbio.structure.Atom

Set element of the atom name, e.g.

setElement(Element) - Method in class org.biojava.nbio.structure.AtomImpl

Set element of the atom name, e.g.

setElement1(T) - Method in class org.biojava.nbio.structure.quaternary.OrderedPair

Sets the first element of an ordered pair.

setElement2(T) - Method in class org.biojava.nbio.structure.quaternary.OrderedPair

Sets the second element of an ordered pair.

setEnd(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

setEnergy(double) - Method in class org.biojava.nbio.structure.secstruc.HBond

setEngineered(String) - Method in class org.biojava.nbio.structure.EntityInfo

setEnsemble(MultipleAlignmentEnsemble) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Set the back-reference to its parent Ensemble.

setEnsemble(MultipleAlignmentEnsemble) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

setEnt(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the ent property.

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setEntityId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

setEntry(Entry) - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation

Sets the value of the entry property.

setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords

setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry

setEvalCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setEvCode(String) - Method in class org.biojava.nbio.structure.Site

sets the REMARK 800 EVIDENCE CODE for the site.

setExperimentalTechnique(String) - Method in class org.biojava.nbio.structure.PDBHeader

Adds the experimental technique to the set of experimental techniques of this header.

setExpression_system_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setExpressionSystem(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemAtccNumber(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemCell(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemCellLine(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemCellularLocation(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemGene(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemOrgan(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemOrganelle(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemOtherDetails(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemPlasmid(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemStrain(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemTaxId(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemTissue(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemVariant(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemVector(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemVectorType(String) - Method in class org.biojava.nbio.structure.EntityInfo

setFamilyId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Set the behavior for fetching files from the server

setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Set the behavior for fetching files from the server.

setFetchCurrent(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Deprecated.
Use FileParsingParameters#setObsoleteBehavior() instead (4.0.0)

setFetchCurrent(boolean) - Method in class org.biojava.nbio.structure.io.PDBFileReader

Deprecated.
Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)

setFetchFileEvenIfObsolete(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Deprecated.
Use FileParsingParameters#setObsoleteBehavior() instead (4.0.0)

setFetchFileEvenIfObsolete(boolean) - Method in class org.biojava.nbio.structure.io.PDBFileReader

Deprecated.
Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)

setFGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setFGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setFile1(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setFile2(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setFileFormat(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setFileLocation(String) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider

setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer

setFileParsingParameters(FileParsingParameters) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer

setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer

setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.PDBFileParser

setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider

setFileParsingParameters(FileParsingParameters) - Method in interface org.biojava.nbio.structure.io.StructureProvider

Set the parameters that should be used for file parsing

setFileParsingParams(FileParsingParameters) - Method in class org.biojava.nbio.structure.align.util.AtomCache

setFirstGroupAsa(GroupAsa) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setFlexible(boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setFlippableSidechain(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the flippableSidechain property.

setFocusAfpList(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFocusAfpn(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFocusRes1(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFocusRes2(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFocusResn(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFoFcCorrelation(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the foFcCorrelation property.

setFold(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setFold(int) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setFoldId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setFormat(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setFormula(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setFormula(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setFormula_weight(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setFormula_weight(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setFragCompat(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setFragLen(Integer) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setFragLen(int) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setFragLen(int) - Method in class org.biojava.nbio.structure.align.model.AFP

setFragLenSq(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setFragment(String) - Method in class org.biojava.nbio.structure.EntityInfo

setFragmentId(Integer) - Method in class org.biojava.nbio.structure.cath.CathFragment

setFragmentLength(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setFragmentMiniDistance(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setFragmentPairs(FragmentPair[]) - Method in class org.biojava.nbio.structure.align.StructurePairAligner

setFragScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setFrom(Integer) - Method in class org.biojava.nbio.structure.domain.pdp.Segment

setGamma(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setGapCreate(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setGapExtCol(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setGapExtCol(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setGapExtend(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setGapExtend(Short) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

setGapExtend(short) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

setGapExtension(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setGapExtension(double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setGapExtension(Double) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setGapExtension(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setGapExtRow(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setGapExtRow(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setGapLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setGapOpen(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setGapOpen(double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setGapOpen(Double) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setGapOpen(Short) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

setGapOpen(short) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

setGapOpen(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setGapOpenCol(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setGapOpenCol(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setGapOpenRow(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setGapOpenRow(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setGaps(Boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setGene(String) - Method in class org.biojava.nbio.structure.EntityInfo

setGene_src_common_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_dev_stage(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_genus(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_species(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_strain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_tissue(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_tissue_fraction(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGenus(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setGroup(Group) - Method in interface org.biojava.nbio.structure.Atom

Set the back-reference to its parent Group.

setGroup(Group) - Method in class org.biojava.nbio.structure.AtomImpl

Set the back-reference to its parent Group.

setGroup_PDB(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setGroupBonds(int, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder

setGroupInfo(String, int, char, String, int) - Method in class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder

setGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setGroups(List<Group>) - Method in class org.biojava.nbio.structure.Site

setHeaderOnly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Parse only the PDB file header out of the files

setHeaderVars(String) - Method in class org.biojava.nbio.structure.EntityInfo

setHeight(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

setHelixRmsdThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setHelixRmsdToRiseRatio(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setHetero(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq

setHetero(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setHGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setHGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setHomologyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setHost_org_common_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setHost_org_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setHost_org_genus(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setHost_org_species(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setHost_org_strain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setIclose(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

setIcode(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the icode property.

setId(long) - Method in class org.biojava.nbio.structure.align.model.AFP

setId(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setId(Long) - Method in interface org.biojava.nbio.structure.Chain

Set the ID used by Hibernate.

setId(Long) - Method in class org.biojava.nbio.structure.ChainImpl

Set the ID used by Hibernate.

setId(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setId(int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

setId(Long) - Method in class org.biojava.nbio.structure.DBRef

Set the ID used by Hibernate.

setId(String) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setId(Long) - Method in class org.biojava.nbio.structure.EntityInfo

set the ID used by Hibernate

setId(long) - Method in class org.biojava.nbio.structure.HetatomImpl

the Hibernate database ID

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setId(int) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setId(int) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

setId(String) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Sets the identifier for this biological assembly transformation.

setId(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setId(Long) - Method in interface org.biojava.nbio.structure.Structure

set the ID used by Hibernate

setId(Long) - Method in class org.biojava.nbio.structure.StructureImpl

set the ID used by Hibernate

setId(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setIdbnsBegin(char) - Method in class org.biojava.nbio.structure.DBRef

Insertion code of initial residue of the segment, if PDB is the reference.

setIdbnsEnd(char) - Method in class org.biojava.nbio.structure.DBRef

Insertion code of the ending residue of the segment, if PDB is the reference.

setIdCode(String) - Method in class org.biojava.nbio.structure.DBRef

Set the idCode for this entry.

setIdCode(String) - Method in class org.biojava.nbio.structure.PDBHeader

The PDB code for this protein structure.

setIdenticalSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setIdentifier(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor

setIdentifier(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier

setIdentity(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setIdxlist(List<int[]>) - Method in class org.biojava.nbio.structure.align.helper.JointFragments

Stores the alignment between the residues of several fragments.

setInChI(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setInChIKey(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setIndex(int) - Method in class org.biojava.nbio.structure.align.helper.GapArray

setInitialK(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setInitials(String) - Method in class org.biojava.nbio.structure.Author

setInsCode(Character) - Method in class org.biojava.nbio.structure.ResidueNumber

setInsCode(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setInsCode(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setInsCode1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setInsCode2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

Sets the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces

setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

Sets the radius of an inscribed sphere, that is tangent to each of the octahedron's faces

setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

Sets the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces

setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Sets the radius of an inscribed sphere, that is tangent to each of the tetrahedron's faces

setInsertBegin(char) - Method in class org.biojava.nbio.structure.DBRef

Initial insertion code of the PDB sequence segment.

setInsertEnd(char) - Method in class org.biojava.nbio.structure.DBRef

Ending insertion code of the PDB sequence segment.

setInstalledDomainDescription(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setInstalledDomainList(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setInstalledDomall(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setInstalledNodeList(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setInt_Tables_number(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry

setInterGroupBonds(int, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder

setInternalChainID(String) - Method in interface org.biojava.nbio.structure.Chain

Sets the internal chain ID that is used in mmCif files

setInternalChainID(String) - Method in class org.biojava.nbio.structure.ChainImpl

setIoTime(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setIoTime(Long) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the IO time to load this object

setIoTime(Long) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setIoTime(long) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setIoverSigma(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the ioverSigma property.

setIsPublished(Boolean) - Method in class org.biojava.nbio.structure.JournalArticle

Sets the publication state of a JournalArticle - TO BE PUBLISHED == false

setJclose(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

setJoinFast(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setJoinPlo(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setJoinRMSCutoff(double) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setJournalArticle(JournalArticle) - Method in class org.biojava.nbio.structure.PDBHeader

Set the associated publication as defined by the JRNL records in a PDB file.

setJournalArticle(JournalArticle) - Method in interface org.biojava.nbio.structure.Structure

Set the associated publication as defined by the JRNL records in a PDB file.

setJournalArticle(JournalArticle) - Method in class org.biojava.nbio.structure.StructureImpl

set the associated publication as defined by the JRNL records in a PDB file.

setJournalName(String) - Method in class org.biojava.nbio.structure.JournalArticle

setKappa(float) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setLabel_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setLabel_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setLabel_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setLabel_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setLabel_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setLabel_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setLabel_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setLabel_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setLabel_entity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setLabel_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setLabel_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setLcmp(int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setLcmp(int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setLength(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathFragment

setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathSegment

setLength1(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setLength2(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setLength_a(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setLength_a_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setLength_b(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setLength_b_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setLength_c(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setLength_c_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setLigands(Set<String>) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setLigRSRnbrMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the ligRSRnbrMean property.

setLigRSRnbrStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the ligRSRnbrStdev property.

setLigRSRnumnbrs(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the ligRSRnumnbrs property.

setLigRSRZ(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the ligRSRZ property.

setLikeSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setLocal(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

setLocalSymmetry(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setLocalTimeLimit(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setLs_d_res_high(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_d_res_low(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_matrix_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_number_parameters(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_number_reflns_all(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_number_reflns_obs(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_number_reflns_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_number_reflns_R_work(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_number_restraints(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_percent_reflns_obs(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_percent_reflns_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_R_factor_all(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_R_factor_obs(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_R_factor_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_R_factor_R_free_error(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_R_factor_R_free_error_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_R_factor_R_work(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_redundancy_reflns_obs(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_wR_factor_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_wR_factor_R_work(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setM(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFP

setMacromolecularSize(int) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

setManual(Boolean) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setMapProperty(TreeMap<Integer, SpaceGroup>) - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot

setMatMatrix(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setMatMatrix(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setMatrix(Matrix) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix(int, int, int, int, Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a submatrix.

setMatrix(int[], int[], Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a submatrix.

setMatrix(int[], int, int, Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a submatrix.

setMatrix(int, int, int[], Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a submatrix.

setMatrix11(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix12(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix13(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix21(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix22(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix23(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix31(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix32(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix33(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatTransform(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

setMaxAtoms(int) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

The maximum numbers of atoms to load in a protein structure (prevents memory overflows)

setMaxGap(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMaxGapFrag(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMaxGapSize(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Set the Max gap size parameter.

