Constant Field Values

Contents

• org.biojava.*

org.biojava.*

org.biojava.nbio.aaproperties.profeat.convertor.Convertor

Modifier and Type	Constant Field	Value
public static final char	group1	49
public static final char	group2	50
public static final char	group3	51
public static final char	unknownGroup	48

org.biojava.nbio.alignment.io.StockholmFileParser

Modifier and Type	Constant Field	Value
public static final int	INFINITY	-1

org.biojava.nbio.alignment.io.StockholmStructure

Modifier and Type	Constant Field	Value
public static final String	PFAM	"PFAM"
public static final String	RFAM	"RFAM"

org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference

Modifier and Type	Constant Field	Value
public static final String	EXPERT	"EXPERT"
public static final String	HOMSTRAD	"HOMSTRAD"
public static final String	INTERPRO	"INTERPRO"
public static final String	LOAD	"LOAD"
public static final String	MIM	"MIM"
public static final String	PDB	"PDB"
public static final String	PFAMB	"PFAMB"
public static final String	PRINTS	"PRINTS"
public static final String	PROSITE	"PROSITE"
public static final String	PROSITE_PROFILE	"PROSITE_PROFILE"
public static final String	SCOP	"SCOP"
public static final String	SMART	"SMART"
public static final String	URL	"URL"

org.biojava.nbio.core.exceptions.Messages

Modifier and Type	Constant Field	Value
public static final String	ENDOFFILE	"end of file"
public static final String	SECTIONKEYNULL	"section key is null"

org.biojava.nbio.core.sequence.io.GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound>

Modifier and Type	Constant Field	Value
protected static final String	ACCESSION_TAG	"ACCESSION"
protected static final String	AUTHORS_TAG	"AUTHORS"
protected static final String	BASE_COUNT_TAG	"BASE"
protected static final String	BASE_COUNT_TAG_FULL	"BASE COUNT"
protected static final String	COMMENT_TAG	"COMMENT"
protected static final String	CONSORTIUM_TAG	"CONSRTM"
protected static final String	DEFINITION_TAG	"DEFINITION"
protected static final String	END_SEQUENCE_TAG	"//"
protected static final String	FEATURE_TAG	"FEATURES"
public static final String	GENBANK_FORMAT	"GENBANK"
protected static final String	JOURNAL_TAG	"JOURNAL"
protected static final String	KEYWORDS_TAG	"KEYWORDS"
protected static final String	LOCUS_TAG	"LOCUS"
protected static final String	MEDLINE_TAG	"MEDLINE"
protected static final String	ORGANISM_TAG	"ORGANISM"
protected static final String	PUBMED_TAG	"PUBMED"
protected static final String	REFERENCE_TAG	"REFERENCE"
protected static final String	REMARK_TAG	"REMARK"
protected static final String	SOURCE_TAG	"SOURCE"
protected static final String	START_SEQUENCE_TAG	"ORIGIN"
protected static final String	TITLE_TAG	"TITLE"
protected static final String	VERSION_TAG	"VERSION"

org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Modifier and Type	Constant Field	Value
public static final String	CIRCULAR_DNA	"circular"
public static final String	LINEAR_DNA	"linear"

org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat<S extends AbstractSequence<C>,C extends Compound>

Modifier and Type	Constant Field	Value
protected static final int	MAX_WIDTH	80
protected static final int	QUALIFIER_INDENT	21
protected static final String	QUALIFIER_INDENT_STR	" "
protected static final String	QUALIFIER_INDENT_TMP	" %s "

org.biojava.nbio.core.sequence.io.IUPACParser

Modifier and Type	Constant Field	Value
public static final String	IUPAC_LOCATION	"org/biojava/nbio/core/sequence/iupac.txt"

org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface<S extends Sequence<?>,C extends Compound>

Modifier and Type	Constant Field	Value
public static final String	UNKNOWN_DNA	"UNK"

org.biojava.nbio.core.sequence.location.InsdcParser<S extends AbstractSequence<C>,C extends Compound>

