Constant Field Values

Contents

• org.biojava.*

org.biojava.*

org.biojava.nbio.structure.AminoAcid

Modifier and Type	Constant Field	Value
public static final String	ATOMRECORD	"ATOM"
public static final String	SEQRESRECORD	"SEQRES"

org.biojava.nbio.structure.AtomImpl

Modifier and Type	Constant Field	Value
public static final int	BONDS_INITIAL_CAPACITY	3

org.biojava.nbio.structure.Group

Modifier and Type	Constant Field	Value
public static final String	SEC_STRUC	"secstruc"

org.biojava.nbio.structure.PDBHeader

Modifier and Type	Constant Field	Value
public static final float	DEFAULT_RESOLUTION	99.0f
public static final float	DEFAULT_RFREE	1.0f

org.biojava.nbio.structure.PDBStatus

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_PDB_SERVER	"www.rcsb.org"
public static final String	PDB_SERVER_PROPERTY	"PDB.SERVER"

org.biojava.nbio.structure.StructureException

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	62946250941673093L

org.biojava.nbio.structure.StructureTools

Modifier and Type	Constant Field	Value
public static final String	C_ATOM_NAME	"C"
public static final String	C1_ATOM_NAME	"C1\'"
public static final String	C2_ATOM_NAME	"C2\'"
public static final String	C3_ATOM_NAME	"C3\'"
public static final String	C4_ATOM_NAME	"C4\'"
public static final String	CA_ATOM_NAME	"CA"
public static final String	CB_ATOM_NAME	"CB"
public static final String	N_ATOM_NAME	"N"
public static final String	NUCLEOTIDE_REPRESENTATIVE	"P"
public static final String	O_ATOM_NAME	"O"
public static final String	O2_ATOM_NAME	"O2\'"
public static final String	O3_ATOM_NAME	"O3\'"
public static final String	O4_ATOM_NAME	"O4\'"
public static final String	O5_ATOM_NAME	"O5\'"
public static final String	OP1_ATOM_NAME	"OP1"
public static final String	OP2_ATOM_NAME	"OP2"
public static final String	P_ATOM_NAME	"P"
public static final double	RATIO_RESIDUES_TO_TOTAL	0.95
public static final char	UNKNOWN_GROUP_LABEL	88

org.biojava.nbio.structure.URLIdentifier

Modifier and Type	Constant Field	Value
public static final String	CHAINID_PARAM	"chainid"
public static final String	FORMAT_PARAM	"format"
public static final String	PDBID_PARAM	"pdbid"
public static final String	RESIDUES_PARAM	"residues"

org.biojava.nbio.structure.align.BioJavaStructureAlignment

Modifier and Type	Constant Field	Value
public static final String	algorithmName	"BioJava_structure"

org.biojava.nbio.structure.align.ClusterAltAligs

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_CLUSTER_CUTOFF	95

org.biojava.nbio.structure.align.ce.CECalculator

Modifier and Type	Constant Field	Value
protected static final boolean	isPrint	false
protected static final int	nIter	1
protected static final double	zThr	-0.1

org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

Modifier and Type	Constant Field	Value
public static final boolean	GLOBAL_ALIGN1	false
public static final boolean	GLOBAL_ALIGN2	false
protected static final boolean	isPrint	true
protected static final int	nIter	1
protected static final double	zThr	-0.1

org.biojava.nbio.structure.align.ce.CeCPMain

Modifier and Type	Constant Field	Value
public static final String	algorithmName	"jCE Circular Permutation"
public static final String	version	"1.5"

org.biojava.nbio.structure.align.ce.CECPParameters

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_MIN_CP_LENGTH	5

org.biojava.nbio.structure.align.ce.CeMain

Modifier and Type	Constant Field	Value
public static final String	algorithmName	"jCE"
public static final String	version	"1.2"

org.biojava.nbio.structure.align.ce.CeParameters

Modifier and Type	Constant Field	Value
protected static final double	DEFAULT_GAP_EXTENSION	0.5
protected static final double	DEFAULT_GAP_OPEN	5.0
protected static final double	DEFAULT_oRmsdThr	2.0
protected static final String	DEFAULT_SUBSTITUTION_MATRIX	"PRLA000101"
protected static final double	DISTANCE_INCREMENT	0.5

org.biojava.nbio.structure.align.ce.CeSideChainMain

Modifier and Type	Constant Field	Value
public static final String	algorithmName	"jCE-sidechain"

org.biojava.nbio.structure.align.ce.OptimalCECPMain

Modifier and Type	Constant Field	Value
public static final String	algorithmName	"jCE Optimal Circular Permutation"
public static final String	version	"1.0"