setMaxGapSize(int) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

CE specific parameter: set the Max gap size parameter G (during AFP extension).

setMaximumLocalCombinations(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMaximumLocalResults(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMaximumLocalSubunits(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMaxIter(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setMaxNrIterationsForOptimization(int) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Set the maximum nr of times the (slow) optimiziation of alignment should iterate.

setMaxOptRMSD(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

set the maximum RMSD cutoff to be applied during alignment optimization.

setMaxOptRMSD(Double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

(jCE specific): maximum RMSD that shall be calculated for the alignment.

setMaxPenalty(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMaxrefine(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setMaxRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setMaxSequenceIdentity(double) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster

setMaxSymmOrder(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setMaxTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setMaxTra(Integer) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

set the maximum number of Twists that are allowed...

setMaxTra(int) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setMaxTra(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Set the maximum number of Twists that are allowed...

setMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the mean property.

setMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.BondOutlier

Sets the value of the mean property.

setMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the mean property.

setMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the mean property.

setMembers(List<StructureInterface>) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

setMethod(String) - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage

setMethod(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setMethod_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setMethod_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly

setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

Sets the radius of radius of a sphere, that is tangent to each of the icosahedron's edges

setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

Sets the radius of radius of a sphere, that is tangent to each of the octahedron's edges

setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Sets the radius of radius of a sphere, that is tangent to each of the tetrahedron's edges

setMinAlignedStructures(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setMinBlockLen(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setMinCoreLength(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setMinCPLength(Integer) - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

setMinCPLength(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

setMindiff(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the mindiff property.

setMindiff(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the mindiff property.

setMinimumHelixAngle(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMinimumHelixRise(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMinimumSequenceLength(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMinimumSequenceLengthFraction(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMinLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setMinRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setMinSequenceIdentity(double) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster

setMinTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setMisCut(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMisLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setMisScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMod_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

setModDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader

setModel(int, List<Chain>) - Method in interface org.biojava.nbio.structure.Structure

A convenience function if one wants to edit and replace the models in a structure.

setModel(int, List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl

A convenience function if one wants to edit and replace the models in a structure.

setModel(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the model property.

setModel_Cartn_x(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setModel_Cartn_y(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setModel_Cartn_z(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setModelCount(int) - Method in class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder

setModelInfo(int, int) - Method in class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder

setMogulIgnore(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the mogulIgnore property.

setMoleculeIds(Pair<String>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setMolecules(Pair<Atom[]>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setMolId(int) - Method in class org.biojava.nbio.structure.EntityInfo

Set the molecule identifier, called entity_id in mmCIF dictionary.

setMon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq

setMon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setMon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setMon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setMon_nstd_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setMon_nstd_parent_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setMultipleAlignment(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Set the back-reference to its parent MultipleAlignment.

setMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

setMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setMultipleAlignments(List<MultipleAlignment>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the List of MultipleAlignments in the ensemble.

setMultipleAlignments(List<MultipleAlignment>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setMultiplicity(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setMutation(String) - Method in class org.biojava.nbio.structure.EntityInfo

setName(String) - Method in interface org.biojava.nbio.structure.Atom

Set atom name, e.g.

setName(String) - Method in class org.biojava.nbio.structure.AtomImpl

Set atom name, e.g.

setName(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setName(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor

setName(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setName(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly

setName(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setName(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setName(String) - Method in interface org.biojava.nbio.structure.Structure

Set biological name of Structure .

setName(String) - Method in class org.biojava.nbio.structure.StructureImpl

Set biological name of Structure .

setName(String) - Method in class org.biojava.nbio.structure.validation.Program

Sets the value of the name property.

setName1(String) - Method in class org.biojava.nbio.structure.align.client.PdbPair

setName1(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setName2(String) - Method in class org.biojava.nbio.structure.align.client.PdbPair

setName2(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setnAtom(int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setnAtom(int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setNatomsEDS(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the natomsEDS property.

setNaturalPos(Integer) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setNcbi_taxonomy_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn

setNclose(int) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

setNcsOperators(Matrix4d[]) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Set the NCS operators.

setNcuts(int) - Method in class org.biojava.nbio.structure.domain.pdp.CutSites

setNdb_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setNdb_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setNmr(boolean) - Method in interface org.biojava.nbio.structure.Structure

Deprecated.

setNmr(boolean) - Method in class org.biojava.nbio.structure.StructureImpl

Deprecated.

setNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathNode

setNormAlignScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setNotObserved(Boolean) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setNrAlignments(int) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setNrCPU(int) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setNrThreads(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setNseg(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setnStart(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setNucleicAcidChainCount(int) - Method in class org.biojava.nbio.structure.symmetry.core.Subunits

setNum(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

setNum(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq

setNumCells(int) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder

Set the number of neighboring crystal cells that will be used in the search for contacts

setNumFreeReflections(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the numFreeReflections property.

setNumHReduce(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the numHReduce property.

setNumHReduce(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the numHReduce property.

setNumMillerIndices(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the numMillerIndices property.

setNumobs(BigInteger) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the numobs property.

setNumobs(BigInteger) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the numobs property.

setNumRes(String) - Method in class org.biojava.nbio.structure.EntityInfo

setObs(BigDecimal) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the obs property.

setObs(BigDecimal) - Method in class org.biojava.nbio.structure.validation.BondOutlier

Sets the value of the obs property.

setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.align.util.AtomCache

[Optional] This method changes the behavior when obsolete entries are requested.

setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

[Optional] This method changes the behavior when obsolete entries are requested.

setObsval(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the obsval property.

setObsval(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the obsval property.

setOccupancy(float) - Method in interface org.biojava.nbio.structure.Atom

Set occupancy.

setOccupancy(float) - Method in class org.biojava.nbio.structure.AtomImpl

setOccupancy(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setOccupancy_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setOccupancy_max(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOccupancy_min(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOligomeric_count(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly

setOligomeric_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly

setOmega(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setOne_letter_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setOper_expression(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen

setOperator(Matrix4d) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper

setOptAln(int[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setOptimization(Boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setOptimizationSteps(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setOptLen(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setOptLength(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

The length of the optimal alignment.

setOptRmsd(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setOrderDetectorMethod(CESymmParameters.OrderDetectorMethod) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setOrgan(String) - Method in class org.biojava.nbio.structure.EntityInfo

setOrganelle(String) - Method in class org.biojava.nbio.structure.EntityInfo

setOrganism_common_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn

setOrganism_scientific(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn

setOrganismCommon(String) - Method in class org.biojava.nbio.structure.EntityInfo

setOrganismScientific(String) - Method in class org.biojava.nbio.structure.EntityInfo

setOrganismTaxId(String) - Method in class org.biojava.nbio.structure.EntityInfo

setOrigGroup(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setOrigGroup(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setORmsdThr(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Set the Original RMSD threshold from which the alignment optimization is started

setOrthologousSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setOutFile(SynchronizedOutFile) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setOutFile(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setOutFile(String) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

setOutputDir(File) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setOutputPDB(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

When writing the results to a file, don;t write as XML but write aligned PDB file

setOverall_FOM_free_R_set(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOverall_FOM_work_R_set(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOverall_SU_B(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOverall_SU_ML(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOverall_SU_R_Cruickshank_DPI(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOverall_SU_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOwab(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the owab property.

setP1(int) - Method in class org.biojava.nbio.structure.align.model.AFP

setP2(int) - Method in class org.biojava.nbio.structure.align.model.AFP

setPair(PdbPair) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setPair(Pair<Atom>) - Method in class org.biojava.nbio.structure.contact.AtomContact

setPair(Pair<Group>) - Method in class org.biojava.nbio.structure.contact.GroupContact

setPairs(SortedSet<PdbPair>) - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.CeMain

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain

setParameters(ConfigStrucAligParams) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner

Set the parameters for this algorithm to use.

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner

setParameters(ConfigStrucAligParams) - Method in interface org.biojava.nbio.structure.align.StructureAlignment

Set the default parameters for this algorithm to use

setParams(FarmJobParameters) - Method in class org.biojava.nbio.structure.align.FarmJob

setParams(StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner

set the parameters to be used for the algorithm

setParams(CESymmParameters) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setParent(Structure) - Method in interface org.biojava.nbio.structure.Chain

Deprecated.
use setStructure instead

setParent(Structure) - Method in class org.biojava.nbio.structure.ChainImpl

Deprecated.

setParent(Structure) - Method in class org.biojava.nbio.structure.DBRef

Set the structure object that this DBRef relates to.

setParentId(String) - Method in class org.biojava.nbio.structure.cath.CathNode

setParentSunid(int) - Method in class org.biojava.nbio.structure.scop.ScopNode

setParseBioAssembly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should the biological assembly info (REMARK 350) be parsed from the PDB file?

setParseCAOnly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Flag if only the C-alpha atoms of the structure should be parsed.

setParseSecStruc(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

A flag to tell the parser to parse the Author's secondary structure assignment from the file default is set to false, i.e.

setPartner(int) - Method in class org.biojava.nbio.structure.secstruc.HBond

setPath(IndexPair[]) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setPath(IndexPair[]) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setPath(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Set the path that is used to cache PDB files.

setPath(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Sets the path for the directory where PDB files are read/written

setPath(String) - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider

directory where to find PDB files

setPathSize(int) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setPathSize(int) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setPdb1(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

mandatory argument to set the first PDB (and optionally chain ID) to be aligned.

setPdb1(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setPdb2(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

mandatory argument to set the second PDB (and optionally chain ID) to be aligned.

setPdb2(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setPdb_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setPdb_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setPdb_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setPdb_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setPdb_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setPdb_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setPdb_strand_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setPdb_strand_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setPdbAln(String[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setPDBCode(String) - Method in interface org.biojava.nbio.structure.Structure

Set PDB code of structure .

setPDBCode(String) - Method in class org.biojava.nbio.structure.StructureImpl

Set PDB code of structure .

setPdbDirSplit(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

Deprecated.
Ignored (4.0.0)

setPdbFilePath(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

mandatory argument to set the location of PDB files.

setPdbFilePath(String) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setPdbFilePath(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setPDBFlag(boolean) - Method in interface org.biojava.nbio.structure.Group

Flag if group has 3D data .

setPDBFlag(boolean) - Method in class org.biojava.nbio.structure.HetatomImpl

flag if group has 3D data.

setPdbGroup(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setPdbGroup(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setPDBHeader(PDBHeader) - Method in interface org.biojava.nbio.structure.Structure

Set the the header information for this PDB file

setPDBHeader(PDBHeader) - Method in class org.biojava.nbio.structure.StructureImpl

Set the the header information for this PDB file

setPdbId(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setPdbId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setPdbId(String) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider

setPdbId(String) - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider

Tell the provider for which PDB ID the quaternary structure should be returned.

setPdbId(String) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider

setPdbId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setPDBName(String) - Method in class org.biojava.nbio.structure.AminoAcidImpl

set three character name of AminoAcid.

setPDBName(String) - Method in interface org.biojava.nbio.structure.Group

Set the PDB 3-letter name for this group.

setPDBName(String) - Method in class org.biojava.nbio.structure.HetatomImpl

Set three character name of Group .