Modifier and Type	Constant Field	Value
protected static final String	locationSplitPattern	",(?=([^\\(|\\)]+\\([^\\(|\\)]+\\))[^\\(|\\)]+)"

org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker<C extends Compound>

Modifier and Type	Constant Field	Value
public static final int	BYTES_PER_INT	32

org.biojava.nbio.core.util.Hashcoder

Modifier and Type	Constant Field	Value
public static final int	PRIME	79
public static final int	SEED	9

org.biojava.nbio.core.util.InputStreamProvider

Modifier and Type	Constant Field	Value
public static final String	CACHE_PROPERTY	"biojava.cache.files"
public static final int	GZIP_MAGIC	8075

org.biojava.nbio.core.util.SequenceTools

Modifier and Type	Constant Field	Value
protected static final String	NUCLEOTIDE_LETTERS	"GCTAUXN"

org.biojava.nbio.core.util.SoftHashMap<K,V>

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_LIMIT	1

org.biojava.nbio.genome.parsers.cytoband.CytobandParser

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_LOCATION	"http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz"

org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_MAPPING_URL	"http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz"

org.biojava.nbio.genome.parsers.genename.GeneNamesParser

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_GENENAMES_URL	"https://www.genenames.org/cgi-bin/download?title=HGNC+output+data&hgnc_dbtag=on&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=md_mim_id&col=gd_pub_refseq_ids&col=md_ensembl_id&col=md_prot_id&col=gd_hgnc_id&status=Approved&status_opt=2&where=((gd_pub_chrom_map%20not%20like%20%27%patch%%27%20and%20gd_pub_chrom_map%20not%20like%20%27%ALT_REF%%27)%20or%20gd_pub_chrom_map%20IS%20NULL)%20and%20gd_locus_group%20%3d%20%27protein-coding%20gene%27&order_by=gd_app_sym_sort&format=text&limit=&submit=submit&.cgifields=&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag"

org.biojava.nbio.genome.util.ChromosomeMappingTools

Modifier and Type	Constant Field	Value
public static final String	CDS	"CDS"
public static final String	CHROMOSOME	"CHROMOSOME"

org.biojava.nbio.ontology.Synonym

Modifier and Type	Constant Field	Value
public static final int	BROAD_SYNONYM	3
public static final int	EXACT_SYNONYM	1
public static final int	NARROW_SYNONYM	2
public static final int	RELATED_SYNONYM	0
public static final int	UNKNOWN_SCOPE	-1

org.biojava.nbio.ontology.obo.OboFileHandler

Modifier and Type	Constant Field	Value
public static final String	ALT_ID	"alt_id"
public static final String	BROAD_SYNONYM	"broad_synonym"
public static final String	COMMENT	"comment"
public static final String	DEF	"def"
public static final String	DISJOINT_FROM	"disjoint_from"
public static final String	EXACT_SYNONYM	"exact_synonym"
public static final String	ID_KEY	"id"
public static final String	INTERSECTION_OF	"intersection_of"
public static final String	IS_A	"is_a"
public static final String	IS_OBSOLETE	"is_obsolete"
public static final String	NAME	"name"
public static final String	NAMESPACE	"namespace"
public static final String	NARROW_SYNONYM	"narrow_synonym"
public static final String	ONTOLOGY	"ontologys"
public static final String	REL_SYNONYM	"related_synonym"
public static final String	RELATIONSHIP	"relationship"
public static final String	SUBSET	"subset"
public static final String	SYNONYM	"synonym"
public static final String	TERM	"Term"
public static final String	TYPEDEF	"Typedef"
public static final String	XREF_ANALOG	"xref_analog"

org.biojava.nbio.phosphosite.Dataset

Modifier and Type	Constant Field	Value
public static final String	ACETYLATION	"https://www.phosphosite.org/downloads/Acetylation_site_dataset.gz"
public static final String	DISEASE_ASSOC	"https://www.phosphosite.org/downloads/Disease-associated_sites.gz"
public static final String	METHYLATION	"https://www.phosphosite.org/downloads/Methylation_site_dataset.gz"
public static final String	PHOSPHORYLATION	"https://www.phosphosite.org/downloads/Phosphorylation_site_dataset.gz"
public static final String	REGULATORY	"https://www.phosphosite.org/downloads/Regulatory_sites.gz"
public static final String	SUMOYLATION	"https://www.phosphosite.org/downloads/Sumoylation_site_dataset.gz"
public static final String	UBIQUITINATION	"https://www.phosphosite.org/downloads/Ubiquitination_site_dataset.gz"

org.biojava.nbio.ronn.RonnConstraint

Modifier and Type	Constant Field	Value
public static final float	DEFAULT_DISORDER	0.5299999713897705f
public static final float	DEFAULT_ORDER	0.4699999988079071f
public static final float	DEFAULT_RANGE_PROBABILITY_THRESHOLD	0.5f