org.biojava.nbio.structure.align.client.FarmJobParameters

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_BATCH_SIZE	100
public static final int	DEFAULT_JOB_TIME	-1
public static final int	DEFAULT_NR_ALIGNMENTS	-1
public static final int	DEFAULT_NR_THREADS	1
public static final String	DEFAULT_PDB_PATH	"/tmp/"

org.biojava.nbio.structure.align.fatcat.FatCat

Modifier and Type	Constant Field	Value
public static final String	algorithmName	"jFatCat"
public static final String	VERSION	"1.1"

org.biojava.nbio.structure.align.fatcat.FatCatFlexible

Modifier and Type	Constant Field	Value
public static final String	algorithmName	"jFatCat_flexible"

org.biojava.nbio.structure.align.fatcat.FatCatRigid

Modifier and Type	Constant Field	Value
public static final String	algorithmName	"jFatCat_rigid"

org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator

Modifier and Type	Constant Field	Value
public static final boolean	debug	false

org.biojava.nbio.structure.align.fatcat.calc.AFPChainer

Modifier and Type	Constant Field	Value
public static final boolean	debug	false

org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer

Modifier and Type	Constant Field	Value
public static final boolean	debug	false

org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor

Modifier and Type	Constant Field	Value
public static final boolean	debug	false

org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner

Modifier and Type	Constant Field	Value
public static final boolean	debug	false
public static final boolean	printTimeStamps	false

org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_FRAGLEN	8

org.biojava.nbio.structure.align.model.AFPChain

Modifier and Type	Constant Field	Value
public static final String	UNKNOWN_ALGORITHM	"unknown"

org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain

Modifier and Type	Constant Field	Value
public static final String	algorithmName	"jMultipleMC"
public static final String	version	"1.1"

org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

Modifier and Type	Constant Field	Value
public static final String	AVGTM_SCORE	"AvgTM-score"
public static final String	CE_SCORE	"CE-score"
public static final String	MC_SCORE	"MC-score"
public static final String	PROBABILITY	"Probability"
public static final String	REF_RMSD	"Ref-RMSD"
public static final String	REFTM_SCORE	"RefTM-score"
public static final String	RMSD	"RMSD"

org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner

Modifier and Type	Constant Field	Value
public static final String	algorithmName	"Smith-Waterman superposition"

org.biojava.nbio.structure.align.util.AtomCache

Modifier and Type	Constant Field	Value
public static final String	BIOL_ASSEMBLY_IDENTIFIER	"BIO:"
public static final String	CHAIN_NR_SYMBOL	":"
public static final String	CHAIN_SPLIT_SYMBOL	"."
public static final String	PDP_DOMAIN_IDENTIFIER	"PDP:"
public static final String	UNDERSCORE	"_"

org.biojava.nbio.structure.align.util.HTTPConnectionTools

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_CONNECTION_TIMEOUT	15000
public static final String	USERAGENT	"JFatCat Java client"

org.biojava.nbio.structure.align.util.UserConfiguration

Modifier and Type	Constant Field	Value
public static final String	MMCIF_FORMAT	"mmCif"
public static final String	PDB_CACHE_DIR	"PDB_CACHE_DIR"
public static final String	PDB_DIR	"PDB_DIR"
public static final String	PDB_FORMAT	"PDB"
public static final String	TMP_DIR	"java.io.tmpdir"

org.biojava.nbio.structure.align.xml.AFPChainXMLParser

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_ALGORITHM_NAME	"jFatCat_rigid"

org.biojava.nbio.structure.align.xml.PdbPairXMLConverter

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_METHOD_NAME	"jFatCat_rigid"

org.biojava.nbio.structure.asa.AsaCalculator

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_N_SPHERE_POINTS	960
public static final int	DEFAULT_NTHREADS	1
public static final double	DEFAULT_PROBE_SIZE	1.4
public static final double	NUC_CARBON_VDW	1.8
public static final double	NUC_NITROGEN_VDW	1.6
public static final double	OXIGEN_VDW	1.4
public static final double	PHOSPHOROUS_VDW	1.9
public static final double	SULFUR_VDW	1.85
public static final double	TETRAHEDRAL_CARBON_VDW	1.87
public static final double	TETRAHEDRAL_NITROGEN_VDW	1.5
public static final double	TRIGONAL_CARBON_VDW	1.76
public static final double	TRIGONAL_NITROGEN_VDW	1.65

org.biojava.nbio.structure.cath.CathDomain

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.biojava.nbio.structure.cath.CathFactory

Modifier and Type	Constant Field	Value
public static final String	LATEST_VERSION	"3.5.0"
public static final String	VERSION_3_5_0	"3.5.0"

org.biojava.nbio.structure.cath.CathFragment

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.biojava.nbio.structure.cath.CathInstallation

Modifier and Type	Constant Field	Value
public static final String	CATH_DOWNLOAD	"http://release.cathdb.info/"
public static final String	DEFAULT_VERSION	"3.5.0"
public static final String	domainDescriptionFileName	"CathDomainDescriptionFile"
public static final String	domainListFileName	"CathDomainList"
public static final String	domallFileName	"CathDomall"
public static final String	nodeListFileName	"CathNames"

org.biojava.nbio.structure.cath.CathNode

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.biojava.nbio.structure.cath.CathSegment

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.biojava.nbio.structure.contact.StructureInterfaceList

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_ASA_SPHERE_POINTS	3000
public static final double	DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF	0.2
public static final int	DEFAULT_MIN_COFACTOR_SIZE	40
public static final double	DEFAULT_MINIMUM_INTERFACE_AREA	35.0

org.biojava.nbio.structure.domain.PDBDomainProvider

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_PDB_API_URL	"http://www.rcsb.org/pdb/rest/"
public static final String	DEFAULT_PDB_HOST	"http://www.rcsb.org"

org.biojava.nbio.structure.domain.RemotePDPProvider

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_SERVER	"http://source.rcsb.org/jfatcatserver/domains/"

org.biojava.nbio.structure.domain.pdp.PDPParameters

Modifier and Type	Constant Field	Value
public static final float	CUT_OFF_VALUE	0.5f
public static final float	CUT_OFF_VALUE1	0.28999999165534973f
public static final float	CUT_OFF_VALUE1M	0.20999999344348907f
public static final float	CUT_OFF_VALUE1S	0.1899999976158142f
public static final float	CUT_OFF_VALUE2	0.4399999976158142f
public static final float	DBL	0.05000000074505806f
public static final int	ENDS	12
public static final int	ENDSEND	9
public static final int	MAX_CUTS	80
public static final int	MAXCONT	900
public static final int	MAXDOM	30
public static final int	MAXLEN	3200
public static final int	MAXSIZE	350
public static final int	MIN_DOMAIN_LENGTH	35
public static final float	RG	0.0f
public static final float	RG1	1.0f
public static final float	TD	25.0f
public static final float	TD1	40.0f

org.biojava.nbio.structure.ecod.EcodInstallation

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_VERSION	"latest"
public static final String	DOMAINS_PATH	"/ecod/distributions/"
public static final String	ECOD_URL	"http://prodata.swmed.edu"

org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

Modifier and Type	Constant Field	Value
public static final String	F_UNCLASSIFIED	"F_UNCLASSIFIED"
public static final String	IS_DOMAIN_ASSEMBLY	"IS_DOMAIN_ASSEMBLY"
public static final String	IS_REPRESENTATIVE	"MANUAL_REP"
public static final String	NOT_DOMAIN_ASSEMBLY	"NOT_DOMAIN_ASSEMBLY"
public static final String	NOT_REPRESENTATIVE	"AUTO_NONREP"

org.biojava.nbio.structure.io.CompoundFinder

Modifier and Type	Constant Field	Value
public static final double	GAP_COVERAGE_THRESHOLD	0.3
public static final double	IDENTITY_THRESHOLD	0.99999
public static final double	RATIO_GAPS_FOR_MISMATCH	0.5

org.biojava.nbio.structure.io.FileParsingParameters

Modifier and Type	Constant Field	Value
public static final int	ATOM_CA_THRESHOLD	500000
public static final int	MAX_ATOMS	2147483647

org.biojava.nbio.structure.io.LocalPDBDirectory

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_PDB_FILE_SERVER	"http://ftp.wwpdb.org"
public static final String	PDB_FILE_SERVER_PROPERTY	"PDB.FILE.SERVER"

org.biojava.nbio.structure.io.PDBParseException

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	219047230178423923L

org.biojava.nbio.structure.io.mmcif.AllChemCompProvider

Modifier and Type	Constant Field	Value
public static final String	COMPONENTS_FILE_LOCATION	"pub/pdb/data/monomers/components.cif.gz"

org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider

Modifier and Type	Constant Field	Value
public static final String	CHEM_COMP_CACHE_DIRECTORY	"chemcomp"
public static final String	SERVER_LOCATION	"http://www.rcsb.org/pdb/files/ligand/"

org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

Modifier and Type	Constant Field	Value
public static final String	MMCIF_DEFAULT_VALUE	"."
public static final String	MMCIF_MISSING_VALUE	"?"

org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

Modifier and Type	Constant Field	Value
public static final String	COMMENT_CHAR	"#"
public static final String	FIELD_LINE	"_"
public static final String	LOOP_START	"loop_"
public static final String	MMCIF_TOP_HEADER	"data_"
public static final String	STRING_LIMIT	";"

org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider

Modifier and Type	Constant Field	Value
public static final String	BIO_ASSEMBLY	"bioAssembly?structureId=%s&nr=%s"
public static final String	DEFAULT_SERVERNAME	"http://pepper.rcsb.org:8080/pdb/rest/biolassembly/"
public static final String	NR_BIOL_APPEND	"nrBiolAssemblies?structureId=%s"

org.biojava.nbio.structure.rcsb.PdbIdLists

Modifier and Type	Constant Field	Value
public static final String	SERVICELOCATION	"http://www.rcsb.org/pdb/rest/search"

org.biojava.nbio.structure.rcsb.RCSBUpdates

Modifier and Type	Constant Field	Value
public static final String	baseURL	"ftp://ftp.rcsb.org/pub/pdb/data/status/latest/"

org.biojava.nbio.structure.scop.RemoteScopInstallation

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_SERVER	"http://source.rcsb.org/jfatcatserver/domains/"

org.biojava.nbio.structure.scop.ScopFactory

Modifier and Type	Constant Field	Value
public static final String	LATEST_VERSION	"2.05"
public static final String	VERSION_1_55	"1.55"
public static final String	VERSION_1_57	"1.57"
public static final String	VERSION_1_59	"1.59"
public static final String	VERSION_1_61	"1.61"
public static final String	VERSION_1_63	"1.63"
public static final String	VERSION_1_65	"1.65"
public static final String	VERSION_1_67	"1.67"
public static final String	VERSION_1_69	"1.69"
public static final String	VERSION_1_71	"1.71"
public static final String	VERSION_1_73	"1.73"
public static final String	VERSION_1_75	"1.75"
public static final String	VERSION_1_75A	"2.01"
public static final String	VERSION_1_75B	"2.02"
public static final String	VERSION_1_75C	"2.03"
public static final String	VERSION_2_0_1	"2.01"
public static final String	VERSION_2_0_2	"2.02"
public static final String	VERSION_2_0_3	"2.03"
public static final String	VERSION_2_0_4	"2.04"
public static final String	VERSION_2_0_5	"2.05"

org.biojava.nbio.structure.scop.ScopInstallation

Modifier and Type	Constant Field	Value
public static final String	claFileName	"dir.cla.scop.txt_"
public static final String	comFileName	"dir.com.scop.txt_"
public static final String	DEFAULT_VERSION	"1.75"
public static final String	desFileName	"dir.des.scop.txt_"
public static final String	hieFileName	"dir.hie.scop.txt_"
public static final String	SCOP_DOWNLOAD	"http://scop.mrc-lmb.cam.ac.uk/scop/parse/"
public static final String	SCOP_DOWNLOAD_ALTERNATE	"http://scop.berkeley.edu/downloads/parse/"

org.biojava.nbio.structure.secstruc.SecStrucCalc

Modifier and Type	Constant Field	Value
public static final double	CA_MIN_DIST	9.0
public static final double	HBONDHIGHENERGY	-500.0
public static final int	HBONDLOWENERGY	-9900
public static final double	MAX_PEPTIDE_BOND_LENGTH	2.5
public static final double	MINDIST	0.5
public static final double	Q	-27888.0

org.biojava.nbio.structure.secstruc.SecStrucInfo

Modifier and Type	Constant Field	Value
public static final String	BIOJAVA_ASSIGNMENT	"BIOJAVA_ASSIGNMENT"
public static final String	DSSP_ASSIGNMENT	"DSSP_ASSIGNMENT"
public static final String	PDB_AUTHOR_ASSIGNMENT	"PDB_AUTHOR_ASSIGNMENT"

org.biojava.nbio.structure.symmetry.internal.CeSymm

Modifier and Type	Constant Field	Value
public static final String	algorithmName	"jCE-symm"
public static final String	version	"2.2"

org.biojava.nbio.structure.symmetry.internal.CESymmParameters

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_SYMMETRY_THRESHOLD	0.4

org.biojava.nbio.structure.xtal.CrystalBuilder

Modifier and Type	Constant Field	Value
public static final int	DEF_NUM_CELLS	12
public static final double	DEFAULT_INTERFACE_DISTANCE_CUTOFF	5.5

org.biojava.nbio.structure.xtal.CrystalCell

Modifier and Type	Constant Field	Value
public static final double	MIN_VALID_CELL_SIZE	10.0

org.biojava.nbio.structure.xtal.SpaceGroup

Modifier and Type	Constant Field	Value
protected static final double	DELTA	1.0E-7