setPdbPath(String) - Static method in class org.biojava.nbio.structure.StructureIO

Utility method to set the location where PDB files can be found

setPdbResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setPdbResNum(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setPdbResNum(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setPdbResNum(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setPDBresnum1(String[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setPDBresnum2(String[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setPDBRevisionNumber(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the pdbRevisionNumber property.

setPDBserial(int) - Method in interface org.biojava.nbio.structure.Atom

Set PDB atom number.

setPDBserial(int) - Method in class org.biojava.nbio.structure.AtomImpl

Set PDB atom number.

setPdbSerial(int) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

setPdbx_align(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_align_begin(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setPdbx_alt_source_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_alt_source_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_ambiguous_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_aromatic_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_aromatic_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setPdbx_atcc(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_auth_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setPdbx_auth_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setPdbx_auth_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setPdbx_auth_seq_align_beg(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_auth_seq_align_end(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_auth_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setPdbx_auth_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_beg_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_beg_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_blank_PDB_chainid_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym

setPdbx_CASP_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

setPdbx_cell(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_cell_line(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_cellular_location(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_component_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_component_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_component_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_data_cutoff_high_absF(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_data_cutoff_high_rms_absF(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_data_cutoff_low_absF(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_db_accession(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setPdbx_db_accession(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_db_align_beg_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_db_align_end_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_description(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setPdbx_description(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_descriptor(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

setPdbx_diffrn_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_dist_value(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ec(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setPdbx_end_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_end_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_evidence_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setPdbx_formal_charge(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setPdbx_formal_charge(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_fragment(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setPdbx_fragment(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_full_space_group_name_H_M(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry

setPdbx_gene_src_atcc(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_cell(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_cell_line(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_cellular_location(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_fragment(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_gene(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_ncbi_taxonomy_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_organ(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_organelle(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_plasmid(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_plasmid_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_scientific_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_variant(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_atcc(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_cell(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_cell_line(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_cellular_location(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_culture_collection(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_gene(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_ncbi_taxonomy_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_organ(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_organelle(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_scientific_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_strain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_tissue(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_tissue_fraction(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_variant(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_vector(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_vector_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_ideal_coordinates_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_ideal_coordinates_missing_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_initial_date(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_isotropic_thermal_model(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_keywords(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords

setPdbx_leaving_atom_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_leaving_atom_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_leaving_atom_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ls_cross_valid_method(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_ls_sigma_F(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_ls_sigma_I(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_method_to_determine_struct(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_model_Cartn_x_ideal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_model_Cartn_y_ideal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_model_Cartn_z_ideal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_model_coordinates_db_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_model_coordinates_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_model_coordinates_missing_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_model_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

setPdbx_model_type_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

setPdbx_modified(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym

setPdbx_modified_date(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_mutation(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setPdbx_ncbi_taxonomy_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_num_res(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setPdbx_num_residues(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setPdbx_number_of_molecules(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setPdbx_ordinal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor

setPdbx_ordinal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_ordinal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setPdbx_ordinal(Integer) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_organ(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_organelle(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_organism_scientific(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_overall_ESU_R(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_overall_ESU_R_Free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_overall_phase_error(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_overall_SU_R_Blow_DPI(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_overall_SU_R_free_Blow_DPI(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_overall_SU_R_free_Cruickshank_DPI(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_PDB_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_PDB_id_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_pdb_id_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_PDB_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setPdbx_pdb_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_PDB_model_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setPdbx_pdb_strand_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_plasmid_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_plasmid_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_polymer_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_processing_site(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_ptnr1_label_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr1_PDB_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr1_standard_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr2_label_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr2_PDB_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr3_label_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr3_label_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr3_label_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr3_label_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr3_label_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr3_PDB_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_R_Free_selection_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_ref_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_refine_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_release_status(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_replaced_by(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_replaces(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_residue_numbering(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_secretion(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_seq_align_beg_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_seq_align_end_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_seq_db_accession_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_seq_db_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_seq_db_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_seq_one_letter_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setPdbx_seq_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_solvent_ion_probe_radii(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_solvent_shrinkage_radii(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_solvent_vdw_probe_radii(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_src_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_src_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_starting_model(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_stereo_config(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_stereo_config(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setPdbx_stereochem_target_val_spec_case(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_stereochemistry_target_values(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_strand_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_subcomponent_list(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_synonyms(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_TLS_residual_ADP_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_unique_axis(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setPdbx_value_order(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_variant(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbxStructAssemblies(List<PdbxStructAssemblyGen>) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer

setPdbxStructAssemblies(List<PdbxStructAssembly>) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer

setPdbxStructOperLists(List<PdbxStructOperList>) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer

setPdpprovider(PDPProvider) - Method in class org.biojava.nbio.structure.align.util.AtomCache

setPercentFreeReflections(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the percentFreeReflections property.

setPercentRamaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the percentRamaOutliers property.

setPercentRotaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the percentRotaOutliers property.

setPercentRSRZOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the percentRSRZOutliers property.

setPercId(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setPermutationSize(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setPhi(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setPhi(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the phi property.

setPlasmid_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPlasmid_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPmid(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of pmid

setPolymerType(PolymerType) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPos1(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setPos2(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setPreferredResult(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

setPrimitiveMultiplicity(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setPrintCE(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

Display the output string in CE style

setPrintConnections(boolean) - Method in class org.biojava.nbio.structure.io.FileConvert

enable/disable printing of connections connections are sometimes buggy in PDB files so there are some cases where one might turn this off.

setPrintFatCat(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setPrintXML(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setProbability(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setProgram(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

setProgram(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor

setProgram(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier

setProgram_version(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

setProgram_version(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor

setProgram_version(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier

setPrograms(Programs) - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation

Sets the value of the programs property.

setProperties(Map<String, Object>) - Method in interface org.biojava.nbio.structure.Group

Properties of this amino acid.

setProperties(Map<String, Object>) - Method in class org.biojava.nbio.structure.HetatomImpl

Properties of this amino acid.

setProperties(String) - Method in class org.biojava.nbio.structure.validation.Program

Sets the value of the properties property.

setProperty(String, Object) - Method in interface org.biojava.nbio.structure.Group

set a single property .

setProperty(String, Object) - Method in class org.biojava.nbio.structure.HetatomImpl

set a single property .

setPseudoSymmetric(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.Subunits

setPsi(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setPsi(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the psi property.

setPtnr1_auth_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_auth_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_auth_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_label_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_label_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_label_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_label_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_symmetry(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_auth_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_auth_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_auth_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_label_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_label_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_label_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_label_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_symmetry(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPublicationDate(int) - Method in class org.biojava.nbio.structure.JournalArticle

setPublished(boolean) - Method in class org.biojava.nbio.structure.JournalArticle

setPublisher(String) - Method in class org.biojava.nbio.structure.JournalArticle

setPx(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setRama(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the rama property.

setRandomSeed(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setRange(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setRanges(List<String>) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setRecordType(String) - Method in interface org.biojava.nbio.structure.AminoAcid

Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.

setRecordType(String) - Method in class org.biojava.nbio.structure.AminoAcidImpl

Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.

setReduceInitialFragments(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setRef(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of the ref.

setRef_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setRefChainId(String) - Method in class org.biojava.nbio.structure.EntityInfo

Return the ref chain id value.

setRefined(boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setRefineMethod(CESymmParameters.RefineMethod) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setRefineResult(boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

Deprecated.

setRefmacVersion(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the refmacVersion property.

setRefn(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of the refn

setRelativePercentileClashscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the relativePercentileClashscore property.

setRelativePercentileDCCRfree(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

setRelativePercentilePercentRamaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the relativePercentilePercentRamaOutliers property.

setRelativePercentilePercentRotaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the relativePercentilePercentRotaOutliers property.

setRelativePercentilePercentRSRZOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the relativePercentilePercentRSRZOutliers property.

setRelativePercentileRNAsuiteness(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

setRemoveCif(boolean) - Method in class org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider

Remove downloaded .cif.gz after adding to zip archive? Default is true.

setRepeatUnits(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setReplaces(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

setRepresentative(String) - Method in class org.biojava.nbio.structure.cath.CathNode

setResidueNumber(ResidueNumber) - Method in interface org.biojava.nbio.structure.Group

sets the ResidueNumber for this Group

setResidueNumber(String, Integer, Character) - Method in interface org.biojava.nbio.structure.Group

Utility method to temporarily set a chainID for a group, if a parent chain object does not exist yet.

setResidueNumber(ResidueNumber) - Method in class org.biojava.nbio.structure.HetatomImpl

setResidueNumber(String, Integer, Character) - Method in class org.biojava.nbio.structure.HetatomImpl

setResidues(List<SiftsResidue>) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

setResidueType(ResidueType) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setResname(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the resname property.

setResNames(String) - Method in class org.biojava.nbio.structure.EntityInfo

setResnum(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the resnum property.

setResnum1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setResnum2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setResolution(Double) - Method in class org.biojava.nbio.structure.cath.CathDomain

setResolution(float) - Method in class org.biojava.nbio.structure.PDBHeader

setResScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setRestypesNotcheckedForBondAngleGeometry(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the restypesNotcheckedForBondAngleGeometry property.

setResultFile(File) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

setRev_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord

setRevisionRecords(List<DatabasePdbrevRecord>) - Method in class org.biojava.nbio.structure.PDBHeader

setRfree(float) - Method in class org.biojava.nbio.structure.PDBHeader

setRise(double) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setRms(double) - Method in class org.biojava.nbio.structure.align.helper.JointFragments

setRms(double) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

the rms in the structurally equivalent regions

setRms(double) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setRmsd(double) - Method in class org.biojava.nbio.structure.align.model.AFP

setRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment

setRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setRmsdCenters(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setRmsdCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

The cutoff to be used during AFP detection

setRmsdCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setRmsdIntra(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setRmsdThr(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setRmsdThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setRmsdThrJoin(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setRnaSuiteness(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

setRndSeed(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setRot(Matrix) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setRota(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the rota property.

setRotationMatrix(double[][]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

setRow(short) - Method in class org.biojava.nbio.structure.align.helper.IndexPair

setRscc(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the rscc property.

setRsr(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the rsr property.

setRsrz(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the rsrz property.

setRunBackground(boolean) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setSaid(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the said property.

setSaveOutputDir(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setScid(BigInteger) - Method in class org.biojava.nbio.structure.validation.SymmClash

Sets the value of the scid property.

setScopDatabase(String) - Static method in class org.biojava.nbio.structure.scop.ScopFactory

Set the default scop version

setScopDatabase(String, boolean) - Static method in class org.biojava.nbio.structure.scop.ScopFactory

Set the default scop version

setScopDatabase(ScopDatabase) - Static method in class org.biojava.nbio.structure.scop.ScopFactory

Set the default scop version and instance

setScopDescription(List<ScopDescription>) - Method in class org.biojava.nbio.structure.scop.server.ScopDescriptions

setScopDomain(List<ScopDomain>) - Method in class org.biojava.nbio.structure.scop.server.ScopDomains

setScopDownloadURL(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

Deprecated.
Use ScopInstallation.addMirror(java.lang.String) instead

setScopId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setScopNode(List<ScopNode>) - Method in class org.biojava.nbio.structure.scop.server.ScopNodes

setScopVersion(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation

setScopVersion(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation

setScopVersion(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

Sets the scop version used.

setScopVersion(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

setScore(double) - Method in class org.biojava.nbio.structure.align.model.AFP

setScore(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setScore(float) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setScore(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setScore(double) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setScore(double) - Method in class org.biojava.nbio.structure.domain.pdp.Segment

setScores(QuatSymmetryScores) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setScores(QuatSymmetryScores) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setScoreThreshold(Double) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setScoringStrategy(CeParameters.ScoringStrategy) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Set the scoring strategy to use.

setScoringStrategy(CeParameters.ScoringStrategy) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setSearchFile(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setSecondGroupAsa(GroupAsa) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setSecretion(String) - Method in class org.biojava.nbio.structure.EntityInfo

setSeedFragmentLength(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setSeedRmsdCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setSegId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

setSegmentId(Integer) - Method in class org.biojava.nbio.structure.cath.CathSegment

setSegments(List<CathSegment>) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSegments(List<Segment>) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setSegments(List<SiftsSegment>) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

setSelfAlignment(AFPChain) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setSeq(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the seq property.

setSeq_align_beg(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setSeq_align_end(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setSeq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setSeq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setSeq_num(Integer) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setSeqBegin(int) - Method in class org.biojava.nbio.structure.DBRef

Initial sequence number of the PDB sequence segment.

setSeqEnd(int) - Method in class org.biojava.nbio.structure.DBRef

Ending sequence number of the PDB sequence segment.

setSeqIdRange(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setSeqMisMatches(List<SeqMisMatch>) - Method in interface org.biojava.nbio.structure.Chain

Set annotated sequence mismatches for this chain.

setSeqMisMatches(List<SeqMisMatch>) - Method in class org.biojava.nbio.structure.ChainImpl

setSeqNum(Integer) - Method in class org.biojava.nbio.structure.ResidueNumber

setSeqNum(Integer) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setSeqNum(Integer) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setSeqResGroups(List<Group>) - Method in interface org.biojava.nbio.structure.Chain

Sets the list of SeqResGroups for this chain.

setSeqResGroups(List<Group>) - Method in class org.biojava.nbio.structure.ChainImpl

Sets the list of SeqResGroups for this chain.

setSeqResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setSequence(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSequence(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

setSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSequenceHeader(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSequenceHeader(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

setSequenceIdentity(double) - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment

setSequenceIdentityThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

setSequenceIdentityThresholds(double[]) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setSequencePseudoSymmetryThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setSequenceString(String) - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList

setSequentialAlignment(boolean) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Set whether this alignment has the normal topology, ie the residues aligned in each block increase sequentially over the original protein.

setSeqWeight(double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.

setSerNum(int) - Method in class org.biojava.nbio.structure.io.SSBondImpl

get serial number of this SSBOND in PDB file

setServer(String) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setServer(String) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider

setServer(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation

setShortAlign(boolean) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setShortSymbol(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setShow3d(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setShowAFPRanges(boolean) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setShowAFPRanges(boolean) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setShowDBresult(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setShowMenu(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setSimilarity(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setSite_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setSiteID(String) - Method in class org.biojava.nbio.structure.Site

setSites(List<Site>) - Method in interface org.biojava.nbio.structure.Structure

setSites(List<Site>) - Method in class org.biojava.nbio.structure.StructureImpl

setSize(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setSmiles(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setSOLID(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSolvent_model_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setSolvent_model_param_bsol(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setSolvent_model_param_ksol(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setSource(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSpace_group_name_H_M(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry

setSpace_group_name_Hall(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry

setSpaceGroup(SpaceGroup) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Set the SpaceGroup

setSparse(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setSpecies(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setSpeciesId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setSrc_method(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setSSBonds(List<Bond>) - Method in interface org.biojava.nbio.structure.Structure

Set the list of SSBonds for this structure

setSSBonds(List<Bond>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the list of SSBonds for this structure

setSSEThreshold(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setStandard(boolean) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setStart(String) - Method in class org.biojava.nbio.structure.cath.CathFragment

setStart(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

setStart(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

setStart_construct_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setStartPage(String) - Method in class org.biojava.nbio.structure.JournalArticle

setStatus(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

setStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the stdev property.

setStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.BondOutlier

Sets the value of the stdev property.

setStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the stdev property.

setStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the stdev property.

setStepSize(int) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setStop(String) - Method in class org.biojava.nbio.structure.cath.CathFragment

setStop(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

setStrain(String) - Method in class org.biojava.nbio.structure.EntityInfo

setStrain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setStrain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn

setStrictSCOP(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Deprecated.
Removed in 4.2.0

setStruct(Struct) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer

setStruct(Struct) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer

setStruct(Struct) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer

setStructure(Structure) - Method in interface org.biojava.nbio.structure.Chain

Sets the back-reference to its parent Structure.

setStructure(Structure) - Method in class org.biojava.nbio.structure.ChainImpl

Sets the back-reference to its parent Structure.

setStructureId(StructureIdentifier) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setStructureIdentifier(StructureIdentifier) - Method in interface org.biojava.nbio.structure.Structure

Set the identifier corresponding to this structure

setStructureIdentifier(StructureIdentifier) - Method in class org.biojava.nbio.structure.StructureImpl

setStructureIdentifiers(List<StructureIdentifier>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).

setStructureIdentifiers(List<StructureIdentifier>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound>) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.

setSubunitRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setSunID(int) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setSunid(Integer) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setSunid(int) - Method in class org.biojava.nbio.structure.scop.ScopNode

setSuperfamilyId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setSurname(String) - Method in class org.biojava.nbio.structure.Author

setSwissprotId(String) - Method in interface org.biojava.nbio.structure.Chain

Sets the Swissprot id of this chain.

setSwissprotId(String) - Method in class org.biojava.nbio.structure.ChainImpl

set the Swissprot id of this chains .

setSymDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setSymmetry(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setSymmetryDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

setSymmetryDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

setSymmGroup(String) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setSymmLevels(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setSymmLevels(int) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setSymmOrder(int) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setSymmType(CESymmParameters.SymmetryType) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setSymop(String) - Method in class org.biojava.nbio.structure.validation.SymmClash

Sets the value of the symop property.

setSynonyms(List<String>) - Method in class org.biojava.nbio.structure.EntityInfo

setSynthetic(String) - Method in class org.biojava.nbio.structure.EntityInfo

setT(double[]) - Method in class org.biojava.nbio.structure.align.model.AFP

setTempFactor(float) - Method in interface org.biojava.nbio.structure.Atom

Set temp factor .

setTempFactor(float) - Method in class org.biojava.nbio.structure.AtomImpl

setText(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark

setText(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords

setTGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setThreads(int) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setThree_letter_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setTime(int) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setTimeout(int) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider

setTissue(String) - Method in class org.biojava.nbio.structure.EntityInfo

setTissue(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setTissue_fraction(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setTitle(String) - Method in class org.biojava.nbio.structure.EntityInfo

setTitle(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

setTitle(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of title

setTitle(String) - Method in class org.biojava.nbio.structure.PDBHeader

setTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setTmIntra(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setTMScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setTo(Integer) - Method in class org.biojava.nbio.structure.domain.pdp.Segment

setTopologyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setTorsionPenalty(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setTotalArea(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setTotalLenIni(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setTotalLenOpt(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setTotalRmsdIni(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

this is the init-RMSD, not the final RMSD after refinement.

setTotalRmsdOpt(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

The RMSD of the final alignment.

setTraceRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setTraceTmScoreMin(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setTrans(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setTransfAlgebraic(List<String>) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setTransformation(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setTransformation(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setTransformationMatrix(Matrix4d) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Sets the transformation using a 4x4 transformation matrix

setTransformations(List<Matrix4d>) - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Set a new superposition for the structures.

setTransformations(List<Matrix4d>) - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

setTransformId(int) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

setTransforms(Pair<CrystalTransform>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setTransforms(List<BiologicalAssemblyTransformation>) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

setTranslation(double[]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

setTransNCS(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the transNCS property.

setTryAllCPs(Boolean) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

setTurn(char, int) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

Set the turn column corresponding to 3,4 or 5 helix patterns.

setTwi(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setTwinFraction(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the twinFraction property.

setTwinL(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the twinL property.

setTwinL2(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the twinL2 property.

setTwistedGroups(Group[]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner

setType(String) - Method in class org.biojava.nbio.structure.EntityInfo

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setType(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

setType(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setType(SecStrucType) - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

setType(CESymmParameters.SymmetryType) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setType_symbol(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setType_symbol(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setUid(Long) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setUnaryOperators(List<String>) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver

setUniProtAccessionId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setUniProtId(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setUniProtId(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setUniProtPos(Integer) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setUniProtResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setUnitv(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setUpdateRemediatedFiles(boolean) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setUpdateRemediatedFiles(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Deprecated.
Properties which impact downloading and caching behavior have been moved to the StructureIOFile implementations. See LocalPDBDirectory.setFetchBehavior(LocalPDBDirectory.FetchBehavior)

setUrl(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Specify a different mirror for the ECOD server.

setUsed(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setUsedAtomNames(String[]) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setUseInternalChainId(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Set the useInternalChainId parsing mode.

setUseMmCif(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

setUsername(String) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setUserOrder(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setValue(int) - Method in class org.biojava.nbio.structure.align.helper.AligMatEl

setValue(int) - Method in class org.biojava.nbio.structure.align.helper.GapArray

setValue_order(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setVariant(String) - Method in class org.biojava.nbio.structure.EntityInfo

setVector(double[]) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setVerbose(boolean) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setVerbose(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setVersion(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setVersion(String) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Sets the version of the algorithm used to generate the MultipleAlignment objects.

setVersion(String) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setVersion(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setVersion(String) - Method in class org.biojava.nbio.structure.validation.Program

Sets the value of the version property.

setVolume(String) - Method in class org.biojava.nbio.structure.JournalArticle

setWaitForAlignments(boolean) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable

setWeight(Double) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setWilsonBaniso(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the wilsonBaniso property.

setWilsonBestimate(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the wilsonBestimate property.

setWinSize(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setWinSize(int) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setX(double) - Method in interface org.biojava.nbio.structure.Atom

Set the X coordinate.

setX(double) - Method in class org.biojava.nbio.structure.AtomImpl

setXGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setXGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setXMLcreationDate(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the xmLcreationDate property.

setXtalInfo(String, List<Float>) - Method in class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder

setXtriageInputColumns(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the xtriageInputColumns property.

setY(double) - Method in interface org.biojava.nbio.structure.Atom

Set the Y coordinate.

setY(double) - Method in class org.biojava.nbio.structure.AtomImpl

setZ(double) - Method in interface org.biojava.nbio.structure.Atom

Set the Z coordinate.

setZ(double) - Method in class org.biojava.nbio.structure.AtomImpl

setZ(BigDecimal) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the z property.

setZ(BigDecimal) - Method in class org.biojava.nbio.structure.validation.BondOutlier

Sets the value of the z property.

setZ_PDB(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setZscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the zscore property.

setZscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the zscore property.

shift(Structure, Atom) - Static method in class org.biojava.nbio.structure.Calc

shift a structure with a vector.

shift(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Shift a vector.

shift(Group, Atom) - Static method in class org.biojava.nbio.structure.Calc

Shift a Group with a vector.

shift(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc

Shift an array of atoms at once.

ShortSegmentRemover - Class in org.biojava.nbio.structure.domain.pdp

ShortSegmentRemover() - Constructor for class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover

shouldCreateAtomBonds() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should we create bonds between atoms when parsing a file?

shouldCreateAtomCharges() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should we create charges on atoms when parsing a file?

showAFPRanges - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

showAFPRanges - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

showAlignmentGUI() - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

showAlignmentImage(AFPChain, Atom[], Atom[], Object) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

showCompound() - Method in class org.biojava.nbio.structure.EntityInfo

showDBResults(StartupParameters) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

showHeader() - Method in class org.biojava.nbio.structure.EntityInfo

Print some debug statements to System.out

showSource() - Method in class org.biojava.nbio.structure.EntityInfo

showStructure(Structure) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

Shows a structure in Jmol

sideChainScoringType - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

SiftsChainEntry - Class in org.biojava.nbio.structure.io.sifts

An entry in the chain-level SIFTS mapping between UniProt and the PDB.

SiftsChainEntry(String, String, String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

SiftsChainToUniprotMapping - Class in org.biojava.nbio.structure.io.sifts

A mapping between UniProt entries and PDB chains.

SiftsEntity - Class in org.biojava.nbio.structure.io.sifts

SiftsEntity() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsEntity

SiftsEntity(String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsEntity

SiftsMappingProvider - Class in org.biojava.nbio.structure.io.sifts

SiftsMappingProvider() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider

SiftsResidue - Class in org.biojava.nbio.structure.io.sifts

SiftsResidue() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsResidue

SiftsSegment - Class in org.biojava.nbio.structure.io.sifts

SiftsSegment() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsSegment

SiftsSegment(String, String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsSegment

SiftsXMLParser - Class in org.biojava.nbio.structure.io.sifts

SiftsXMLParser() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsXMLParser

SigEva - Class in org.biojava.nbio.structure.align.fatcat.calc

SigEva() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.SigEva

SimpleMMcifConsumer - Class in org.biojava.nbio.structure.io.mmcif

A MMcifConsumer implementation that builds an in-memory representation of the content of a mmcif file as a BioJava Structure object.

SimpleMMcifConsumer() - Constructor for class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer

SimpleMMcifParser - Class in org.biojava.nbio.structure.io.mmcif

A simple mmCif file parser Usage:

SimpleMMcifParser() - Constructor for class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

SingularValueDecomposition - Class in org.biojava.nbio.structure.jama

Singular Value Decomposition.

SingularValueDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.SingularValueDecomposition

Construct the singular value decomposition.

Site - Class in org.biojava.nbio.structure

Holds the data of sites presented in PDB files.

Site() - Constructor for class org.biojava.nbio.structure.Site

Site(String, List<Group>) - Constructor for class org.biojava.nbio.structure.Site

site2 - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues

size() - Method in interface org.biojava.nbio.structure.align.multiple.Block

Returns the number of aligned structures (rows) in the Block.

size() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

size() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Returns the number of aligned structures in the BlockSet.

size() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

size() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Returns the number of aligned structures in the MultipleAlignment.

size() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Returns the number of aligned structures in the MultipleAlignments.

size() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

size() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

size() - Method in class org.biojava.nbio.structure.contact.AtomContactSet

size() - Method in class org.biojava.nbio.structure.contact.GroupContactSet

size() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

size() - Method in interface org.biojava.nbio.structure.Group

Get number of atoms.

size() - Method in class org.biojava.nbio.structure.HetatomImpl

Get number of atoms.

size() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

Returns the number of mapped entries.

size() - Method in class org.biojava.nbio.structure.math.SparseVector

size() - Method in class org.biojava.nbio.structure.math.SymbolTable

How many keys are in the table?

size() - Method in interface org.biojava.nbio.structure.Structure

Return number of Chains in this Structure.

size(int) - Method in interface org.biojava.nbio.structure.Structure

Return number of chains of model.

size() - Method in class org.biojava.nbio.structure.StructureImpl

return number of chains , if NMR return number of chains of first model .

size(int) - Method in class org.biojava.nbio.structure.StructureImpl

return number of chains of model.

size() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

SmithWaterman3Daligner - Class in org.biojava.nbio.structure.align.seq

provides a 3D superimposition based on the sequence alignment

SmithWaterman3Daligner() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner

SmithWaterman3DParameters - Class in org.biojava.nbio.structure.align.seq

SmithWaterman3DParameters() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

SmithWatermanStartupParams() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

SmithWatermanUserArgumentProcessor - Class in org.biojava.nbio.structure.align.seq

SmithWatermanUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor

SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams - Class in org.biojava.nbio.structure.align.seq

solve(Matrix) - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition

Solve A*X = B

solve(Matrix) - Method in class org.biojava.nbio.structure.jama.LUDecomposition

Solve A*X = B

solve(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Solve A*X = B

solve(Matrix) - Method in class org.biojava.nbio.structure.jama.QRDecomposition

Least squares solution of A*X = B

solveTranspose(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Solve X*A = B, which is also A'*X' = B'

sort() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Sorts the interface list and reassigns ids based on new sorting

sortAfps(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator

sortBlocks(List<Block>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Sort blocks so that the specified row is in sequential order.

sortByFoldDecending() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

sortSequenceClustersBySize(List<SequenceAlignmentCluster>) - Static method in class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer

SpaceGroup - Class in org.biojava.nbio.structure.xtal

A crystallographic space group.

SpaceGroup(int, int, int, String, String, BravaisLattice) - Constructor for class org.biojava.nbio.structure.xtal.SpaceGroup

SpaceGroupMapElements - Class in org.biojava.nbio.structure.xtal.io

SpaceGroupMapElements(Integer, SpaceGroup) - Constructor for class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements

SpaceGroupMapRoot - Class in org.biojava.nbio.structure.xtal.io

SpaceGroupMapRoot() - Constructor for class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot

SparseSquareMatrix - Class in org.biojava.nbio.structure.math

A sparse, square matrix, implementing using two arrays of sparse vectors, one representation for the rows and one for the columns.

SparseSquareMatrix(int) - Constructor for class org.biojava.nbio.structure.math.SparseSquareMatrix

initialize an N-by-N matrix of all 0s

SparseVector - Class in org.biojava.nbio.structure.math

A sparse vector, implemented using a symbol table.

SparseVector(int) - Constructor for class org.biojava.nbio.structure.math.SparseVector

Constructor.

SphereSampler - Class in org.biojava.nbio.structure.symmetry.geometry

splitBlocksByTopology(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

SSBondImpl - Class in org.biojava.nbio.structure.io

A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.

SSBondImpl() - Constructor for class org.biojava.nbio.structure.io.SSBondImpl

StandardAminoAcid - Class in org.biojava.nbio.structure

A class that provides a set of standard amino acids.

startingAlignment(String, Atom[], String, Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener

StartupParameters - Class in org.biojava.nbio.structure.align.ce

a simple bean that contains the parameters that can get set at startup

StartupParameters() - Constructor for class org.biojava.nbio.structure.align.ce.StartupParameters

stdev - Variable in class org.biojava.nbio.structure.validation.AngleOutlier

stdev - Variable in class org.biojava.nbio.structure.validation.BondOutlier

stdev - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier

stdev - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier

storeUnAlignedSeqRes(Structure, List<Chain>, boolean) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner

Storing unaligned SEQRES groups in a Structure.

StrCompAlignment - Class in org.biojava.nbio.structure.align.pairwise

StrCompAlignment(int, int) - Constructor for class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

STRING_LIMIT - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

Quoting character ; (multi-line quoting)

StrucAligParameters - Class in org.biojava.nbio.structure.align

A class that contains all the parameters of the structure alignment algorithm.

StrucAligParameters() - Constructor for class org.biojava.nbio.structure.align.StrucAligParameters

Struct - Class in org.biojava.nbio.structure.io.mmcif.model

a bean to contain the data of the _struct lines

Struct() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Struct

StructAsym - Class in org.biojava.nbio.structure.io.mmcif.model

Contains the data for _struct_asym

StructAsym() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructAsym

StructConn - Class in org.biojava.nbio.structure.io.mmcif.model

A bean that stores data from the mmcif category _struct_conn

StructConn() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructConn

StructKeywords - Class in org.biojava.nbio.structure.io.mmcif.model

StructKeywords() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructKeywords

StructNcsOper - Class in org.biojava.nbio.structure.io.mmcif.model

A class containing the _struct_ncs_oper data

StructNcsOper() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper

StructRef - Class in org.biojava.nbio.structure.io.mmcif.model

A class to containt the _struct_ref field data

StructRef() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructRef

StructRefSeq - Class in org.biojava.nbio.structure.io.mmcif.model

StructRefSeq() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

StructRefSeqDif - Class in org.biojava.nbio.structure.io.mmcif.model

A class to store sequence mismatch annotations

StructRefSeqDif() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

StructSite - Class in org.biojava.nbio.structure.io.mmcif.model

Created by Matt on 11/1/2015.

StructSite() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructSite

StructSiteGen - Class in org.biojava.nbio.structure.io.mmcif.model

Created by Matt on 10/31/2015.

StructSiteGen() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

Structure - Interface in org.biojava.nbio.structure

Interface for a structure object.

StructureAlignment - Interface in org.biojava.nbio.structure.align

StructureAlignmentFactory - Class in org.biojava.nbio.structure.align

StructureAlignmentFactory() - Constructor for class org.biojava.nbio.structure.align.StructureAlignmentFactory

StructureAlignmentOptimizer - Class in org.biojava.nbio.structure.align.fatcat.calc

StructureAlignmentOptimizer(int, int, Atom[], int, int, Atom[], int, int[][]) - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer

optimize the structural alignment by update the equivalent residues and then run dynamic programming input: len1 the length of structure 1; c1: the structure information of 1 len2 the length of structure 2; c2: the structure information of 2 iniLen and iniSet is the length and list of initial equivalent residues

StructureException - Exception in org.biojava.nbio.structure

An exception during the parsing of a PDB file.

StructureException(String) - Constructor for exception org.biojava.nbio.structure.StructureException

Constructs a StructureException object.

StructureException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.StructureException

Constructs a StructureException object.

StructureException(Throwable) - Constructor for exception org.biojava.nbio.structure.StructureException

Constructs a StructureException object.

StructureIdentifier - Interface in org.biojava.nbio.structure

An identifier that uniquely identifies a whole Structure or arbitrary substructure.

StructureImpl - Class in org.biojava.nbio.structure

Implementation of a PDB Structure.

StructureImpl() - Constructor for class org.biojava.nbio.structure.StructureImpl

Constructs a StructureImpl object.

StructureImpl(Group) - Constructor for class org.biojava.nbio.structure.StructureImpl

construct a Structure object that only contains a single group

StructureImpl(Chain) - Constructor for class org.biojava.nbio.structure.StructureImpl

construct a Structure object that contains a particular chain

StructureInterface - Class in org.biojava.nbio.structure.contact

An interface between 2 molecules (2 sets of atoms).

StructureInterface(Atom[], Atom[], String, String, AtomContactSet, CrystalTransform, CrystalTransform) - Constructor for class org.biojava.nbio.structure.contact.StructureInterface

Constructs a StructureInterface

StructureInterface() - Constructor for class org.biojava.nbio.structure.contact.StructureInterface

Constructs an empty StructureInterface

StructureInterfaceCluster - Class in org.biojava.nbio.structure.contact

StructureInterfaceCluster() - Constructor for class org.biojava.nbio.structure.contact.StructureInterfaceCluster

StructureInterfaceList - Class in org.biojava.nbio.structure.contact

A list of interfaces between 2 molecules (2 sets of atoms)

StructureInterfaceList() - Constructor for class org.biojava.nbio.structure.contact.StructureInterfaceList

StructureIO - Class in org.biojava.nbio.structure

A class that provides static access methods for easy lookup of protein structure related components

StructureIO() - Constructor for class org.biojava.nbio.structure.StructureIO

StructureIO.StructureFiletype - Enum in org.biojava.nbio.structure

StructureIOFile - Interface in org.biojava.nbio.structure.io

StructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem.

StructureName - Class in org.biojava.nbio.structure.align.client

A utility class that makes working with names of structures, domains and ranges easier.

StructureName(String) - Constructor for class org.biojava.nbio.structure.align.client.StructureName

Create a new StructureName from the given identifier, which may be a domain name, a substructure identifier, etc.

StructureName.Source - Enum in org.biojava.nbio.structure.align.client

StructurePairAligner - Class in org.biojava.nbio.structure.align

Perform a pairwise protein structure superimposition.

StructurePairAligner() - Constructor for class org.biojava.nbio.structure.align.StructurePairAligner

StructureProvider - Interface in org.biojava.nbio.structure.io

A class that can provide a protein structure object from somewhere.

StructureSequenceMatcher - Class in org.biojava.nbio.structure.io

A utility class with methods for matching ProteinSequences with Structures.

StructureSequenceMatcher() - Constructor for class org.biojava.nbio.structure.io.StructureSequenceMatcher

StructureTools - Class in org.biojava.nbio.structure

A class that provides some tool methods.

StructureTools() - Constructor for class org.biojava.nbio.structure.StructureTools

substitutionMatrix - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

SubstructureIdentifier - Class in org.biojava.nbio.structure

This is the canonical way to identify a part of a structure.

SubstructureIdentifier(String) - Constructor for class org.biojava.nbio.structure.SubstructureIdentifier

Create a new identifier from a string.

SubstructureIdentifier(String, List<ResidueRange>) - Constructor for class org.biojava.nbio.structure.SubstructureIdentifier

Create a new identifier based on a set of ranges.

subtract(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

subtract two atoms ( a - b).

SubunitGraph - Class in org.biojava.nbio.structure.symmetry.core

SubunitGraph(List<Point3d[]>) - Constructor for class org.biojava.nbio.structure.symmetry.core.SubunitGraph

Subunits - Class in org.biojava.nbio.structure.symmetry.core

A bean to represent info about the set of subunits being considered for a QuatSymmetryDetector alignment.

Subunits(List<Point3d[]>, List<Integer>, List<Boolean>, List<Double>, List<Double>, List<Integer>, List<String>, List<Integer>) - Constructor for class org.biojava.nbio.structure.symmetry.core.Subunits

All inputs should contain one element per subunit.

suggestDomains(Structure) - Static method in class org.biojava.nbio.structure.domain.LocalProteinDomainParser

Suggest domains for a protein structure

suggestDomains(Atom[]) - Static method in class org.biojava.nbio.structure.domain.LocalProteinDomainParser

Suggest domains for a set of Calpha atoms

SULFUR_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

superimpose(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer

superimpose(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer

Superimpose all structures from a MultipleAlignment.

superimpose(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer

superpose(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

superposeAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

superposeAtOrigin(Point3d[], Point3d[], AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

superposeWithTranslation(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

SuperPosition - Class in org.biojava.nbio.structure.symmetry.geometry

SuperPosition() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

SuperPositionQCP - Class in org.biojava.nbio.structure.symmetry.geometry

SuperPositionQCP() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP

svd() - Method in class org.biojava.nbio.structure.jama.Matrix

Singular Value Decomposition

SVDSuperimposer - Class in org.biojava.nbio.structure

A class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class...

SVDSuperimposer(Atom[], Atom[]) - Constructor for class org.biojava.nbio.structure.SVDSuperimposer

Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.

SymbolTable<Key extends Comparable<Key>,Value> - Class in org.biojava.nbio.structure.math

Sorted symbol table implementation using a java.util.TreeMap.

SymbolTable() - Constructor for class org.biojava.nbio.structure.math.SymbolTable

Create an empty symbol table.

symmClash - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

SymmClash - Class in org.biojava.nbio.structure.validation

Java class for anonymous complex type.

SymmClash() - Constructor for class org.biojava.nbio.structure.validation.SymmClash

Symmetry - Class in org.biojava.nbio.structure.io.mmcif.model

Symmetry() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Symmetry

SymmetryAxes - Class in org.biojava.nbio.structure.symmetry.internal

Data Structure that stores all the symmetry axis that describe the symmetry of a structure.

SymmetryAxes() - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Constructor.

symmetryCoefficient() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia

SymmetryRefiner - Interface in org.biojava.nbio.structure.symmetry.internal

Interface for all symmetry refinement implementations.

SymmetryTools - Class in org.biojava.nbio.structure.symmetry.utils

Utility methods for the internal symmetry identification and manipulation.

SymmOptimizer - Class in org.biojava.nbio.structure.symmetry.internal

Optimizes a symmetry alignment by a Monte Carlo score optimization of the repeat multiple alignment.

SymmOptimizer(CeSymmResult) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmOptimizer

Constructor with a seed MultipleAligment storing a refined symmetry alignment of the repeats.

symop - Variable in class org.biojava.nbio.structure.validation.SymmClash

SymoplibParser - Class in org.biojava.nbio.structure.xtal

A class containing static methods to parse the symop.lib file from the CCP4 package.

SymoplibParser() - Constructor for class org.biojava.nbio.structure.xtal.SymoplibParser

SynchronizedOutFile - Class in org.biojava.nbio.structure.align.util

SynchronizedOutFile(File, boolean) - Constructor for class org.biojava.nbio.structure.align.util.SynchronizedOutFile

Create a thread safe wrapper for writing to this file, the file will be gzip compressed.

SynchronizedOutFile(File) - Constructor for class org.biojava.nbio.structure.align.util.SynchronizedOutFile

create a thread safe wrapper for working with this file

SystematicSolver - Class in org.biojava.nbio.structure.symmetry.core

SystematicSolver(Subunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.SystematicSolver

T

TD - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

TD1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

terminate() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable

Send signal to terminate calculations

terminate() - Method in class org.biojava.nbio.structure.align.FarmJob

TETRAHEDRAL_CARBON_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

TETRAHEDRAL_NITROGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

Tetrahedron - Class in org.biojava.nbio.structure.symmetry.geometry

Tetrahedron() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

times(double) - Method in class org.biojava.nbio.structure.jama.Matrix

Multiply a matrix by a scalar, C = s*A

times(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Linear algebraic matrix multiplication, A * B

times(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix

timesEquals(double) - Method in class org.biojava.nbio.structure.jama.Matrix

Multiply a matrix by a scalar in place, A = s*A

TMP_DIR - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration

TMScore(Point3d[], Point3d[], int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

Returns the TM-Score for two superimposed sets of coordinates Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)

to3DFormat(MultipleAlignment, int, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Outputs a pairwise alignment in I-TASSER's 3D Format for target-template alignment.

toAlignedPairs(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

Prints the alignment in the simplest form: a list of aligned residues.

toAlignedResidues(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts the alignment to its simplest form: a list of groups of aligned residues.

toCanonical() - Method in class org.biojava.nbio.structure.align.client.StructureName

toCanonical() - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier

toCanonical() - Method in class org.biojava.nbio.structure.cath.CathDomain

toCanonical() - Method in class org.biojava.nbio.structure.domain.PDPDomain

toCanonical() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

toCanonical() - Method in class org.biojava.nbio.structure.PassthroughIdentifier

toCanonical() - Method in class org.biojava.nbio.structure.scop.ScopDomain

toCanonical() - Method in interface org.biojava.nbio.structure.StructureIdentifier

Convert to a canonical SubstructureIdentifier.

toCanonical() - Method in class org.biojava.nbio.structure.SubstructureIdentifier

Return itself.

toCanonical() - Method in class org.biojava.nbio.structure.URLIdentifier

toCE(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

toCE(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toConciseAlignmentString(Map<S, T>, Map<T, S>) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Print an alignment map in a concise representation.

toConciseAlignmentString(Map<T, T>) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

toDASStructure(XMLWriter) - Method in class org.biojava.nbio.structure.io.FileConvert

Convert a protein Structure to a DAS Structure XML response .

toDBSearchResult() - Method in class org.biojava.nbio.structure.align.model.AFPChain

toDBSearchResult(AFPChain) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toDoubleArray(Collection<Number>) - Static method in class org.biojava.nbio.structure.align.util.CollectionTools

toFASTA(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts the MultipleAlignment into a multiple sequence alignment String in FASTA format.

toFatcat(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

toFatCat(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toFatCat(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts the MultipleAlignment into a FatCat String format.

toFatCatCore(AFPChain, Atom[], Atom[], boolean, boolean, boolean, boolean) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

Output in FatCatCore format

toFullAlignment(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Method that converts a repeats symmetric alignment into an alignment of whole structures.

toIntArray(Collection<Number>) - Static method in class org.biojava.nbio.structure.align.util.CollectionTools

toLoopMmCifHeaderString(String, String) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

Produces a mmCIF loop header string for the given categoryName and className.

toMMCIF() - Method in interface org.biojava.nbio.structure.Chain

Convert this Chain to a String in mmCIF format

toMMCIF() - Method in class org.biojava.nbio.structure.ChainImpl

toMMCIF() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Return a String representing the 2 molecules of this interface in mmCIF format.

toMMCIF() - Method in class org.biojava.nbio.structure.io.FileConvert

toMMCIF(Chain, String, String, boolean) - Static method in class org.biojava.nbio.structure.io.FileConvert

toMMCIF(Chain, boolean) - Static method in class org.biojava.nbio.structure.io.FileConvert

toMMCIF(String, Object) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

Converts a mmCIF bean (see org.biojava.nbio.structure.io.mmcif.model to a String representing it in mmCIF (single-record) format.

toMMCIF(List<Object>) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

Converts a list of mmCIF beans (see org.biojava.nbio.structure.io.mmcif.model to a String representing them in mmCIF loop format with one record per line.

toMMCIF() - Method in interface org.biojava.nbio.structure.Structure

Create a String that contains this Structure's contents in MMCIF file format.

toMMCIF() - Method in class org.biojava.nbio.structure.StructureImpl

Create a String that contains this Structure's contents in MMCIF file format.

toPDB(Structure, Structure) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

converts the alignment to a PDB file each of the structures will be represented as a model.

toPDB() - Method in class org.biojava.nbio.structure.AtomImpl

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.AtomImpl

toPDB() - Method in interface org.biojava.nbio.structure.Chain

Convert this Chain to a String in PDB format

toPDB() - Method in class org.biojava.nbio.structure.ChainImpl

toPDB() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Return a String representing the 2 molecules of this interface in PDB format.

toPDB() - Method in class org.biojava.nbio.structure.DBRef

Convert the DBRef object to a DBREF record as it is used in PDB files

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.DBRef

Append the PDB representation of this DBRef to the provided StringBuffer

toPDB() - Method in class org.biojava.nbio.structure.io.FileConvert

Convert a structure into a PDB file.

toPDB(Atom) - Static method in class org.biojava.nbio.structure.io.FileConvert

Prints the content of an Atom object as a PDB formatted line.

toPDB(Atom, String) - Static method in class org.biojava.nbio.structure.io.FileConvert

toPDB(Chain) - Static method in class org.biojava.nbio.structure.io.FileConvert

Convert a Chain object to PDB representation

toPDB(Group) - Static method in class org.biojava.nbio.structure.io.FileConvert

Convert a Group object to PDB representation

toPDB(Atom, StringBuffer, String) - Static method in class org.biojava.nbio.structure.io.FileConvert

Print ATOM record in the following syntax

toPDB(Atom, StringBuffer) - Static method in class org.biojava.nbio.structure.io.FileConvert

toPDB() - Method in class org.biojava.nbio.structure.io.SSBondImpl

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.io.SSBondImpl

Append the PDB representation of this SSBOND to the provided StringBuffer

toPDB() - Method in class org.biojava.nbio.structure.PDBHeader

Return a PDB representation of the PDB Header

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.PDBHeader

Appends a PDB representation of the PDB header to the provided StringBuffer

toPDB() - Method in interface org.biojava.nbio.structure.PDBRecord

Returns a PDB file like representation of this record.

toPDB(StringBuffer) - Method in interface org.biojava.nbio.structure.PDBRecord

Appends a PDB file like representation of this record to the provided StringBuffer.

toPDB() - Method in class org.biojava.nbio.structure.ResidueNumber

toPDB() - Method in class org.biojava.nbio.structure.Site

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.Site

toPDB() - Method in interface org.biojava.nbio.structure.Structure

Create a String that contains this Structure's contents in PDB file format.

toPDB() - Method in class org.biojava.nbio.structure.StructureImpl

Create a String that contains this Structure's contents in PDB file format.

toProteinMSA(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid residues.

toRepeatsAlignment(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Method that converts a symmetry alignment into an alignment of the repeats only, as new independent structures.

toRotMat() - Method in class org.biojava.nbio.structure.align.model.AFPChain

toRotMat(AFPChain) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

torsionAngle(Atom, Atom, Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Calculate the torsion angle, i.e.

toScoresList(AFPChain) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toSDF() - Method in interface org.biojava.nbio.structure.Group

Function to get the Group as an MDL molblock

toSDF() - Method in class org.biojava.nbio.structure.HetatomImpl

toSsBond(Bond) - Static method in class org.biojava.nbio.structure.io.SSBondImpl

Converts the given Bond object into a SSBondImpl.

toString() - Method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

toString() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

toString() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

toString() - Method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

toString() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

toString() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

toString() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

toString() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

toString() - Method in class org.biojava.nbio.structure.align.client.CountProgressListener

toString() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

toString() - Method in class org.biojava.nbio.structure.align.client.PdbPair

toString() - Method in class org.biojava.nbio.structure.align.client.StructureName

toString() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

toString() - Method in class org.biojava.nbio.structure.align.fatcat.FatCat

toString() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl

toString() - Method in class org.biojava.nbio.structure.align.helper.IndexPair

toString() - Method in class org.biojava.nbio.structure.align.helper.JointFragments

toString() - Method in class org.biojava.nbio.structure.align.model.AFP

toString() - Method in class org.biojava.nbio.structure.align.model.AFPChain

toString() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

toString() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

toString() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

toString() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Return a summary of the MultipleAlignment, containing the structures, the lengths and the cached scores.

toString() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

toString() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

toString() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

print the idx positions of this alignment

toString() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

toString() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

toString() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

toString() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage

toString() - Method in class org.biojava.nbio.structure.AminoAcidImpl

string representation.

toString() - Method in class org.biojava.nbio.structure.AtomImpl

toString() - Method in class org.biojava.nbio.structure.Author

toString() - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier

toString() - Method in class org.biojava.nbio.structure.BondImpl

toString() - Method in enum org.biojava.nbio.structure.cath.CathCategory

toString() - Method in class org.biojava.nbio.structure.cath.CathDomain

toString() - Method in class org.biojava.nbio.structure.cath.CathNode

toString() - Method in class org.biojava.nbio.structure.cath.CathSegment

toString() - Method in interface org.biojava.nbio.structure.Chain

toString() - Method in class org.biojava.nbio.structure.ChainImpl

String representation.

toString() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

toString() - Method in class org.biojava.nbio.structure.contact.BoundingBox

toString() - Method in class org.biojava.nbio.structure.contact.GroupContact

toString() - Method in class org.biojava.nbio.structure.contact.Pair

toString() - Method in class org.biojava.nbio.structure.contact.StructureInterface

toString() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

toString() - Method in class org.biojava.nbio.structure.DBRef

String representation of a DBRef.

toString() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites

toString() - Method in class org.biojava.nbio.structure.domain.pdp.CutValues

toString() - Method in class org.biojava.nbio.structure.domain.pdp.Domain

toString() - Method in class org.biojava.nbio.structure.domain.pdp.Segment

toString() - Method in class org.biojava.nbio.structure.domain.PDPDomain

toString() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

toString() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

toString() - Method in class org.biojava.nbio.structure.EntityInfo

toString() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique

toString() - Method in enum org.biojava.nbio.structure.GroupType

toString() - Method in class org.biojava.nbio.structure.HetatomImpl

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.AbstractBean

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

toString() - Method in class org.biojava.nbio.structure.io.SSBondImpl

toString() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

toString() - Method in class org.biojava.nbio.structure.jama.Matrix

toString() - Method in class org.biojava.nbio.structure.JournalArticle

toString() - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix

toString() - Method in class org.biojava.nbio.structure.math.SparseVector

toString() - Method in class org.biojava.nbio.structure.NucleotideImpl

toString() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

toString() - Method in class org.biojava.nbio.structure.PDBHeader

String representation

toString() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

toString() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

toString() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair

toString() - Method in class org.biojava.nbio.structure.ResidueNumber

toString() - Method in class org.biojava.nbio.structure.ResidueRange

toString(List<? extends ResidueRange>) - Static method in class org.biojava.nbio.structure.ResidueRange

toString() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet

toString() - Method in enum org.biojava.nbio.structure.scop.ScopCategory

toString() - Method in class org.biojava.nbio.structure.scop.ScopDescription

toString() - Method in class org.biojava.nbio.structure.scop.ScopDomain

toString() - Method in class org.biojava.nbio.structure.scop.ScopNode

toString() - Method in enum org.biojava.nbio.structure.secstruc.BridgeType

toString() - Method in class org.biojava.nbio.structure.secstruc.HBond

toString() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc

toString() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement

toString() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

toString() - Method in enum org.biojava.nbio.structure.secstruc.SecStrucType

toString() - Method in interface org.biojava.nbio.structure.SeqMisMatch

toString() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

toString() - Method in class org.biojava.nbio.structure.Site

toString() - Method in interface org.biojava.nbio.structure.Structure

String representation of object.

toString() - Method in class org.biojava.nbio.structure.StructureImpl

string representation.

toString() - Method in class org.biojava.nbio.structure.SubstructureIdentifier

toString() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer

toString() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

toString() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

toString() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment

toString() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

toString() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

toString() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

toString() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

toString() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

toString() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

toString() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster

toString() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList

toString() - Method in class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus

toString() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

toString() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

toString() - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector

toString() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

toString() - Method in class org.biojava.nbio.structure.xtal.CrystalCell

toString() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

toString() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

toStrings(List<? extends ResidueRange>) - Static method in class org.biojava.nbio.structure.ResidueRange

toTransformMatrices(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts the transformation Matrices of the alignment into a String output.

toUnixPath(String) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils

Converts path to Unix convention and adds a terminating slash if it was omitted

toWebSiteDisplay(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.

toWebSiteDisplay(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.

toXML(MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts all the information of a multiple alignment ensemble into an XML String format.

toXML(PrintWriter) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

convert Configuration to an XML file so it can be serialized

toXML(XMLWriter) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

convert Configuration to an XML file so it can be serialized add to an already existing xml file.

toXML(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

Convert an afpChain to a simple XML representation

toXML(AFPChain, StringWriter, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

Write the XML representation to a StringWriter

toXML(AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

toXML(boolean) - Method in class org.biojava.nbio.structure.align.xml.HasResultXMLConverter

return flag if the server has a result

toXML(int) - Method in class org.biojava.nbio.structure.align.xml.PositionInQueueXMLConverter

toXML(SortedSet<String>) - Static method in class org.biojava.nbio.structure.align.xml.RepresentativeXMLConverter

toXML() - Method in class org.biojava.nbio.structure.domain.AssignmentXMLSerializer

toXML() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer

toXML() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer

toXML() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer

toXML() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

toXML(PrettyXMLWriter) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

toXML() - Method in class org.biojava.nbio.structure.scop.server.ListStringWrapper

toXML() - Method in class org.biojava.nbio.structure.scop.server.ScopDescriptions

toXML() - Method in class org.biojava.nbio.structure.scop.server.ScopDomains

toXML() - Method in class org.biojava.nbio.structure.scop.server.ScopNodes

toXML() - Method in class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper

toXML() - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot

toXML() - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

toXML() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

toXYZString() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

Expresses this transformation in terms of x,y,z fractional coordinates.

trace() - Method in class org.biojava.nbio.structure.jama.Matrix

Matrix trace.

trace1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

trace1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

trace2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

trace2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

traceFragmentMatrix(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

traceFragmentMatrix(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

TransfAlgebraicAdapter - Class in org.biojava.nbio.structure.xtal.io

TransfAlgebraicAdapter() - Constructor for class org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter

transform(Atom[], Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transform an array of atoms at once.

transform(Atom, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms an atom object, given a Matrix4d (i.e.

transform(Group, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms a group object, given a Matrix4d (i.e.

transform(Structure, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms a structure object, given a Matrix4d (i.e.

transform(Chain, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms a chain object, given a Matrix4d (i.e.

transform(Matrix4d, Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

transformAtoms(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Transforms atoms according to the superposition stored in the alignment.

transformPoint(double[]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Applies the transformation to given point.

TransformType - Enum in org.biojava.nbio.structure.xtal

transfToCrystal(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Transform given Matrix4d in orthonormal basis to the crystal basis using the PDB axes convention (NCODE=1)

transfToCrystal(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Transforms the given orthonormal basis coordinates into crystal coordinates.

transfToOriginCell(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Converts the coordinates in pt so that they occur within the (0,0,0) unit cell

transfToOriginCell(Tuple3d[], Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Converts a set of points so that the reference point falls in the unit cell.

transfToOriginCellCrystal(Matrix4d[], Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

transfToOriginCellOrthonormal(Matrix4d[], Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

transfToOrthonormal(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Transform given Matrix4d in crystal basis to the orthonormal basis using the PDB axes convention (NCODE=1)

transfToOrthonormal(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Transforms the given crystal basis coordinates into orthonormal coordinates.

translate(Atom, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates an atom object, given a Vector3d (i.e.

translate(Group, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates a group object, given a Vector3d (i.e.

translate(Chain, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates a chain object, given a Vector3d (i.e.

translate(Structure, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates a Structure object, given a Vector3d (i.e.

translate(Vector3d) - Method in class org.biojava.nbio.structure.contact.BoundingBox

translate(Point3d, Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

translate(Matrix4d, Vector3d) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder

translate(Point3i) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

translVecToString(Matrix4d) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

transNCS - Variable in class org.biojava.nbio.structure.validation.Entry

transpose() - Method in class org.biojava.nbio.structure.jama.Matrix

Matrix transpose.

traverseHierarchy() - Method in class demo.DemoSCOP

Traverse throught the SCOP hierarchy

TreeMapSpaceGroupWrapper - Class in org.biojava.nbio.structure.xtal.io

TreeMapSpaceGroupWrapper() - Constructor for class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

TreeSetStringWrapper - Class in org.biojava.nbio.structure.scop.server

TreeSetStringWrapper() - Constructor for class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper

triggerDocumentEnd() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerDocumentStart() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerGeneric(String, List<String>, List<String>) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewChemCompDescriptor(ChemCompDescriptor) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewEntity(Entity) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewEntityPolySeq(EntityPolySeq) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewEntitySrcGen(EntitySrcGen) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewEntitySrcNat(EntitySrcNat) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewEntitySrcSyn(EntitySrcSyn) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewPdbxEntityNonPoly(PdbxEntityNonPoly) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewPdbxStructOper(PdbxStructOperList) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewRefine(Refine) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewStructAsym(StructAsym) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewStructKeywords(StructKeywords) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewStructNcsOper(StructNcsOper) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

TRIGONAL_CARBON_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

TRIGONAL_NITROGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

trimToSize() - Method in interface org.biojava.nbio.structure.Group

attempts to reduce the memory imprint of this group by trimming all internal Collection objects to the required size.

trimToSize() - Method in class org.biojava.nbio.structure.HetatomImpl

attempts to reduce the memory imprint of this group by trimming all internal Collection objects to the required size.

trimToValidResidues(ResidueRange) - Method in class org.biojava.nbio.structure.AtomPositionMap

Trims a residue range so that both endpoints are contained in this map.

tryAllCPs - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

If true, ignores OptimalCECPParameters.cpPoint and tries all possible cp points.

twinFraction - Variable in class org.biojava.nbio.structure.validation.Entry

twinL - Variable in class org.biojava.nbio.structure.validation.Entry

twinL2 - Variable in class org.biojava.nbio.structure.validation.Entry

twistOptimized(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.AFPTwister

superimposing according to the optimized alignment

twistPDB(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.AFPTwister

calculate the total rmsd of the blocks output a merged pdb file for both proteins protein 1, in chain A protein 2 is twisted according to the twists detected, in chain B

type - Static variable in class org.biojava.nbio.structure.AminoAcidImpl

this is an Amino acid.

type - Static variable in class org.biojava.nbio.structure.HetatomImpl

The GroupType is HETATM

type - Static variable in class org.biojava.nbio.structure.NucleotideImpl

this is a "nucleotide", a special occurance of a Hetatom.

type - Variable in enum org.biojava.nbio.structure.secstruc.BridgeType

type - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo

type - Variable in enum org.biojava.nbio.structure.secstruc.SecStrucType

U

uminus() - Method in class org.biojava.nbio.structure.jama.Matrix

Unary minus

UNDERSCORE - Static variable in class org.biojava.nbio.structure.align.util.AtomCache

uniProtEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

UniqueSequenceList - Class in org.biojava.nbio.structure.symmetry.core

Bean for a single sequence.

UniqueSequenceList(Atom[], String, int, int, String) - Constructor for class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList

UnitCellBoundingBox - Class in org.biojava.nbio.structure.xtal

A class to contain the BoundingBoxes of all molecules in a full unit cell

UnitCellBoundingBox(int, int) - Constructor for class org.biojava.nbio.structure.xtal.UnitCellBoundingBox

unitVector(Atom) - Static method in class org.biojava.nbio.structure.Calc

Returns the unit vector of vector a .

UNKNOWN_ALGORITHM - Static variable in class org.biojava.nbio.structure.align.model.AFPChain

UNKNOWN_GROUP_LABEL - Static variable in class org.biojava.nbio.structure.StructureTools

The character to use for unknown compounds in sequence strings

unmarshal(String[]) - Method in class org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter

updateAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

Force the atom arrays to regenerate based on MultipleAlignmentEnsembleImpl.getStructureIdentifiers().

updateAxis(Integer, Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Updates an axis of symmetry, after the superposition changed.

updateCache() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

updateCache() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

Updates all cached properties

updateChainInfo(String, int) - Method in class org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder

updateCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

updateCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

updateCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

Force recalculation of the core length (ungapped columns) based on the BlockSet core lengths.

updateDistanceMatrix() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

Force recalculation of the distance matrices.

updateLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

updateLength() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

Force recalculation of the length (aligned columns) based on the BlockSet lengths.

updateMatrixWithSequenceConservation(double[][], Atom[], Atom[], CeParameters) - Static method in class org.biojava.nbio.structure.align.ce.CECalculator

Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.

updateMatrixWithSequenceConservation(double[][], Atom[], Atom[], CeParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.

updateScore(FatCatParameters, AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer

to update the chaining score after block delete and merge processed the blockScore value is important for significance evaluation

updateSuperposition(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

After the alignment changes (optAln, optLen, blockNum, at a minimum), many other properties which depend on the superposition will be invalid.

updateSymmetryScores(MultipleAlignment) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Update the scores (TM-score and RMSD) of a symmetry multiple alignment.

updateSymmetryTransformation(SymmetryAxes, MultipleAlignment, Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Calculates the set of symmetry operation Matrices (transformations) of the new alignment, based on the symmetry relations in the SymmetryAxes object.

url - Variable in class org.biojava.nbio.structure.domain.RemoteDomainProvider

URLIdentifier - Class in org.biojava.nbio.structure

Represents a structure loaded from a URL (including a file URL) A few custom query parameters are supported: format=[pdb|cif] Specify the file format (will otherwise be guessed from the extension) pdbId=[String] Specify the PDB ID (also guessed from the filename) chainID=[String] A single chain from the structure residues=[String] Residue ranges, in a form understood by SubstructureIdentifier

URLIdentifier(URL) - Constructor for class org.biojava.nbio.structure.URLIdentifier

URLIdentifier(String) - Constructor for class org.biojava.nbio.structure.URLIdentifier

USERAGENT - Static variable in class org.biojava.nbio.structure.align.util.HTTPConnectionTools

UserArgumentProcessor - Interface in org.biojava.nbio.structure.align.ce

UserConfiguration - Class in org.biojava.nbio.structure.align.util

A container to persist config to the file system

UserConfiguration() - Constructor for class org.biojava.nbio.structure.align.util.UserConfiguration

Default UserConfiguration: split directory autofetch files default download location.

V

value - Variable in class org.biojava.nbio.structure.align.helper.GapArray

value - Variable in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements

valueOf(String) - Static method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.align.client.StructureName.Source

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.BondType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.Element

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.ElementType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.GroupType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.PDBStatus.Status

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.scop.ScopCategory

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.StructureIO.StructureFiletype

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia.SymmetryClass

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.xtal.TransformType

Returns the enum constant of this type with the specified name.

valueOfIgnoreCase(String) - Static method in enum org.biojava.nbio.structure.Element

Returns the Element that corresponds to the specified element symbol.

values() - Static method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.align.client.StructureName.Source

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.BondType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.cath.CathCategory

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.Element

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.ElementType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.GroupType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

values() - Static method in enum org.biojava.nbio.structure.PDBStatus.Status

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.scop.ScopCategory

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.StructureIO.StructureFiletype

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia.SymmetryClass

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.xtal.TransformType

Returns an array containing the constants of this enum type, in the order they are declared.

vectorProduct(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Vector product (cross product).

verbose - Static variable in class org.biojava.nbio.structure.domain.pdp.CutDomain

version - Static variable in class org.biojava.nbio.structure.align.ce.CeCPMain

version history: 1.5 - Added more parameters to the command line, including -maxOptRMSD 1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain 1.3 - Short CPs are now discarded 1.2 - now supports check AlignmentTools.isSequentialAlignment.

version - Static variable in class org.biojava.nbio.structure.align.ce.CeMain

version history: 1.2 - Added more parameters to the command line, including -maxOptRMSD 1.1 - Additional parameters 1.0 - Initial port from C code

version - Static variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain

version history: 1.0 - Initial version

VERSION - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat

version history: 1.1 - Added more parameters to the command line 1.0 - Initial version

version - Static variable in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain

Version history:

version - Static variable in class org.biojava.nbio.structure.symmetry.internal.CeSymm

Version History:

version - Variable in class org.biojava.nbio.structure.validation.Program

VERSION_1_55 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_57 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_59 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_61 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_63 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_65 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_67 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_69 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_71 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_73 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_75 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_75A - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_75B - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_75C - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_1 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_2 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_3 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_4 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_5 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_3_5_0 - Static variable in class org.biojava.nbio.structure.cath.CathFactory

W

WATERNAMES - Static variable in enum org.biojava.nbio.structure.GroupType

The 3-letter codes used in the PDB to identify water molecules

wilsonBaniso - Variable in class org.biojava.nbio.structure.validation.Entry

wilsonBestimate - Variable in class org.biojava.nbio.structure.validation.Entry

winSize - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

winSize - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

write(String) - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile

WwPDBValidationInformation - Class in org.biojava.nbio.structure.validation

Java class for anonymous complex type.

WwPDBValidationInformation() - Constructor for class org.biojava.nbio.structure.validation.WwPDBValidationInformation

X

xmax - Variable in class org.biojava.nbio.structure.contact.BoundingBox

xmin - Variable in class org.biojava.nbio.structure.contact.BoundingBox

xmLcreationDate - Variable in class org.biojava.nbio.structure.validation.Entry

XMLUtil - Class in org.biojava.nbio.structure.scop.server

Utility classes for the XML serialization and de-serialization of SCOP.

XMLUtil() - Constructor for class org.biojava.nbio.structure.scop.server.XMLUtil

xtriageInputColumns - Variable in class org.biojava.nbio.structure.validation.Entry

Y

ymax - Variable in class org.biojava.nbio.structure.contact.BoundingBox

ymin - Variable in class org.biojava.nbio.structure.contact.BoundingBox

Z

z - Variable in class org.biojava.nbio.structure.validation.AngleOutlier

z - Variable in class org.biojava.nbio.structure.validation.BondOutlier

ZipChemCompProvider - Class in org.biojava.nbio.structure.io.mmcif

This chemical component provider retrieves and caches chemical component definition files from a zip archive specified in its construction.

ZipChemCompProvider(String, String) - Constructor for class org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider

ZipChemCompProvider is a Chemical Component provider that stores chemical components in a zip archive.

zmax - Variable in class org.biojava.nbio.structure.contact.BoundingBox

zmin - Variable in class org.biojava.nbio.structure.contact.BoundingBox

zscore - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier

zscore - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier

zStrAlign(int, int, double, int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

zStrAlign(int, int, double, int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

zThr - Static variable in class org.biojava.nbio.structure.align.ce.CECalculator

zThr - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z