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 double	DEFAULT_LIGAND_PROXIMITY_CUTOFF	5.0
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.gui.ChooseDirAction

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	0L

org.biojava.nbio.structure.align.gui.MemoryMonitor

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	56289234782130L

org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	2387409854370432908L

org.biojava.nbio.structure.align.gui.MenuCreator

Modifier and Type	Constant Field	Value
public static final String	ALIGNMENT_PANEL	"Alignment Panel"
public static final String	DIST_MATRICES	"Show Distance Matrices"
public static final String	DOT_PLOT	"Show Dot Plot"
public static final String	EQR_COLOR	"Color By EQR"
public static final String	FASTA_FORMAT	"View FASTA Alignment"
public static final String	FATCAT_BLOCK	"Color By Alignment Block"
public static final String	FATCAT_TEXT	"View as FATCAT result"
public static final String	LOAD_ALIGNMENT_XML	"Load Alignment XML"
public static final String	LOAD_DB_RESULTS	"Load DB search results"
public static final String	MULTIPLE_ALIGN	"New Multiple Alignment"
public static final String	PAIRS_ONLY	"View Aligned Pairs"
public static final String	PAIRWISE_ALIGN	"New Pairwise Alignment"
public static final String	PHYLOGENETIC_TREE	"Phylogenetic Tree"
public static final String	PRINT	"Print"
public static final String	SAVE_ALIGNMENT_XML	"Save Alignment XML"
public static final String	SELECT_EQR	"Select Equivalent Positions"
public static final String	SIMILARITY_COLOR	"Color By Similarity"
public static final String	TEXT_ONLY	"View Text Only"

org.biojava.nbio.structure.align.gui.SystemInfo

Modifier and Type	Constant Field	Value
public static final String	defaultProperties	"browser file.separator java.class.version java.vendor java.vendor.url java.version line.separator os.arch os.name os.version path.separator "
public static final String	hexPropertyNames	" file.separator line.separator path.separator "
public static final String	urlPropertyNames	" browser.vendor.url java.class.path java.home user.dir user.home user.name "

org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_CHAR_SIZE	12
public static final int	DEFAULT_LINE_LENGTH	70
public static final int	DEFAULT_LINE_SEPARATION	20
public static final int	DEFAULT_RIGHT_SPACER	10
public static final int	DEFAULT_X_SPACE	20
public static final int	DEFAULT_Y_SPACE	40
public static final int	DEFAULT_Y_STEP	60
public static final int	SUMMARY_POS	20

org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_CHAR_SIZE	12
public static final int	DEFAULT_LINE_LENGTH	70
public static final int	DEFAULT_LINE_SEPARATION	20
public static final int	DEFAULT_RIGHT_SPACER	10
public static final int	DEFAULT_X_SPACE	20
public static final int	DEFAULT_Y_SPACE	40
public static final int	SUMMARY_POS	20

org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

Modifier and Type	Constant Field	Value
protected static final String	COMMAND_LINE_HELP	"enter Jmol scripting command..."
protected static final int	DEFAULT_HEIGHT	500
protected static final int	DEFAULT_WIDTH	500

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 boolean	DEFAULT_BIOASSEMBLY_STYLE	false
public static final String	PDP_DOMAIN_IDENTIFIER	"PDP:"
public static final String	UNDERSCORE	"_"

org.biojava.nbio.structure.align.util.URLConnectionTools

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_CONNECTION_TIMEOUT	30000

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

Modifier and Type	Constant Field	Value
public static final String	MMCIF_FORMAT	"mmCif"
public static final String	MMTF_FORMAT	"mmtf"
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.basepairs.MismatchedBasePairParameters

