- 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(QuatSymmetrySubunits, 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(K, V) - Method in class org.biojava.nbio.structure.domain.SerializableCache
-
This will not cache null values.
- 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, Matrices, Point3d, etc.
- Calc() - Constructor for class org.biojava.nbio.structure.Calc
-
- 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.axis.HelixAxisAligner
-
- calcGlobalSymmetry(Structure, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Calculate GLOBAL symmetry results.
- calcGlobalSymmetry(List<Subunit>, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Calculate GLOBAL symmetry results.
- calcGlobalSymmetry(Stoichiometry, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Calculate GLOBAL symmetry results.
- 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.
- calcLocalSymmetries(Structure, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Returns a List of LOCAL symmetry results.
- calcLocalSymmetries(List<Subunit>, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Returns a List of LOCAL symmetry results.
- calcLocalSymmetries(Stoichiometry, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Returns a List of LOCAL symmetry results.
- CalcPoint - Class in org.biojava.nbio.structure.geometry
-
Utility operations on Point3d.
- 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(QuatSymmetrySubunits, 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
-
- calculateDsspSecondaryStructure(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Generate the secondary structure for a Biojava structure object.
- 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
-
- calculateTp(Matrix4d) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method calculates pairing and step parameters from 4x4 transformation matrices (used internally)
that comes out as a Matrix4d.
- 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
-
- canonical - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
- 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_ALL_RELEASES_DIR - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
-
- CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
-
- CATH_DOWNLOAD_URL - 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
-
- 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
- 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
-
- 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.
- 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.geometry.CalcPoint
-
Center a cloud of points.
- 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.
- centered - Variable in class org.biojava.nbio.structure.geometry.SuperPositionAbstract
-
- centerOfMass(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
-
Returns the center of mass of the set of atoms.
- centroid(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
-
Calculate the centroid of the point cloud.
- 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 of a
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(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_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
-
- chainEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
-
- 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.
- chainName - Variable in class org.biojava.nbio.structure.align.client.StructureName
-
- 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
-
A class to add appropriate charge information to a structure.
- ChargeAdder() - Constructor for class org.biojava.nbio.structure.io.ChargeAdder
-
- checkDoFirstInstall() - Method in class org.biojava.nbio.structure.chem.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
-
- checkInput(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionAbstract
-
Check that the input to the superposition algorithms is valid.
- 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.chem.DownloadChemCompProvider
-
- chem_comp_type - Variable in enum org.biojava.nbio.structure.chem.ResidueType
-
String value of the type
- ChemComp - Class in org.biojava.nbio.structure.chem
-
Properties of a chemical component.
- ChemComp() - Constructor for class org.biojava.nbio.structure.chem.ChemComp
-
- chemComp - Variable in class org.biojava.nbio.structure.HetatomImpl
-
- ChemCompAtom - Class in org.biojava.nbio.structure.chem
-
Properties of an atom of a chemical component.
- ChemCompAtom() - Constructor for class org.biojava.nbio.structure.chem.ChemCompAtom
-
- ChemCompBond - Class in org.biojava.nbio.structure.chem
-
Properties of a bond in a chemical component.
- ChemCompBond() - Constructor for class org.biojava.nbio.structure.chem.ChemCompBond
-
- ChemCompConsumer - Interface in org.biojava.nbio.structure.io.cif
-
- ChemCompConsumerImpl - Class in org.biojava.nbio.structure.io.cif
-
- ChemCompConsumerImpl() - Constructor for class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
-
- ChemCompConverter - Class in org.biojava.nbio.structure.io.cif
-
Convert CifFiles to chem comps.
- ChemCompConverter() - Constructor for class org.biojava.nbio.structure.io.cif.ChemCompConverter
-
- ChemCompDescriptor - Class in org.biojava.nbio.structure.chem
-
Properties of the chemical component descriptor.
- ChemCompDescriptor() - Constructor for class org.biojava.nbio.structure.chem.ChemCompDescriptor
-
- ChemCompDistribution - Class in demo
-
- ChemCompDistribution() - Constructor for class demo.ChemCompDistribution
-
- ChemCompGroupFactory - Class in org.biojava.nbio.structure.chem
-
- ChemCompGroupFactory() - Constructor for class org.biojava.nbio.structure.chem.ChemCompGroupFactory
-
- ChemCompProvider - Interface in org.biojava.nbio.structure.chem
-
Interface that is implemented by all classes that can provide
ChemComp definitions.
- ChemCompTools - Class in org.biojava.nbio.structure.chem
-
- ChemCompTools() - Constructor for class org.biojava.nbio.structure.chem.ChemCompTools
-
- ChemicalComponentDictionary - Class in org.biojava.nbio.structure.chem
-
A representation of the Chemical Component Dictionary.
- ChemicalComponentDictionary() - Constructor for class org.biojava.nbio.structure.chem.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.
- CIF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.BcifFileReader
-
- CIF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.CifFileReader
-
- CIF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.BcifFileReader
-
- CIF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.CifFileReader
-
- CifBean - Interface in org.biojava.nbio.structure.io.cif
-
Flag for BioJava beans that resemble categories defined by the mmCIF schema.
- CifChainSupplierImpl - Class in org.biojava.nbio.structure.io.cif
-
Convert a chain to a CifFile.
- CifChainSupplierImpl() - Constructor for class org.biojava.nbio.structure.io.cif.CifChainSupplierImpl
-
- CifFileConsumer<S> - Interface in org.biojava.nbio.structure.io.cif
-
Defines a rather generic interface which allows to populate some data structure with data parsed from a CIF file.
- CifFileReader - Class in org.biojava.nbio.structure.io
-
Parse text Cif files and provide capabilities to store them locally.
- CifFileReader() - Constructor for class org.biojava.nbio.structure.io.CifFileReader
-
Constructs a new CifFileReader, initializing the extensions member variable.
- CifFileReader(String) - Constructor for class org.biojava.nbio.structure.io.CifFileReader
-
Constructs a new CifFileReader, initializing the extensions member variable.
- CifFileSupplier<S> - Interface in org.biojava.nbio.structure.io.cif
-
Create a CifFile instance for a given container of structure data.
- CifStructureConsumer - Interface in org.biojava.nbio.structure.io.cif
-
Defines the categories to consume during CIF parsing.
- CifStructureConsumerImpl - Class in org.biojava.nbio.structure.io.cif
-
An implementation of a CifFileConsumer for BioJava.
- CifStructureConsumerImpl(FileParsingParameters) - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- CifStructureConverter - Class in org.biojava.nbio.structure.io.cif
-
Convert BioJava structures to CifFiles and vice versa.
- CifStructureConverter() - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureConverter
-
- CifStructureSupplierImpl - Class in org.biojava.nbio.structure.io.cif
-
Convert a structure to a CifFile.
- CifStructureSupplierImpl() - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureSupplierImpl
-
- claFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
-
- cleanup(List<Domain>) - Static method in class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
-
- cleanUpAltLocs(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Cleans up the structure's alternate location (altloc) groups.
- 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
-
- clearCache() - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory
-
Force the in-memory cache to be reset.
- clearExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
clear the supported file extensions
- 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.internal.CESymmParameters
-
- cloneAtomArray(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Provides an equivalent copy of Atoms in a new array.
- cloneAtomsAndBonds(Group) - Method in class org.biojava.nbio.structure.HetatomImpl
-
- 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.geometry.CalcPoint
-
Clone an array of points.
- 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(Structure, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.cluster.SubunitClusterer
-
- cluster(List<Subunit>, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.cluster.SubunitClusterer
-
- 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
-
- 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
-
- 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(Stoichiometry) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
Make a combined Stoichiometry object of this and the other.
- 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
-
- 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(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- 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(BiologicalAssemblyTransformation) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
- compareTo(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber
-
Compare residue numbers by chain, sequence number, and insertion code
- compareTo(Site) - Method in class org.biojava.nbio.structure.Site
-
- compareTo(ChainSignature) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- compareToPositional(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber
-
Compare residue numbers by sequence number and insertion code,
ignoring the chain
- complementBase(char, boolean) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the complement of a base.
- 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.chem.AllChemCompProvider
-
- COMPOSED_OPERATOR_SEPARATOR - Static variable in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
-
The character separating operator ids that are composed.
- 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.
- consume(Category) - Method in interface org.biojava.nbio.structure.io.cif.MetalBondConsumer
-
- consume(Category) - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl
-
- consumeAtomSite(AtomSite) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeAtomSite(AtomSite) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeAtomSites(AtomSites) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeAtomSites(AtomSites) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeAuditAuthor(AuditAuthor) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeAuditAuthor(AuditAuthor) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeCell(Cell) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeCell(Cell) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer
-
Consume a particular Cif category.
- consumeChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
-
- consumeChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeChemCompAtom(ChemCompAtom) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer
-
Consume a particular Cif category.
- consumeChemCompAtom(ChemCompAtom) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
-
- consumeChemCompBond(ChemCompBond) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer
-
Consume a particular Cif category.
- consumeChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
-
- consumeChemCompBond(ChemCompBond) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeDatabasePDBRemark(DatabasePDBRemark) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeDatabasePDBRemark(DatabasePDBRemark) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeDatabasePDBRev(DatabasePDBRev) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeDatabasePDBRev(DatabasePDBRev) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeDatabasePDBRevRecord(DatabasePDBRevRecord) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeDatabasePDBRevRecord(DatabasePDBRevRecord) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeEntity(Entity) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeEntity(Entity) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeEntityPoly(EntityPoly) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeEntityPoly(EntityPoly) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeEntityPolySeq(EntityPolySeq) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeEntityPolySeq(EntityPolySeq) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeEntitySrcGen(EntitySrcGen) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeEntitySrcGen(EntitySrcGen) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeEntitySrcNat(EntitySrcNat) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeEntitySrcNat(EntitySrcNat) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeEntitySrcSyn(PdbxEntitySrcSyn) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeEntitySrcSyn(PdbxEntitySrcSyn) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeExptl(Exptl) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeExptl(Exptl) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxAuditRevisionHistory(PdbxAuditRevisionHistory) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxAuditRevisionHistory(PdbxAuditRevisionHistory) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxChemCompIdentifier(PdbxChemCompIdentifier) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxChemCompIdentifier(PdbxChemCompIdentifier) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxDatabaseStatus(PdbxDatabaseStatus) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxDatabaseStatus(PdbxDatabaseStatus) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxEntityBranchDescriptor(PdbxEntityBranchDescriptor) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxEntityBranchDescriptor(PdbxEntityBranchDescriptor) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxMolecule(PdbxMolecule) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxMolecule(PdbxMolecule) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxMoleculeFeatures(PdbxMoleculeFeatures) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxMoleculeFeatures(PdbxMoleculeFeatures) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxNonpolyScheme(PdbxNonpolyScheme) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxNonpolyScheme(PdbxNonpolyScheme) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxReferenceEntityLink(PdbxReferenceEntityLink) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxReferenceEntityLink(PdbxReferenceEntityLink) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxReferenceEntityList(PdbxReferenceEntityList) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxReferenceEntityList(PdbxReferenceEntityList) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxReferenceEntityPolyLink(PdbxReferenceEntityPolyLink) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxReferenceEntityPolyLink(PdbxReferenceEntityPolyLink) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxStructAssembly(PdbxStructAssembly) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxStructAssembly(PdbxStructAssembly) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxStructAssemblyGen(PdbxStructAssemblyGen) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxStructAssemblyGen(PdbxStructAssemblyGen) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxStructModResidue(PdbxStructModResidue) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxStructModResidue(PdbxStructModResidue) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumePdbxStructOperList(PdbxStructOperList) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxStructOperList(PdbxStructOperList) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeRefine(Refine) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeRefine(Refine) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeStruct(Struct) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStruct(Struct) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeStructAsym(StructAsym) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructAsym(StructAsym) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeStructConf(StructConf) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructConf(StructConf) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeStructConn(StructConn) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructConn(StructConn) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeStructConnType(StructConnType) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructConnType(StructConnType) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeStructKeywords(StructKeywords) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructKeywords(StructKeywords) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeStructNcsOper(StructNcsOper) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructNcsOper(StructNcsOper) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeStructRef(StructRef) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructRef(StructRef) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeStructRefSeq(StructRefSeq) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructRefSeq(StructRefSeq) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeStructRefSeqDif(StructRefSeqDif) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructRefSeqDif(StructRefSeqDif) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeStructSheetRange(StructSheetRange) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructSheetRange(StructSheetRange) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeStructSite(StructSite) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructSite(StructSite) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeStructSiteGen(StructSiteGen) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructSiteGen(StructSiteGen) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- consumeSymmetry(Symmetry) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeSymmetry(Symmetry) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- Contact - Class in org.biojava.nbio.structure.contact
-
A simple class to store contacts in the form of pairs of indices and a distance associated to them.
- Contact(int, int, double) - Constructor for class org.biojava.nbio.structure.contact.Contact
-
- contacts(Point3d[], Point3d[], double) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
-
- contains(ResidueNumber) - Method in class org.biojava.nbio.structure.AugmentedResidueRange
-
- contains(Point3d) - Method in class org.biojava.nbio.structure.contact.BoundingBox
-
Check if a given point falls within this box
- 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
-
- 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(File, File) - Static method in class demo.DemoMmcifToPdbConverter
-
- 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
-
- convertPairsToXML(SortedSet<PdbPair>, String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
-
- convertToDoubleArray(Matrix4d) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Convert a four-d matrix to a double array.
- convertXMLtoPairs(String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
-
- copy() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Make a deep copy of a matrix
- copyLigandsByProximity(Structure, Structure) - Static method in class org.biojava.nbio.structure.SubstructureIdentifier
-
Supplements the reduced structure with ligands from the full structure based on
a distance cutoff.
- copyLigandsByProximity(Structure, Structure, double, int, int) - Static method in class org.biojava.nbio.structure.SubstructureIdentifier
-
Supplements the reduced structure with ligands from the full structure based on
a distance cutoff.
- 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.
- 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.
- createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
- createPurelyNonPolyEntities(List<List<Chain>>, List<List<Chain>>, List<EntityInfo>) - Static method in class org.biojava.nbio.structure.io.EntityFinder
-
Given all chains of all models find entities for the nonpolymers and water chains within them,
assigning entity ids, types and descriptions to them.
- createVirtualCBAtom(AminoAcid) - Static method in class org.biojava.nbio.structure.Calc
-
creates a virtual C-beta atom.
- 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, Map<String, String>, Map<String, Matrix4d>) - Constructor for class org.biojava.nbio.structure.xtal.CrystalBuilder
-
Special constructor for NCS-aware CrystalBuilder.
- 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
-
- GAP_COVERAGE_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.EntityFinder
-
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(Chain) - Method in class org.biojava.nbio.structure.io.cif.CifChainSupplierImpl
-
- get(S) - Method in interface org.biojava.nbio.structure.io.cif.CifFileSupplier
-
Convert some model instance describing structure information to a CifFile instance.
- get(Structure) - Method in class org.biojava.nbio.structure.io.cif.CifStructureSupplierImpl
-
- 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.
- 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.
- 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.cluster.SubunitClustererParameters
-
If the shortest subunit sequence length is higher or equal the
minimumSequenceLengthFraction times the median subunit sequence length,
then the minimumSequenceLength is set to shortest subunit sequence
length, but not shorter than the absoluteMinimumSequenceLength.
- 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.
- 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
-
- 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.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
-
- 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
-
- getAlignedAtomsForSubunits1(int) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
- getAlignedAtomsForSubunits2(int) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
- getAlignedAtomsSubunit(int) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
- getAlignedAtomsSubunits() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
- getAlignedModel(Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
get an artificial List of chains containing the Atoms and groups.
- getAlignedResIndex(Group, Chain) - Method in class org.biojava.nbio.structure.EntityInfo
-
Given a Group g of Chain c (member of this EntityInfo) 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(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
Get an artificial Structure containing a different model for every
input structure, so that the alignment result can be viewed in Jmol.
- 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.
- getAlignedStructure(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Get an artifical Structure containing both chains.
- getAlignedSubunits1() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
Return the aligned subunits of the first Subunit group, in the alignment
order.
- getAlignedSubunits2() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
Return the aligned subunits of the second Subunit group, in the alignment
order.
- 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.align.quaternary.QsAlignResult
-
The alignment that specifies the residue equivalencies of the equivalent
Subunits.
- getAlignmentAtoms(Structure) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
Returns the atoms that are being used for the alignment.
- 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
-
- getAlignResCounts() - Method in interface org.biojava.nbio.structure.align.multiple.Block
-
Returns the number of non null positions (residues) of each structure in
the alignment Block.
- getAlignResCounts() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
-
- getAlignResCounts() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
-
Returns the number of non null positions (residues) of each structure in
the alignment Block Set.
- getAlignResCounts() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
-
- getAlignResCounts() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Returns the number of non null positions (residues) of each structure in
the alignment.
- getAlignResCounts() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- getAlignScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlignScoreUpdate() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- 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 (all models) into an Atom array
- getAllAtomArray(Structure, int) - Static method in class org.biojava.nbio.structure.StructureTools
-
Convert all atoms of the structure (specified 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, including
Hydrogens (if present) and all HETATOMs.
- getAllAtoms() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
-
- getAllChains() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
-
- 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
- getAllGroupsFromSubset(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Expand a set of atoms into all groups from the same structure.
- getAllGroupsFromSubset(Atom[], GroupType) - Static method in class org.biojava.nbio.structure.StructureTools
-
Expand a set of atoms into all groups from the same structure.
- getAllInterfaces() - Method in class org.biojava.nbio.structure.contact.InterfaceFinder
-
Find all inter polymer-chain interfaces in the structure.
- 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(Structure, boolean, int) - 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.
- getAllNonHCoordsArray(Chain, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns and array of all non-Hydrogen atoms coordinates 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
-
- 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.cluster.SubunitCluster
-
A letter that is assigned to this cluster in stoichiometry.
- getAlpha() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getAlpha() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getAlphabet() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
- getAltAligNumber() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
returns the sequential number of this alternative alignment
- getAltAtomId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getAltLoc() - Method in interface org.biojava.nbio.structure.Atom
-
Get alternate Location.
- getAltLoc() - Method in class org.biojava.nbio.structure.AtomImpl
-
- 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 other alternate location groups.
- 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.chem.ChemCompTools
-
- getAminoThreeLetter(Character) - Static method in class org.biojava.nbio.structure.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(Matrix4d) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Quickly compute the rotation angle from a rotation matrix.
- getAngle(Matrix3d) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Quickly compute the rotation angle from a rotation 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.
- getAngleDiff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getAngleThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- 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
- getAssemblyId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getAssignment() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
-
- getAsymmetryParameter(double) - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
- 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.io.cif.AbstractCifFileSupplier.WrappedAtom
-
- 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() - Static method in class org.biojava.nbio.structure.StructureIO
-
- 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.Grid
-
Returns all contacts, i.e.
- 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
-
- getAtomGroups(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl
-
- 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.
- getAtomId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getAtomId() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom
-
- getAtomId1() - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- getAtomId2() - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- 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
-
- 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 class org.biojava.nbio.structure.chem.ChemComp
-
- 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.symmetry.internal.CeSymmResult
-
- 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
-
- getAtomsForGroup(Group) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get a list of atoms for a group.
- 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.
- getAtomType1() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
-
- getAtomType2() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
-
- 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
- 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.
- 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
- 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
- getAxisEnds(Atom[]) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Find a segment of the axis that covers the specified set of atoms.
- 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
-
- 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.
- getBiologicalAssemblies(String, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns all biological assemblies for given PDB id.
- getBiologicalAssemblies(String, boolean) - Static method in class org.biojava.nbio.structure.StructureIO
-
Returns all biological assemblies for the given PDB id.
- getBiologicalAssemblies(String) - Static method in class org.biojava.nbio.structure.StructureIO
-
Returns all biological assemblies for the given PDB id,
using multiModel=
- getBiologicalAssembly(String, int, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the
assembly from the biounit annotations found in
Structure.getPDBHeader()
- getBiologicalAssembly(String, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns the default biological unit (bioassemblyId=1, known in PDB as pdb1.gz).
- getBiologicalAssembly(String, boolean) - Static method in class org.biojava.nbio.structure.StructureIO
-
Returns the first biological assembly that is available for the given PDB id.
- getBiologicalAssembly(String) - Static method in class org.biojava.nbio.structure.StructureIO
-
Returns the first biological assembly that is available for the given PDB id,
using multiModel=
- getBiologicalAssembly(String, int, boolean) - Static method in class org.biojava.nbio.structure.StructureIO
-
Returns the biological assembly for the given PDB id and bioassembly identifier.
- getBiologicalAssembly(String, int) - Static method in class org.biojava.nbio.structure.StructureIO
-
Returns the biological assembly for the given PDB id and bioassembly identifier,
using multiModel=
- 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() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getBioUnitTransformationList(PdbxStructAssembly, int, PdbxStructAssemblyGen, 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.
- 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.
- 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.chem.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
-
- getBuckle(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the buckle in degrees for the given base pair
- 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 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
-
- getCacheFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- 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
-
- getCalphaCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- 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.
- getCECalculator() - Method in class org.biojava.nbio.structure.align.ce.CeMain
-
- getCell() - Method in class org.biojava.nbio.structure.EntityInfo
-
- 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.AlignUtils
-
Get the centroid for the set of atoms starting from position 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
-
- getCenterOfMass() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
- getCenters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- 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
- getCentroid(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
-
Returns the centroid of the set of atoms.
- getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- 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(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a Chain (polymeric, non-polymeric or water) based on
the 'internal' chain id (asymId) for the first model
- getChain(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a Chain (polymeric, non-polymeric or water) based on
the 'internal' chain id (asymId) for the given model index
- getChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Retrieve a Chain (polymeric, non-polymeric or water) based on
the 'internal' chain id (asymId) for the given model index
- getChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
Retrieve a Chain (polymeric, non-polymeric or water) based on
the 'internal' chain id (asymId) for the first model
- 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
- getChainByIndex(int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a chain by its index within the Structure .
- getChainByIndex(int, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a chain by its indices within the Structure and model.
- getChainByIndex(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Retrieve a chain by its index within the Structure .
- getChainByIndex(int, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Retrieve a chain by its indices within the Structure and model.
- getChainByPDB(String) - Method in interface org.biojava.nbio.structure.Structure
-
- getChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
- getChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a chain by its public id (author id) for the given model index.
- getChainByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a chain by its public id (author id) for 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
-
- getChainID() - Method in class org.biojava.nbio.structure.ChainImpl
-
Gets the 'private' asymId of this chain.
- getChainId() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
-
- 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.cif.AbstractCifFileSupplier.WrappedAtom
-
- 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 (asym id) that this transformation should be applied to.
- 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 (asym ids) that are described by this EntityInfo,
only unique chain IDs are contained in the list.
- getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
This method is provisional and should only be used for coloring Subunits.
- getChainIds() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- getChainIdsInEntry(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
-
- getChainIdToIndexMap() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
-
- getChainLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getChainName() - Method in class org.biojava.nbio.structure.DBRef
-
The name of the corresponding chain.
- getChainName() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom
-
- getChainName() - Method in class org.biojava.nbio.structure.ResidueNumber
-
- getChainName() - Method in class org.biojava.nbio.structure.ResidueRange
-
- 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 EntityInfo.
- getChains() - Method in class org.biojava.nbio.structure.Model
-
Get all chains: polymeric, non-polymeric and water
- 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 for 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 for 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.chem.ChemCompAtom
-
- getChemComp(String) - Method in class org.biojava.nbio.structure.chem.AllChemCompProvider
-
Returns a new instance of a chemical component definition.
- getChemComp(String) - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory
-
- getChemComp(String) - Method in interface org.biojava.nbio.structure.chem.ChemCompProvider
-
Returns a new instance of a chemical component definition.
- getChemComp(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
-
- getChemComp(String) - Method in class org.biojava.nbio.structure.chem.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.chem.ReducedChemCompProvider
-
- getChemComp(String) - Method in class org.biojava.nbio.structure.chem.ZipChemCompProvider
-
(non-Javadoc)
- 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
-
- getChemCompProvider() - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory
-
- getChildren() - Method in class org.biojava.nbio.structure.scop.ScopNode
-
- 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
-
- 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
-
- getClustererMethod() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
- getClustererMethod() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Method to cluster subunits.
- getClusterIds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- 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.
- getClusters() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
- getClustersNcs() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Get the interface clusters for this StructureInterfaceList grouped by NCS-equivalence.
- 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 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
-
- getCommonValence() - Method in enum org.biojava.nbio.structure.Element
-
Returns the common valence for this Element.
- getCompId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getCompId() - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- getCompId() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
-
- getComplexSignature() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
-
- getComplexStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
-
- getComponent(int) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
Make a Stoichiometry object that corresponds to a single component.
- getCompositionId() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- getCompositionId(String) - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
-
- getCompoundById(int) - Method in interface org.biojava.nbio.structure.Structure
-
- getCompoundById(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a particular entity by its entity id (mol id in legacy PDB format)
- getComURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
-
- getConn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getConnectedFrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getConnectedTo() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- 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
-
- getContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getContacts() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getContactsToOtherCell(GridCell) - 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 Contacts containing the indices of the pair and the calculated distance.
- getContactsWithinCell() - 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 Contacts containing the indices of the pair and the calculated distance.
- 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.
- getContainer() - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
-
- getContainer() - Method in interface org.biojava.nbio.structure.io.cif.CifFileConsumer
-
Retrieve the created container representing a CIF file.
- getContainer() - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
-
- getContainer() - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl
-
- 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.
- getCoordsAsPoint3d() - Method in interface org.biojava.nbio.structure.Atom
-
Get the coordinates.
- getCoordsAsPoint3d() - 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
- 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
- getCoverages() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Returns the coverage of the alignment for each structure in the
alignment as a fraction between 0.0 and 1.0.
- getCoverages() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- 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
- 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 all current PDB IDs
- 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.xtal.io.TreeMapSpaceGroupWrapper
-
- getDatabase() - Method in class org.biojava.nbio.structure.DBRef
-
The database of the db-ref.
- getDate() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- 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.
- getdCutoff() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
-
The maximum allowed distance between the centroids of two equivalent
Subunits, in A.
- 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
-
Return the deposition date of the structure in the PDB.
- 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.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.chem.ChemCompDescriptor
-
- getDescriptors() - Method in class org.biojava.nbio.structure.chem.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.DatabasePDBRevRecord
-
- getDetails() - Method in class org.biojava.nbio.structure.EntityInfo
-
- 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.AlignUtils
-
Get distances along diagonal k from coordinate array coords.
- getDiagonalDistance() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getDiagonalDistance2() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getDimension() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getDimension() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getDimension() - Method in class org.biojava.nbio.structure.symmetry.axis.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
-
- 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
-
- getDistance() - Method in class org.biojava.nbio.structure.contact.Contact
-
- 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.AlignUtils
-
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.chem.ChemCompTools
-
- getDNATwoLetter(Character) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools
-
- getDoi() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the value of DOI field.
- 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 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
- 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 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
-
- 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
- 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 the operator for 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.
- getElementaryAxesObjects() - 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.
- getElementaryAxis(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- 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.geometry.MomentsOfInertia
-
The effective value of this distance for a certain body is known as its
radius of / gyration with respect to the given axis.
- getEmptyChemComp() - Static method in class org.biojava.nbio.structure.chem.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
-
- getEntities() - Method in class org.biojava.nbio.structure.io.sifts.SiftsXMLParser
-
- getEntityById(int) - Method in interface org.biojava.nbio.structure.Structure
-
Request a particular entity by its entity id (mol id in legacy PDB format)
- getEntityById(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a particular entity by its entity id (mol id in legacy PDB format)
- getEntityId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- getEntityInfo() - Method in interface org.biojava.nbio.structure.Chain
-
Returns the EntityInfo for this chain.
- getEntityInfo() - Method in class org.biojava.nbio.structure.ChainImpl
-
Returns the EntityInfo for this chain.
- getEntityInfos() - Method in interface org.biojava.nbio.structure.Structure
-
Get all the EntityInfo for this Structure.
- getEntityInfos() - Method in class org.biojava.nbio.structure.StructureImpl
-
Get all the EntityInfo for this Structure.
- getEntityType() - Method in interface org.biojava.nbio.structure.Chain
-
Returns the EntityType of this chain.
- getEntityType() - Method in class org.biojava.nbio.structure.ChainImpl
-
- getEntityType() - Method in enum org.biojava.nbio.structure.EntityType
-
Returns the type of the Entity as a String
- getEnumValuesAsString(Class<T>) - Static method in class org.biojava.nbio.structure.align.util.CliTools
-
Constructs a comma-separated list of values for an enum.
- 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
- 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 enum org.biojava.nbio.structure.io.StructureFiletype
-
- getExtensions() - Method in interface org.biojava.nbio.structure.io.StructureIOFile
-
Returns a list of extensions supported by this class
- 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
-
- getFileFormat() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- getFilename(String) - Method in class org.biojava.nbio.structure.io.BcifFileReader
-
- getFilename(String) - Method in class org.biojava.nbio.structure.io.CifFileReader
-
- 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.MMTFFileReader
-
- 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.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
-
- getFiletype() - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns the currently active file type that will be parsed.
- 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.
- getFirstRepeat() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
Get the index of the first repeat used by this axis
- getFirstRepeats(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Get the first repeat index of each axis of a specified level.
- 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
-
- 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.QuatSymmetrySubunits
-
- 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.chem.ChemComp
-
- getFormulaWeight() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- 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.AlignUtils
-
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.AlignUtils
-
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.AlignUtils
-
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
-
- 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.
- 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
-
- getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
Returns a transformation matrix transform polyhedra for Cn structures.
- getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
Returns a transformation matrix transform polyhedra for Cn structures.
- getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
Returns the geometric center of polyhedron.
- getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
Returns the geometric center of polyhedron.
- 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
-
- 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.chem.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
-
- 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.axis.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
-
- 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
-
- 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.
- getI() - Method in class org.biojava.nbio.structure.contact.Contact
-
- getIAtoms() - Method in class org.biojava.nbio.structure.contact.Grid
-
- getIclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- 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 'private' asymId (internal chain IDs in mmCif) for this chain.
- getId() - Method in class org.biojava.nbio.structure.ChainImpl
-
Get the 'private' asymId (internal chain IDs in mmCif) for this chain.
- getId() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- 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.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 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.cluster.Subunit
-
The standard identifier of the Subunit.
- getIdentifier() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- 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
- getIndex() - Method in class org.biojava.nbio.structure.align.helper.GapArray
-
- getIndex() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement
-
Returns the index of the SSE for its type.
- getIndexPair() - Method in class org.biojava.nbio.structure.contact.Contact
-
- getIndicesContacts() - Method in class org.biojava.nbio.structure.contact.Grid
-
Returns all contacts, i.e.
- getInertiaTensor() - Method in class org.biojava.nbio.structure.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.URLConnectionTools
-
Connect to server and return result as an InputStream.
- getInputStream(URL) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools
-
Connect to a URL and return result as an InputStream.
- getInputStream(URL, boolean, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools
-
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.axis.AxisAligner
-
Returns an instance of AxisAligner for differnt type of QuatSymmetryResults (factory method)
- 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.
- getInternal(Structure, List<AbstractCifFileSupplier.WrappedAtom>) - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier
-
- getInternalChainID() - Method in interface org.biojava.nbio.structure.Chain
-
- 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
-
- getJ() - Method in class org.biojava.nbio.structure.contact.Contact
-
- getJAtoms() - Method in class org.biojava.nbio.structure.contact.Grid
-
- 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
- getLargestSubunit() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- 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
-
- 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 class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the total number of base pairs that were found, used after the call to analyze().
- 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.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
-
- 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.
- getLevel() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
- getLfrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getLigands() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getLigandsByProximity(Collection<Group>, Atom[], double) - Static method in class org.biojava.nbio.structure.StructureTools
-
Finds all ligand groups from the target which fall within the cutoff distance
of some atom from the query set.
- 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
-
- getList() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
- 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.chem.DownloadChemCompProvider
-
Returns the file name that contains the definition for this
ChemComp
- getLocalTimeLimit() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getLocalTimeStart() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getLogger() - Static method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- getLowerBound() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getLowerLimit() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
-
- 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
-
Returns the macromolecular size of this biological assembly, i.e.
- 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>, boolean) - 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(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.
- 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
-
- 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.
- getMaxOrientationAngle() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
-
The maximum orientation angle between two equivalent Subunits, in
radians.
- getMaxPenalty() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getMaxPropeller() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This method returns the maximum propeller twist between bases used as criteria for the characterization of two bases as being paired.
- getMaxPropeller() - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
-
This method returns the maximum propeller twist between bases used as criteria for the characterization of two bases as being paired.
- getMaxrefine() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getMaxRmsd() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
-
The maximum allowed RMSD of the alignment, in A.
- getMaxRmsd() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getMaxRmsd() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
-
- getMaxRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getMaxShear() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This method returns the maximum shear between bases used as criteria for the characterization of two bases as being paired.
- getMaxStagger() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This method returns the maximum stagger between bases used as criteria for the characterization of two bases as being paired.
- getMaxStagger() - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
-
This method returns the maximum stagger between bases used as criteria for the characterization of two bases as being paired.
- getMaxStretch() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This method returns the maximum stretch between bases used as criteria for the characterization of two bases as being paired.
- 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.
- getMembers() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
-
- getMetalBondDefinitions() - Static method in class org.biojava.nbio.structure.io.cif.MetalBondConverter
-
- getMethod() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
-
- getMethod() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- 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
-
- 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.cluster.SubunitClustererParameters
-
Get the minimum number of residues of a subunits to be considered in the
clusters.
- getMinimumSequenceLengthFraction() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
If the shortest subunit sequence length is higher or equal the
minimumSequenceLengthFraction times the median subunit sequence length,
then the minimumSequenceLength is set to shortest subunit sequence
length, but not shorter than the absoluteMinimumSequenceLength.
- 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
-
- getMinLen() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getMinLen() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
-
- 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
-
- 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
-
- getModDate() - Method in class org.biojava.nbio.structure.PDBHeader
-
Return the latest modification date of the structure.
- getModel() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom
-
- 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 .
- getModelCartnX() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getModelCartnY() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getModelCartnZ() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
This method is provisional and should only be used for coloring Subunits.
- 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.QuatSymmetrySubunits
-
- getMonNstdFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getMonNstdParentCompId() - Method in class org.biojava.nbio.structure.chem.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.cluster.SubunitCluster
-
The multiple alignment is calculated from the equivalent residues in the
SubunitCluster.
- 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 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 interface org.biojava.nbio.structure.Chain
-
Get the 'public' authId (chain ID in PDB file)
- getName() - Method in class org.biojava.nbio.structure.ChainImpl
-
Get the 'public' authId (chain ID in PDB file)
- getName() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getName() - Method in class org.biojava.nbio.structure.cluster.Subunit
-
The Name of a Subunit is a free-text field, user defined.
- getName() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique
-
- 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 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
-
- getNaturalPos() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getNavMap() - Method in class org.biojava.nbio.structure.AtomPositionMap
-
- getNclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- getNcsAsArray(Matrix4d[]) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get a list of length N*16 of a list of Matrix4d*N.
- getNcsAsMatrix4d(double[][]) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get a list of N 4*4 matrices from a single list of doubles of length 16*N.
- getNcsOperators() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Get the NCS operators.
- getNcuts() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
-
- 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.PermutationGenerator
-
- 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
-
- getNonPolyChain(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a non-polymeric Chain based on the 'internal' chain
id (asymId) for the first model
- getNonPolyChain(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a non-polymeric Chain based on the 'internal' chain
id (asymId) for the given model index
- getNonPolyChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getNonPolyChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getNonPolyChains() - Method in class org.biojava.nbio.structure.Model
-
- getNonPolyChains() - Method in interface org.biojava.nbio.structure.Structure
-
Return all non-polymeric chains for the first model
- getNonPolyChains(int) - Method in interface org.biojava.nbio.structure.Structure
-
Return all non-polymeric chains for the given model index.
- getNonPolyChains() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getNonPolyChains(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getNonPolyChainsByPDB(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve all non-polymeric Chains corresponding to the given 'public' chain
name (authId) for the first model.
- getNonPolyChainsByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve all non-polymeric Chains corresponding to the 'public' chain
name (authId) and the given model index.
- getNonPolyChainsByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getNonPolyChainsByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getNormAlignScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getNotObserved() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- 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
- 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
- getNucleicChains(boolean) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method reports all the nucleic acid chains and has an option to remove duplicates if you
are considering an analysis of only unique DNA or RNA helices in the Structure.
- getNumAtomContacts() - Method in class org.biojava.nbio.structure.contact.GroupContact
-
- getNumBonds() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
-
- getNumBondsInGroup(List<Atom>) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Find the number of bonds in a group
- getNumericalBondOrder() - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
Converts this ChemCompBond's value_order attribute into an int using the
conversion:
- getNumGroups(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Count the total number of groups in the structure
- 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.PermutationGenerator
-
- getNumLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getNumOperators() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets the number of symmetry operators corresponding to this SpaceGroup (counting
the identity operator)
- getNumRepeats() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
Return the symmetry order determined by the order detector if the
symmetry is significant.
- getNumRepeats() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Get the number of repeats.
- 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
- 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.BcifFileReader
-
- getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.CifFileReader
-
- 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.MMTFFileReader
-
- getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.PDBFileReader
-
- getOccupancy() - Method in interface org.biojava.nbio.structure.Atom
-
Get occupancy.
- getOccupancy() - Method in class org.biojava.nbio.structure.AtomImpl
-
- getOmega() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getOneLetterCode() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getOneLetterCode(ChemComp) - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory
-
- getOneLetterCode(ChemComp, ChemicalComponentDictionary) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools
-
- getOpening(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the opening in degrees for the given base pair
- getOperator() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
Get the transformation operator for this axis as an homogeneous matrix
- 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.axis.AxisAligner
-
- getOrbits() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getOrbits() - Method in class org.biojava.nbio.structure.symmetry.axis.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
-
- getOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
Get the order of this axis (closed symm) or the number of repeats
(open symm)
- 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
-
- 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
-
- getOrientationMatrix() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
The orientation Matrix is a 3x3 Matrix with a column for each principal
axis.
- 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.QuatSymmetrySubunits
-
- 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.
- getOutFile() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- getOutFile() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- 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
-
- getPairingNames() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the names of the pairs in terms of A, G, T/U, and C for each base pair group in the
list.
- getPairingParameters() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method reports all the pair parameters, in the order of:
buckle, propeller, opening (in degrees), shear, stagger, stretch (in Å).
- getPairs() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
-
- getPairSequence() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the primary strand's sequence where parameters were found.
- 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.StructurePairAligner
-
get the parameters.
- getParams() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
- getParent() - Method in interface org.biojava.nbio.structure.Chain
-
- getParent() - Method in class org.biojava.nbio.structure.ChainImpl
-
- getParent(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
-
Get the parent of a component.
- getParent() - Method in class org.biojava.nbio.structure.DBRef
-
Get the structure object that this DBRef relates to.
- 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 entities 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() - Static method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
-
Get this provider's cache path
- 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
-
- 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.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.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.scop.ScopDomain
-
- getPdbId() - Method in interface org.biojava.nbio.structure.Structure
-
- 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
-
- 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
-
- 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
-
- getPdbxAlign() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxAmbiguousFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxAromaticFlag() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxAromaticFlag() - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- getPdbxComponentAtomId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxComponentCompId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxComponentId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxFormalCharge() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxIdealCoordinatesDetails() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxIdealCoordinatesMissingFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxInitialDate() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxLeavingAtomFlag() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxModelCartnXIdeal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxModelCartnYIdeal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxModelCartnZIdeal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxModelCoordinatesDbCode() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxModelCoordinatesDetails() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxModelCoordinatesMissingFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxModifiedDate() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxOrdinal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxOrdinal() - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- getPdbxPolymerType() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxProcessingSite() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxRefId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxReleaseStatus() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxReplacedBy() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxReplaces() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxResidueNumbering() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxStereoConfig() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- getPdbxStereoConfig() - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- getPdbxSubcomponentList() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxSynonyms() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPdbxType() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- 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
-
- getPivot() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
-
Return pivot permutation vector
- 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
-
- getPolyChain(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a polymeric Chain based on the 'internal' chain
id (asymId) for the first model
- getPolyChain(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a polymeric Chain based on the 'internal' chain
id (asymId) for the given model index
- getPolyChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPolyChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPolyChainByPDB(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a polymeric Chain based on the 'public' chain
name (authId) for the first model
- getPolyChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a polymeric Chain based on the 'public' chain
name (authId) for the given model index.
- getPolyChainByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPolyChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPolyChains() - Method in class org.biojava.nbio.structure.Model
-
- getPolyChains() - Method in interface org.biojava.nbio.structure.Structure
-
Return all polymeric chains for the first model
- getPolyChains(int) - Method in interface org.biojava.nbio.structure.Structure
-
Return all polymeric chains for the given model index.
- getPolyChains() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPolyChains(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- 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
- getPolymerType() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getPolymerType(ResidueType) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools
-
- getPolymerType() - Method in enum org.biojava.nbio.structure.chem.ResidueType
-
Gets the associated PolymerType, which are less specific
- 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
- getPredominantGroupType() - Method in interface org.biojava.nbio.structure.Chain
-
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
, 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
- getPredominantGroupType() - Method in class org.biojava.nbio.structure.ChainImpl
-
- getPredominantGroupType(Chain) - Static method in class org.biojava.nbio.structure.StructureTools
-
- getPrimitiveMultiplicity() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getPrincipalAxes() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
The principal axes of intertia
- getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getPrincipalAxisIndex() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- getPrincipalMomentsOfInertia() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
- getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.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.chem.ChemCompDescriptor
-
- getProgramVersion() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
-
- 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
- getPropeller(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the propeller ("propeller-twist") in degrees for the given base pair
- getProperties() - Method in interface org.biojava.nbio.structure.Group
-
Return properties.
- getProperties() - Method in class org.biojava.nbio.structure.HetatomImpl
-
- getProperty(String) - Method in interface org.biojava.nbio.structure.Group
-
Get a single property .
- getProperty(String) - Method in class org.biojava.nbio.structure.HetatomImpl
-
- getProteinSequence() - Method in class org.biojava.nbio.structure.cluster.Subunit
-
Get the protein sequence of the Subunit.
- 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.
- getProteinSequenceString() - Method in class org.biojava.nbio.structure.cluster.Subunit
-
Get the protein sequence of the Subunit as String.
- 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
-
- 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
-
- 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.axis.AxisAligner
-
Returns the radius for drawing polyhedra
- getRadius() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getRadius() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
Returns the radius for drawing the minor rotation axis in the xy-plane
- getRadiusOfGyration() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
- getRandomSeed() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
-
- 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
-
- 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
- getReason() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
Return a String describing the reasons for the CE-Symm final decision in
this particular result.
- 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.
- 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
-
- getRef() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the value of REF field.
- getRefChainId() - Method in class org.biojava.nbio.structure.EntityInfo
-
Return the ref chain id value.
- getReferenceFrames() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
- getRefinedScoreThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getRefineMethod() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- 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.
- getRelation() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
The quaternary structure relation
QsRelation between the two
groups of Subunits.
- 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.
- getRelDate() - Method in class org.biojava.nbio.structure.PDBHeader
-
Return the release date of the structure in the PDB.
- getRepeatRelation(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Get the indices of participating repeats in Cauchy two-line form.
- getRepeatRelation(SymmetryAxes.Axis) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getRepeatRelation(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getRepeatsCyclicForm(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Get the indices of participating repeats in cyclic form.
- getRepeatsCyclicForm(SymmetryAxes.Axis) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getRepeatsCyclicForm(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getRepeatsCyclicForm(SymmetryAxes.Axis, List<?>) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getRepeatsCyclicForm(List<List<Integer>>, List<?>) - Static method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- 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
repeat in order to superimpose onto repeat 0.
- getRepeatTransform(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Return the transformation that needs to be applied to
repeat x in order to superimpose onto repeat y.
- 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.chem.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.chem.ChemicalComponentDictionary
-
- getReplacer(ChemComp) - Method in class org.biojava.nbio.structure.chem.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.chem.ChemicalComponentDictionary
-
- 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 EntityInfo.
- 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
-
- getRepresentativeAtoms() - Method in class org.biojava.nbio.structure.cluster.Subunit
-
Get all the representative Atoms of the Subunit.
- getRepresentativeAtoms(Structure) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
-
Returns the representative Atom Array of the first model, if the
structure is NMR, or the Array for each model, if it is a biological
assembly with multiple models.
- 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.
- 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
-
- 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.chem.ChemComp
-
- getResidueTypeFromString(String) - Static method in enum org.biojava.nbio.structure.chem.ResidueType
-
Get ResidueType by chem_comp_type
- getResidueTypes() - Method in enum org.biojava.nbio.structure.GroupType
-
Get a set of ResidueTypes loosely equivalent to this GroupType.
- 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
-
- 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
-
- getReverse() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getRevisionRecords() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getRevNum() - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord
-
- getRfree() - Method in class org.biojava.nbio.structure.PDBHeader
-
- 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(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the rise for the given base pair, relative to the one before it.
- 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
-
- 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.align.quaternary.QsAlignResult
-
The RMSD between the equivalent residues of the equivalent Subunits after
superposition of the Subunit groups.
- getRmsd(Point3d[], Point3d[]) - Method in interface org.biojava.nbio.structure.geometry.SuperPosition
-
Calculate the RMSD between two arrays of equivalent points that are not
superposed.
- getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP
-
- getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQuat
-
- getRmsd(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
-
- getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionSVD
-
- getRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getRmsdAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
-
- 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.cluster.SubunitClustererParameters
-
Structure similarity threshold (measured with RMSD) to consider for the
structural subunit clustering.
- 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
- getRndSeed() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getRoll(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the roll for the given base pair, relative to the one before it.
- 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
-
- 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(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
- getRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
Get the transformation operator as a rotation axis.
- getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getRotationJAMA(Matrix4d) - Static method in class org.biojava.nbio.structure.geometry.Matrices
-
Convert a transformation matrix into a JAMA rotation matrix.
- 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.geometry.Matrices
-
Convert a transformation matrix into a rotation matrix.
- getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- 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.axis.AxisAligner
-
- getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.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
-
- getRwork() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getS() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
-
Return the diagonal matrix of singular values
- getSaveOutputDir() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getScaleableMatrixPanel(Matrix) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
-
- getSCOP() - Static method in class org.biojava.nbio.structure.scop.ScopFactory
-
Get the current default instance for the default version
- getSCOP(String) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
-
Gets an instance of the specified scop version.
- 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
-
- 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
-
- getScopId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- 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
-
- 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)
- 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.
- getSecStructType(Group) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get the secondary structure as defined by DSSP.
- getSecStructTypeFromDsspIndex(int) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Set the DSSP type based on a numerical index.
- 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
-
- 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
-
Gets 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
-
- 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
-
- 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
-
- getSeqResOneLetterSeq() - Method in class org.biojava.nbio.structure.ChainImpl
-
Get the one letter sequence so that Sequence is guaranteed to
be the same length as seqResGroups.
- 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.
- 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.
- getSequenceCoverageThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
The minimum coverage of the sequence alignment between two subunits to be
clustered together.
- 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
-
- getSequenceIdentityThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Sequence identity threshold to consider for the subunits clustering.
- getSequences() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
-
Gets the protein sequences read from the Fasta file.
- 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
-
- 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://).
- getShear(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the shear in Å for the given base pair
- 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
- getShift(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
Return the shift for the given base pair, relative to the one before it.
- 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
-
Return the SIFTS mappings by getting the info from individual SIFTS xml files at URL
- getSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Returns the similarity score for the alignment.
- getSingularValues() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
-
Return the one-dimensional array of singular values
- 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
-
- getSlide(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the slide for the given base pair, relative to the one before it.
- getSOILD() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getSource() - Method in class org.biojava.nbio.structure.align.client.StructureName
-
- getSource() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- 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.
- getSpaceGroupAsString(SpaceGroup) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get the string representation of a space group.
- getSparse() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- 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.BcifFileReader
-
- getSplitDirPath() - Method in class org.biojava.nbio.structure.io.CifFileReader
-
- 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.MMTFFileReader
-
- 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
-
- 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
-
- getStagger(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the stagger in Å for the given base pair
- 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
-
- 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(String) - Static method in class org.biojava.nbio.structure.PDBStatus
-
Get the status of a PDB id.
- getStatus(String[]) - Static method in class org.biojava.nbio.structure.PDBStatus
-
Get the status of a collection of PDB ids (in a single API query).
- getStepParameters() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method reports all the base-pair step parameters, in the order of:
tilt, roll, twist (in degrees), shift, slide, rise (in Å).
- getStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- 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
-
- getStrategy() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
- getStretch(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the stretch in Å for the given base pair
- getString(String) - Method in class org.biojava.nbio.structure.align.util.ResourceManager
-
- 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
-
- 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() - Method in class org.biojava.nbio.structure.cluster.Subunit
-
The parent Structure from which the Subunit atoms were obtained.
- getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.BcifFileReader
-
- getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.CifFileReader
-
- 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.mmtf.MmtfStructureReader
-
Gets the structure.
- getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.MMTFFileReader
-
- 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
-
- getStructure(String, PDBFileParser, AtomCache) - Static method in class org.biojava.nbio.structure.StructureTools
-
Flexibly get a structure from an input String.
- getStructure() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- 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
- getStructureCoverageThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
The minimum coverage of the structure alignment between two subunits to be
clustered together.
- getStructureFiletype() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- getStructureForCathDomain(StructureName) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- 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
-
- getStructureForDomain(ScopDomain, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForDomain(ScopDomain, ScopDatabase, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForDomain(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForDomain(String, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- 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.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
-
- getStructureInfo(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get summary information for the structure.
- getStructures() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
-
Gets the protein structures mapped from the Fasta file.
- 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.
- getSubunitClusters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
Returns the List of SubunitCluster used to calculate symmetry.
- getSubunitCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
Return the number of Subunits involved in the symmetry.
- getSubunitCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getSubunitMap() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
Map of Subunit equivalencies from the first to the second group.
- getSubunitRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getSubunits() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
Subunits contained in the SubunitCluster.
- getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
Returns the List of Subunits used to calculate symmetry.
- getSubunits1() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
Original Subunits of the first group.
- getSubunits2() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
Original Subunits of the second group.
- 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
-
- getSuperpositionAlgorithm() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Method to superpose subunits (i.e., structural aligner).
- 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
-
- getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- 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.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
-
- 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
-
- getSymmType() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getSymmType() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
- getSynonyms() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getSynthetic() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getT() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- 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
-
- 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.
- getThreeLetterCode() - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- getTilt(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the tilt for the given base pair, relative to the one before it.
- getTissue() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getTitle() - Method in class org.biojava.nbio.structure.EntityInfo
-
- 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(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.util.AFPChainScorer
-
- getTMScore(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.Calc
-
Calculate the TM-Score for the superposition.
- getTMScore(Atom[], Atom[], int, int, boolean) - Static method in class org.biojava.nbio.structure.Calc
-
Calculate the TM-Score for the superposition.
- getTMThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Structure similarity threshold (measured with TMScore) to consider for the
structural subunit clustering.
- 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.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.QuatSymmetrySubunits
-
- 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
-
- getTransform() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
The transformation 4D matrix that needs to be applied to the second group
of Subunits to superimpose them onto the first group of Subunits, given
the equivalent residues in the SubunitCluster and the Subunit
equivalencies.
- getTransformation(Matrix, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Convert JAMA rotation and translation to a Vecmath transformation matrix.
- getTransformation(Matrix, Matrix) - Static method in class org.biojava.nbio.structure.geometry.Matrices
-
Convert JAMA rotation and translation to a Vecmath transformation matrix.
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- 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.
- 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.
- getTransformId() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
- getTransformMap(BioAssemblyInfo, Map<String, Integer>) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Convert a bioassembly information into a map of transform, chainindices it relates to.
- 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
-
- 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.align.util.RotationAxis
-
- getTranslationVector(Matrix4d) - Static method in class org.biojava.nbio.structure.Calc
-
Extract the translational vector as an Atom of a transformation matrix.
- getTranslationVector(Matrix4d) - Static method in class org.biojava.nbio.structure.geometry.Matrices
-
Extract the translational vector of a transformation matrix.
- 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.
- 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 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
-
- getTwist(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the twist for the given base pair, relative to the one before it.
- 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.chem.ChemComp
-
- getType() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
-
- getType() - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord
-
- getType() - Method in class org.biojava.nbio.structure.EntityInfo
-
Get the type of entity this EntityInfo describes.
- getType() - Method in interface org.biojava.nbio.structure.Group
-
- getType() - Method in class org.biojava.nbio.structure.HetatomImpl
-
- 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.secstruc.BetaBridge
-
- getType() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement
-
- getType() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
-
- getTypeSymbol() - Method in class org.biojava.nbio.structure.chem.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.
- getUnitCellAsArray(PDBCrystallographicInfo) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get the length six array of the unit cell information.
- getUnitv() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getUnitVectors() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getUnrefinedScoreThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getUpdateFrequency() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
The expected ECOD update frequency determines whether the version
"latest" should be re-downloaded
- getUpperBound() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getUpperLimit() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
-
- 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
-
- 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.utils.SymmetryTools
-
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
-
- getValueOrder() - Method in class org.biojava.nbio.structure.chem.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.
- 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.
- 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.
- getWaterChain(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a water Chain based on the 'internal' chain id (asymId)
for the first model
- getWaterChain(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a water chain based on the 'internal' chain id (asymId)
for the given model index
- getWaterChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getWaterChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getWaterChainByPDB(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a water Chain based on the 'public' chain name (authId)
for the first model
- getWaterChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a water Chain based on the 'public' chain name (authId)
for the given model index
- getWaterChainByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getWaterChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getWaterChains() - Method in class org.biojava.nbio.structure.Model
-
- getWaterChains() - Method in interface org.biojava.nbio.structure.Structure
-
Return all water chains for the first model
- getWaterChains(int) - Method in interface org.biojava.nbio.structure.Structure
-
Return all water chains for the given model index
- getWaterChains() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getWaterChains(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getWeightedRmsd(Point3d[], Point3d[], double[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP
-
- 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
- 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
-
- 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.
- 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 a spatial hashing algorithm.
- Grid(double) - Constructor for class org.biojava.nbio.structure.contact.Grid
-
Creates a Grid, the cutoff is in the same units as the coordinates
(Angstroms if they are atom coordinates) and can
be specified to a precision of 0.01.
- GridCell - Class in org.biojava.nbio.structure.contact
-
A grid cell to be used in contact calculation via spatial hashing algorithm.
- GridCell(Grid) - 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 over all models
- GroupIterator(Structure, int) - Constructor for class org.biojava.nbio.structure.GroupIterator
-
Constructs a GroupIterator object over a specific model
- 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.geometry.CalcPoint
-
- 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
-
- s_min - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
-
- 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)
- 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
-
- 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
-
- 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
-
- 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
-
- 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.
- 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
-
- serverBaseUrl - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
-
- set(int, int, double) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Set a single element.
- setA(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- setAbsoluteMinimumSequenceLength(int) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
If the shortest subunit sequence length is higher or equal the
minimumSequenceLengthFraction times the median subunit sequence length,
then the minimumSequenceLength is set to shortest subunit sequence
length, but not shorter than the absoluteMinimumSequenceLength.
- 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).
- 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.
- 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_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(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
The alignment that specifies the residue equivalencies of the equivalent
Subunits.
- 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.
- setAllAtoms(List<Atom>) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
-
- setAllChains(List<Chain>) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
-
- 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(String) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
A letter that is assigned to this cluster in stoichiometry.
- setAlpha(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- setAlphabet(String) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
Change alphabet used for string representation of a stoichiometry.
- setAltAligNumber(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- setAltAtomId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setAltLoc(Character) - Method in interface org.biojava.nbio.structure.Atom
-
Set alternate Location.
- setAltLoc(Character) - Method in class org.biojava.nbio.structure.AtomImpl
-
- 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 .
- setAngleDiff(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setAngleThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- 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
-
- setAsaU(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
- setAssemblyId(Long) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- setAtcc(String) - Method in class org.biojava.nbio.structure.EntityInfo
-
- 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) - 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.
- setAtomId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setAtomId1(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- setAtomId2(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- setAtomInfo(String, int, char, float, float, float, float, float, String, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
-
- setAtoms(List<ChemCompAtom>) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- 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(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
- setAtomType1(String) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
-
- setAtomType2(String) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
-
- 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
-
- setAverageScore(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
-
- 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
-
- 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
-
- setBioAssemblyTrans(int, int[], double[], String) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
-
- 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
-
- 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.chem.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
-
- 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.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
-
- 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
-
- setCell(String) - Method in class org.biojava.nbio.structure.EntityInfo
-
- 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.geometry.SuperPositionAbstract
-
- 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.
- 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
-
- setChainID(String) - Method in class org.biojava.nbio.structure.ChainImpl
-
Sets the 'private' asymId 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.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 identifier (asym id) that this transformation should be applied to.
- setChainID1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl
-
- setChainID2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl
-
- setChainIdToIndexMap(Map<String, Integer>) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
-
- setChainInfo(String, String, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
-
- setChainLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setChainName(String) - Method in class org.biojava.nbio.structure.DBRef
-
The name of the corresponding chain.
- setChainName(String) - Method in class org.biojava.nbio.structure.ResidueNumber
-
- setChainOrigNamesMap(Map<String, String>) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Sets a map with mapping from NCS chain names to original chain names.
- 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 EntityInfo
- setChains(List<Chain>) - Method in class org.biojava.nbio.structure.Model
-
- 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(int) - Method in class org.biojava.nbio.structure.chem.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.chem.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
-
- 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
- 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
-
- setClustererMethod(SubunitClustererMethod) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Method to cluster subunits.
- setClusters(List<SubunitCluster>) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
- setCol(short) - Method in class org.biojava.nbio.structure.align.helper.IndexPair
-
- setComment(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- setCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
-
- setCompositionId(String) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- setConn(Double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- 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.
- 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
- setCustomStringGenerator(Function<List<SubunitCluster>, String>) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
Let a user-defined function handle the entire string representation of a stoichiometry.
- setCut_sites(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
-
- setCutoff(double) - Method in class org.biojava.nbio.structure.contact.InterfaceFinder
-
Set the contact distance cutoff.
- setData(TreeMap<Integer, SpaceGroup>) - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
-
- setDatabase(String) - Method in class org.biojava.nbio.structure.DBRef
-
Specifies the database value.
- setDate(Date) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- 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
- setdCutoff(double) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
-
The maximum allowed distance between the centroids of two equivalent
Subunits, in A.
- setDefault() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
- setDefaultSuperPosition(SuperPositionAbstract) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
-
- setDensityCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setDepDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader
-
The deposition date of the structure in the PDB
- 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.chem.ChemCompDescriptor
-
- setDescriptors(List<ChemCompDescriptor>) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setDetails(String) - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord
-
- setDetails(String) - Method in class org.biojava.nbio.structure.EntityInfo
-
- 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
-
- 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
-
- 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.chem.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
-
- 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
-
- setEntityId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- setEntityInfo(EntityInfo) - Method in interface org.biojava.nbio.structure.Chain
-
Sets the Entity information
- setEntityInfo(EntityInfo) - Method in class org.biojava.nbio.structure.ChainImpl
-
Sets the Entity information
- setEntityInfo(int[], String, String, String) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
-
- setEntityInfos(List<EntityInfo>) - Method in interface org.biojava.nbio.structure.Structure
-
Set the EntityInfo
- setEntityInfos(List<EntityInfo>) - Method in class org.biojava.nbio.structure.StructureImpl
-
Set the EntityInfo
- 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.
- 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.
- 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.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
-
- setFiletype(StructureFiletype) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Set the file type that will be parsed.
- setFirstGroupAsa(GroupAsa) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- setFirstRepeat(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
- setFlexible(boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- 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
-
- 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.chem.ChemComp
-
- setFormulaWeight(double) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- 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
-
- 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.
- setGroupBond(int, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
-
- setGroupInfo(String, int, char, String, int, int, char, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
-
- setGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- setGroups(List<Group>) - Method in class org.biojava.nbio.structure.Site
-
- setHeaderInfo(float, float, float, String, String, String, String[]) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
-
- 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
-
- setHetAtomInFile(boolean) - Method in interface org.biojava.nbio.structure.Group
-
Sets the field isHetAtomInFile which is intented only for
helping in infering if a polymeric group is in a ligand chain
or in a polymeric chain.
- setHetAtomInFile(boolean) - Method in class org.biojava.nbio.structure.HetatomImpl
-
- 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
-
- setIclose(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- 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(String) - Method in interface org.biojava.nbio.structure.Chain
-
Set the 'private' asymId (internal chain IDs in mmCif) for this chain.
- setId(String) - Method in class org.biojava.nbio.structure.ChainImpl
-
Set the 'private' asymId (internal chain IDs in mmCif) for this chain.
- setId(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- 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(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(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
-
- 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.
- 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
-
- setInterGroupBond(int, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
-
- setInternalChainID(String) - Method in interface org.biojava.nbio.structure.Chain
-
- setInternalChainID(String) - Method in class org.biojava.nbio.structure.ChainImpl
-
- setInternalSymmetry(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
The internal symmetry option divides each
Subunit of each
SubunitCluster into its internally symmetric repeats.
- 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
-
- 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
-
- 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
-
- setLevel(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
- setLigands(Set<String>) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- setLikeSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setLocalTimeLimit(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setLowerLimit(float) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
-
- setM(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFP
-
- setMacromolecularSize(int) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
-
- setMacromolecularSizes() - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser
-
Set the macromolecularSize fields of the parsed bioassemblies.
- 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(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.
- 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
-
- 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.
- setMaxOrientationAngle(double) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
-
The maximum orientation angle between two equivalent Subunits, in
radians.
- setMaxPenalty(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setMaxPropeller(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This method sets the maximum propeller allowed for a base pair, prior to analyze() call
- setMaxPropeller(double) - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
-
This method sets the maximum propeller allowed for a base pair, prior to analyze() call
- setMaxrefine(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setMaxRmsd(double) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
-
The maximum allowed RMSD of the alignment, in A.
- setMaxRmsd(Double) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- setMaxRmsd(double) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
-
- setMaxRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- setMaxShear(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This method sets the maximum shear allowed for a base pair, prior to analyze() call
- setMaxStagger(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This method sets the maximum stagger allowed for a base pair, prior to analyze() call
- setMaxStagger(double) - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
-
This method sets the maximum stagger allowed for a base pair, prior to analyze() call
- setMaxStretch(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This method sets the maximum stretch allowed for a base pair, prior to analyze() call.
- 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...
- setMembers(List<StructureInterface>) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
-
- setMethod(String) - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
-
- 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
-
- 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.cluster.SubunitClustererParameters
-
Set the minimum number of residues of a subunits to be considered in the
clusters.
- setMinimumSequenceLengthFraction(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
If the shortest subunit sequence length is higher or equal the
minimumSequenceLengthFraction times the median subunit sequence length,
then the minimumSequenceLength is set to shortest subunit sequence
length, but not shorter than the absoluteMinimumSequenceLength.
- setMinLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setMinLen(Integer) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- setMinLen(int) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
-
- setMinRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- 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
-
- setModDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader
-
The latest modification date of the structure.
- 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.
- setModelCartnX(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setModelCartnY(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setModelCartnZ(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setModelInfo(int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
-
- 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.
- setMonNstdFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setMonNstdParentCompId(String) - Method in class org.biojava.nbio.structure.chem.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 interface org.biojava.nbio.structure.Chain
-
Set the 'public' authId (chain ID in PDB file)
- setName(String) - Method in class org.biojava.nbio.structure.ChainImpl
-
Set the 'public' authId (chain ID in PDB file)
- setName(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setName(String) - Method in class org.biojava.nbio.structure.cluster.Subunit
-
The Name of a Subunit is a free-text field, user defined.
- 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 .
- 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
-
- setNaturalPos(Integer) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- 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
-
- setNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathNode
-
- setNonStandardCoordFrameConvention(boolean) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Set the non-standard coordinate frame convention field
- setNonStandardSg(boolean) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Set the non-standard space group field
- setNormAlignScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setNotObserved(Boolean) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- 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
-
- setNumBonds(int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
-
- 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
- setNumRepeats(int) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
- setNumRes(String) - Method in class org.biojava.nbio.structure.EntityInfo
-
- 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.
- setOccupancy(float) - Method in interface org.biojava.nbio.structure.Atom
-
Set occupancy.
- setOccupancy(float) - Method in class org.biojava.nbio.structure.AtomImpl
-
- setOmega(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- setOneLetterCode(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
On-the-fly Jmol bioassembly generation.
- setOperator(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
- 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
-
- setOptimizeAlignment(boolean) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Whether the CE algorithm should extend the best found trace with dynamic programming,
while keeping RMSD at about the same level.
- setOptimizeAlignment(boolean) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
Whether the alignment algorithm should try its best to optimize the alignment,
or we are happy with a quick and dirty result.
- setOptimizeAlignment(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Whether the alignment algorithm should try its best to optimize the alignment,
or we are happy with a quick and dirty result.
- 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
-
- 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
-
- 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
- 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(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
-
- 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
-
- 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 .
- 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.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
-
- 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.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
-
- 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
-
- 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
-
- setPdbxAlign(int) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxAmbiguousFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxAromaticFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxAromaticFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- setPdbxComponentAtomId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxComponentCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxComponentId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxFormalCharge(int) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxIdealCoordinatesDetails(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxIdealCoordinatesMissingFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxInitialDate(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxLeavingAtomFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxModelCartnXIdeal(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxModelCartnYIdeal(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxModelCartnZIdeal(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxModelCoordinatesDbCode(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxModelCoordinatesDetails(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxModelCoordinatesMissingFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxModifiedDate(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxOrdinal(int) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxOrdinal(int) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- setPdbxPolymerType(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxProcessingSite(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxRefId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxReleaseStatus(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxReplacedBy(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxReplaces(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxResidueNumbering(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxStereoConfig(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
-
- setPdbxStereoConfig(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- setPdbxSubcomponentList(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxSynonyms(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setPdbxType(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- 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
-
- setPmid(String) - Method in class org.biojava.nbio.structure.JournalArticle
-
Set the value of pmid
- setPolymerType(PolymerType) - Method in class org.biojava.nbio.structure.chem.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
-
- 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.chem.ChemCompDescriptor
-
- setProgramVersion(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
-
- 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.
- 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
-
- setPsi(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- 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
-
- 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.
- 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
-
- setRefinedScoreThreshold(Double) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- 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.
- setRefn(String) - Method in class org.biojava.nbio.structure.JournalArticle
-
Set the value of the refn
- setRelation(QsRelation) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
The quaternary structure relation
QsRelation between the two
groups of Subunits.
- setRelDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader
-
The release date of the structure in the PDB.
- setRemoveCif(boolean) - Method in class org.biojava.nbio.structure.chem.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
-
- 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.chem.ChemComp
-
- setResNames(String) - Method in class org.biojava.nbio.structure.EntityInfo
-
- 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
-
- setRevisionRecords(List<DatabasePDBRevRecord>) - Method in class org.biojava.nbio.structure.PDBHeader
-
- setRevNum(String) - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord
-
- 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.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.cluster.SubunitClustererParameters
-
Structure similarity threshold (measured with RMSD) to consider for the
structural subunit clustering.
- setRmsdThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setRmsdThrJoin(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- setRndSeed(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- setRot(Matrix) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setRotationMatrix(double[][]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
- setRow(short) - Method in class org.biojava.nbio.structure.align.helper.IndexPair
-
- setRwork(float) - Method in class org.biojava.nbio.structure.PDBHeader
-
- setSaveOutputDir(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setScopDatabase(String) - 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
- setScopId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- 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
-
- 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
-
- setSecStructType(Group, int) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get the secondary structure as defined by DSSP.
- 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
-
- 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
-
Sets 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
-
- setSequenceCoverageThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
The minimum coverage of the sequence alignment between two subunits to be
clustered together.
- 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
-
- setSequenceIdentityThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Sequence identity threshold to consider for the sequence subunit
clustering.
- 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
- 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
-
- 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
-
- setSOLID(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setSource(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- 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
-
- setSpeciesId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- 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
-
- 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
-
- setStartPage(String) - Method in class org.biojava.nbio.structure.JournalArticle
-
- 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
-
- setStrategy(Stoichiometry.StringOverflowStrategy) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
Change string representation of a stoichiometry in case number of clusters exceeds number of letters in the alphabet.
- 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.
- setStructure(Structure) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- setStructureCoverageThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
The minimum coverage of the structure alignment between two subunits to be
clustered together.
- 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.
- setSubunitMap(Map<Integer, Integer>) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
Map of Subunit equivalencies from the first to the second group.
- 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
-
- setSuperpositionAlgorithm(String) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Method to cluster subunits.
- 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
-
- 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
-
- setSymmType(CESymmParameters.SymmetryType) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- 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
-
- setTGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- setThreeLetterCode(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setTissue(String) - Method in class org.biojava.nbio.structure.EntityInfo
-
- setTitle(String) - Method in class org.biojava.nbio.structure.EntityInfo
-
- 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
-
- setTMThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Structure similarity threshold (measured with TMScore) to consider for the
structural subunit clustering.
- 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
-
- 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
-
- setTwistedGroups(Group[]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
-
- setType(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
-
- setType(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
-
- setType(String) - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord
-
- setType(EntityType) - Method in class org.biojava.nbio.structure.EntityInfo
-
Set the type of entity this EntityInfo describes.
- setType(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- setType(SecStrucType) - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
-
- setTypeSymbol(String) - Method in class org.biojava.nbio.structure.chem.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
-
- setUnrefinedScoreThreshold(Double) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- setUpBioJava() - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Set up the configuration parameters for BioJava.
- setUpBioJava(String) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Set up the configuration parameters for BioJava.
- setUpdateFrequency(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
- setUpperLimit(float) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
-
- 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
-
- setUseEntityIdForSeqIdentityDetermination(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Whether to use the entity id of subunits to infer that sequences are identical.
- setUseGlobalMetrics(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Use metrics calculated relative to the whole sequence or structure,
rather than the aligned part only
- setUseRMSD(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Use RMSD for evaluating structure similarity
- setUserOrder(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- setUseSequenceCoverage(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Use sequence coverage for evaluating sequence similarity
- setUseStructureCoverage(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Use structure coverage for evaluating sequence similarity
- setUseTMScore(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Use TMScore for evaluating structure similarity
- setValue(int) - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
-
- setValue(int) - Method in class org.biojava.nbio.structure.align.helper.GapArray
-
- setValueOrder(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
-
- setVariant(String) - Method in class org.biojava.nbio.structure.EntityInfo
-
- 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
-
- setVolume(String) - Method in class org.biojava.nbio.structure.JournalArticle
-
- 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
-
- setXtalInfo(String, float[], double[][]) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
-
- 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
-
- 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.
- shiftCA2(AFPChain, Atom[], Matrix, Atom, Group[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
only shift CA positions.
- 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
-
- 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
-
- 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.chem.ChemicalComponentDictionary
-
Returns the number of ChemComps in this dictionary
- size() - Method in class org.biojava.nbio.structure.cluster.Subunit
-
The size of a Subunit is the number of residues it contains.
- size() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
- 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 class org.biojava.nbio.structure.Model
-
Returns the total number of chains in this model: polymeric, non-polymeric and water
- size() - Method in interface org.biojava.nbio.structure.Structure
-
Return number of polymer Chains in this Structure for first model.
- 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
-
- 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 of two structures based on their 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
-
- 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
-
Sample possible orientations.
- 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
-
- STANDARD_BASES - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
- 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
-
- STATUS_ENDPOINT - Static variable in class org.biojava.nbio.structure.PDBStatus
-
- STATUS_LIST_ENDPOINT - Static variable in class org.biojava.nbio.structure.PDBStatus
-
- stepParameters - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
- Stoichiometry - Class in org.biojava.nbio.structure.symmetry.core
-
A utility object that describes Stoichiometry (composition of a protein assembly),
determined via clustering procedure
SubunitClusterer,
and implements human-readable representation using various strategies.
- Stoichiometry(List<SubunitCluster>) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
Constructor for Stoichiometry.
- Stoichiometry(List<SubunitCluster>, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
Constructor for Stoichiometry.
- Stoichiometry(List<SubunitCluster>, Stoichiometry.StringOverflowStrategy) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
Constructor for Stoichiometry.
- Stoichiometry(List<SubunitCluster>, Stoichiometry.StringOverflowStrategy, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
Constructor for Stoichiometry.
- Stoichiometry(List<SubunitCluster>, Function<List<SubunitCluster>, String>) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
Constructor for Stoichiometry.
- Stoichiometry.StringOverflowStrategy - Enum in org.biojava.nbio.structure.symmetry.core
-
What to do when the number of
SubunitCluster exceeds the length of the alphabet.
- 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
-
- 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
-
- structure - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
- 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.
- StructureFiletype - Enum in org.biojava.nbio.structure.io
-
An enum of supported file formats.
- 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
-
- 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).
- Subunit - Class in org.biojava.nbio.structure.cluster
-
A Subunit consists of a set of residues from a Structure, which may
correspond to an entire Chain, a Domain, or any subset or combination of
residues from them.
- Subunit(Atom[], String, StructureIdentifier, Structure) - Constructor for class org.biojava.nbio.structure.cluster.Subunit
-
A Subunit is solely defined by the coordinates of the representative
Atoms of its residues.
- SubunitCluster - Class in org.biojava.nbio.structure.cluster
-
- SubunitCluster(Subunit) - Constructor for class org.biojava.nbio.structure.cluster.SubunitCluster
-
A constructor from a single Subunit.
- SubunitCluster(SubunitCluster, List<Integer>) - Constructor for class org.biojava.nbio.structure.cluster.SubunitCluster
-
A copy constructor with the possibility of removing subunits.
- SubunitClusterer - Class in org.biojava.nbio.structure.cluster
-
- SubunitClustererMethod - Enum in org.biojava.nbio.structure.cluster
-
The SubunitClustererMethod ennummerates all methods that can be used to
cluster
Subunit in the
SubunitCluster.
- SubunitClustererParameters - Class in org.biojava.nbio.structure.cluster
-
The SubunitClustererParameters specifies the options used for the clustering
of the subunits in structures using the
SubunitClusterer.
- SubunitClustererParameters(boolean) - Constructor for class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
"Local" metrics are scoring
SubunitClustererMethod.SEQUENCE: sequence identity of a local alignment
(normalised by the number of aligned residues)
sequence coverage of the alignment
(normalised by the length of the longer sequence)
SubunitClustererMethod.STRUCTURE: RMSD of the aligned substructures
and structure coverage of the alignment
(normalised by the length of the larger structure)
Two thresholds for each method are required.
- SubunitClustererParameters() - Constructor for class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Initialize with "local" metrics by default.
- SubunitExtractor - Class in org.biojava.nbio.structure.cluster
-
The SubunitExtractor extracts the information of each protein
Chain
in a
Structure and converts them into a List of
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(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer
-
- superpose(Point3d[], Point3d[]) - Method in interface org.biojava.nbio.structure.geometry.SuperPosition
-
Obtain the superposition matrix that minimizes the RMSD between two
arrays of equivalent points.
- superpose(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP
-
- superpose(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQuat
-
- superpose(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
-
- superpose(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionSVD
-
- superposeAfterRmsd() - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP
-
The QCP method can be used as a two-step calculation: first compute the
RMSD (fast) and then compute the superposition.
- superposeAndTransform(Point3d[], Point3d[]) - Method in interface org.biojava.nbio.structure.geometry.SuperPosition
-
Transform an array of points so that the coordinates of its points
minimize the RMSD to the other array of equivalent points, and return the
transformation matrix applied.
- superposeAndTransform(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionAbstract
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- superposeAndTransform(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
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- superposeAndTransformAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
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- superposeAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
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- SuperPosition - Interface in org.biojava.nbio.structure.geometry
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The SuperPosition interface defines and documents the required methods for
any superpostion algorithm implementation, so that the input and expected
output are uniform.
- SuperPositionAbstract - Class in org.biojava.nbio.structure.geometry
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The SuperPositionAbstract contains common code shared by all SuperPosition
algorithm implementations.
- SuperPositionAbstract(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionAbstract
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- SuperPositionQCP - Class in org.biojava.nbio.structure.geometry
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Implementation of the Quaternion-Based Characteristic Polynomial algorithm
for RMSD and Superposition calculations.
- SuperPositionQCP(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionQCP
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Default constructor for the quaternion based superposition algorithm.
- SuperPositionQCP(boolean, double, double) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionQCP
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Constructor with option to set the precision values.
- SuperPositionQuat - Class in org.biojava.nbio.structure.geometry
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The SuperPositionQuat implements a quaternion based algorithm to superpose
arrays of Points in 3D.
- SuperPositionQuat(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionQuat
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Constructor for the quaternion based superposition algorithm.
- SuperPositions - Class in org.biojava.nbio.structure.geometry
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SuperPositions is a Class that provides static helper methods and an easy
access to the whole family of
SuperPosition algorithms.
- SuperPositionSVD - Class in org.biojava.nbio.structure.geometry
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A class that calculates the superposition between two sets of points using an
SVD Matrix Decomposition.
- SuperPositionSVD(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionSVD
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Constructor for the SVD superposition algorithm.
- svd() - Method in class org.biojava.nbio.structure.jama.Matrix
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Singular Value Decomposition
- SYM_CHAIN_ID_SEPARATOR - Static variable in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
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The character separating the original chain identifier from the operator id.
- SymbolTable<Key extends Comparable<Key>,Value> - Class in org.biojava.nbio.structure.math
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Sorted symbol table implementation using a java.util.TreeMap.
- SymbolTable() - Constructor for class org.biojava.nbio.structure.math.SymbolTable
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Create an empty symbol table.
- SymmetryAxes - Class in org.biojava.nbio.structure.symmetry.internal
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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
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Constructor.
- SymmetryAxes.Axis - Class in org.biojava.nbio.structure.symmetry.internal
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Represents an axis of symmetry
- symmetryCoefficient() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
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- SymmetryPerceptionMethod - Enum in org.biojava.nbio.structure.symmetry.core
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- SymmetryRefiner - Interface in org.biojava.nbio.structure.symmetry.internal
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Interface for all symmetry refinement implementations.
- SymmetryTools - Class in org.biojava.nbio.structure.symmetry.utils
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Utility methods for symmetry (quaternary and internal) detection and result
manipulation.
- SymmOptimizer - Class in org.biojava.nbio.structure.symmetry.internal
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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
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Constructor with a seed MultipleAligment storing a refined symmetry
alignment of the repeats.
- SymoplibParser - Class in org.biojava.nbio.structure.xtal
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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
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- SynchronizedOutFile - Class in org.biojava.nbio.structure.align.util
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- SynchronizedOutFile(File, boolean) - Constructor for class org.biojava.nbio.structure.align.util.SynchronizedOutFile
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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
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create a thread safe wrapper for working with this file
- SystematicSolver - Class in org.biojava.nbio.structure.symmetry.core
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- SystematicSolver(QuatSymmetrySubunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.SystematicSolver
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