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_MAX_PROPELLER	60.0
public static final double	DEFAULT_MAX_SHEAR	5.0
public static final double	DEFAULT_MAX_STAGGER	2.0
public static final double	DEFAULT_MAX_STRETCH	5.0

org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_MAX_PROPELLER	60.0
public static final double	DEFAULT_MAX_STAGGER	2.0

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	DEFAULT_VERSION	"4_2_0"
public static final String	LATEST_VERSION	"4_2_0"
public static final String	VERSION_3_5_0	"3_5_0"
public static final String	VERSION_4_0_0	"4_0_0"
public static final String	VERSION_4_1_0	"4_1_0"
public static final String	VERSION_4_2_0	"4_2_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_ALL_RELEASES_DIR	"all-releases"
public static final String	CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR	"cath-classification-data"
public static final String	CATH_DOWNLOAD_URL	"http://download.cathdb.info/cath/releases/"
public static final String	DEFAULT_VERSION	"4_2_0"
public static final String	domainDescriptionFileName	"cath-domain-description-file-v%s.txt"
public static final String	domainListFileName	"cath-domain-list-v%s.txt"
public static final String	domallFileName	"cath-domain-boundaries-v%s.txt"
public static final String	nodeListFileName	"cath-names-v%s.txt"

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.EcodFactory

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_VERSION	"latest"

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.gui.BiojavaJmol

Modifier and Type	Constant Field	Value
public static final String	adapter	"org.jmol.api.JmolAdapter"
public static final String	smartAdapter	"org.jmol.adapter.smarter.SmarterJmolAdapter"
public static final String	viewer	"org.jmol.api.JmolSimpleViewer"

org.biojava.nbio.structure.gui.JmolViewerImpl

Modifier and Type	Constant Field	Value
public static final String	adapter	"org.jmol.api.JmolAdapter"
public static final String	smartAdapter	"org.jmol.adapter.smarter.SmarterJmolAdapter"
public static final String	viewer	"org.jmol.api.JmolSimpleViewer"

org.biojava.nbio.structure.gui.ScaleableMatrixPanel

Modifier and Type	Constant Field	Value
protected static final int	SLIDER_STEPS	8

org.biojava.nbio.structure.gui.SequenceDisplay

Modifier and Type	Constant Field	Value
public static final int	MAX_SCALE	10

org.biojava.nbio.structure.gui.util.AlignedPosition

Modifier and Type	Constant Field	Value
public static final int	EQUIVALENT	1
public static final int	NOT_ALIGNED	0

org.biojava.nbio.structure.gui.util.SequenceScalePanel

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_X_RIGHT_BORDER	40
public static final int	DEFAULT_X_START	10
public static final int	DEFAULT_Y_BOTTOM	16
public static final int	DEFAULT_Y_HEIGHT	8
public static final int	DEFAULT_Y_START	0
public static final int	DEFAULT_Y_STEP	10
public static final int	LINE_HEIGHT	10
public static final int	MINIMUM_HEIGHT	20
public static final int	SIZE	20

org.biojava.nbio.structure.gui.util.color.GradientMapper

Modifier and Type	Constant Field	Value
public static final int	BLACK_WHITE_GRADIENT	1
public static final int	RAINBOW_GRADIENT	4
public static final int	RAINBOW_INTENSITY_GRADIENT	5
public static final int	RED_BLUE_GRADIENT	3
public static final int	WHITE_BLACK_GRADIENT	2

org.biojava.nbio.structure.gui.util.color.HSVColorSpace

Modifier and Type	Constant Field	Value
public static final int	CS_HSV	1007

org.biojava.nbio.structure.io.EntityFinder

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	DEFAULT_SERVER_URL	"http://files.rcsb.org/ligands/download/"

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.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	"2.07"
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"
public static final String	VERSION_2_0_6	"2.06"
public static final String	VERSION_2_0_7	"2.07"

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.berkeley.edu/downloads/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

org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties

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

org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties

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

org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService

Modifier and Type	Constant Field	Value
public static final long	WAIT_INCREMENT	3000L

org.biojava.nbio.ws.hmmer.RemoteHmmerScan

Modifier and Type	Constant Field	Value
public static final String	HMMER_SERVICE	"https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan"