Constant Field Values
Contents
org.biojava.*
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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
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org.biojava.nbio.alignment.io.StockholmFileParser Modifier and Type Constant Field Value public static final int
INFINITY
-1
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org.biojava.nbio.alignment.io.StockholmStructure Modifier and Type Constant Field Value public static final String
PFAM
"PFAM"
public static final String
RFAM
"RFAM"
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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"
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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"
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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"
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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"
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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 "
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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"
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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"
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org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader<C extends Compound> Modifier and Type Constant Field Value public static final String
DEFAULT_UNIPROT_BASE_URL
"https://www.uniprot.org"
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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
",(?=([^\\(|\\)]+\\([^\\(|\\)]+\\))[^\\(|\\)]+)"
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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
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org.biojava.nbio.core.util.Hashcoder Modifier and Type Constant Field Value public static final int
PRIME
79
public static final int
SEED
9
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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
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org.biojava.nbio.core.util.SequenceTools Modifier and Type Constant Field Value protected static final String
NUCLEOTIDE_LETTERS
"GCTAUXN"
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org.biojava.nbio.core.util.SoftHashMap<K,V> Modifier and Type Constant Field Value public static final int
DEFAULT_LIMIT
1
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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"
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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"
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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"
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org.biojava.nbio.genome.util.ChromosomeMappingTools Modifier and Type Constant Field Value public static final String
CDS
"CDS"
public static final String
CHROMOSOME
"CHROMOSOME"
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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
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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
REPLACED_BY
"replaced_by"
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"
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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"
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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
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org.biojava.nbio.structure.AminoAcid Modifier and Type Constant Field Value public static final String
ATOMRECORD
"ATOM"
public static final String
SEQRESRECORD
"SEQRES"
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org.biojava.nbio.structure.AtomImpl Modifier and Type Constant Field Value public static final int
BONDS_INITIAL_CAPACITY
3
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org.biojava.nbio.structure.Group Modifier and Type Constant Field Value public static final String
SEC_STRUC
"secstruc"
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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
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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"
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org.biojava.nbio.structure.StructureException Modifier and Type Constant Field Value public static final long
serialVersionUID
62946250941673093L
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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
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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"
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org.biojava.nbio.structure.align.BioJavaStructureAlignment Modifier and Type Constant Field Value public static final String
algorithmName
"BioJava_structure"
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org.biojava.nbio.structure.align.ClusterAltAligs Modifier and Type Constant Field Value public static final int
DEFAULT_CLUSTER_CUTOFF
95
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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
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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
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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"
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org.biojava.nbio.structure.align.ce.CECPParameters Modifier and Type Constant Field Value public static final int
DEFAULT_MIN_CP_LENGTH
5
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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"
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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
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org.biojava.nbio.structure.align.ce.CeSideChainMain Modifier and Type Constant Field Value public static final String
algorithmName
"jCE-sidechain"
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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"
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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/"
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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"
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org.biojava.nbio.structure.align.fatcat.FatCatFlexible Modifier and Type Constant Field Value public static final String
algorithmName
"jFatCat_flexible"
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org.biojava.nbio.structure.align.fatcat.FatCatRigid Modifier and Type Constant Field Value public static final String
algorithmName
"jFatCat_rigid"
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org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator Modifier and Type Constant Field Value public static final boolean
debug
false
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org.biojava.nbio.structure.align.fatcat.calc.AFPChainer Modifier and Type Constant Field Value public static final boolean
debug
false
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org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer Modifier and Type Constant Field Value public static final boolean
debug
false
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org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor Modifier and Type Constant Field Value public static final boolean
debug
false
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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
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org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters Modifier and Type Constant Field Value public static final int
DEFAULT_FRAGLEN
8
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org.biojava.nbio.structure.align.gui.ChooseDirAction Modifier and Type Constant Field Value public static final long
serialVersionUID
0L
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org.biojava.nbio.structure.align.gui.MemoryMonitor Modifier and Type Constant Field Value public static final long
serialVersionUID
56289234782130L
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org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface Modifier and Type Constant Field Value public static final long
serialVersionUID
2387409854370432908L
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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"
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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 "
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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
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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
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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
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org.biojava.nbio.structure.align.model.AFPChain Modifier and Type Constant Field Value public static final String
UNKNOWN_ALGORITHM
"unknown"
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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"
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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"
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org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner Modifier and Type Constant Field Value public static final String
algorithmName
"Smith-Waterman superposition"
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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
"_"
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org.biojava.nbio.structure.align.util.URLConnectionTools Modifier and Type Constant Field Value public static final int
DEFAULT_CONNECTION_TIMEOUT
30000
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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"
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org.biojava.nbio.structure.align.xml.AFPChainXMLParser Modifier and Type Constant Field Value public static final String
DEFAULT_ALGORITHM_NAME
"jFatCat_rigid"
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org.biojava.nbio.structure.align.xml.PdbPairXMLConverter Modifier and Type Constant Field Value public static final String
DEFAULT_METHOD_NAME
"jFatCat_rigid"
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org.biojava.nbio.structure.asa.AsaCalculator Modifier and Type Constant Field Value public static final int
DEFAULT_N_SPHERE_POINTS
1000
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
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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
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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
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org.biojava.nbio.structure.cath.CathDomain Modifier and Type Constant Field Value public static final long
serialVersionUID
1L
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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"
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org.biojava.nbio.structure.cath.CathFragment Modifier and Type Constant Field Value public static final long
serialVersionUID
1L
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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"
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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 long
MIN_PDB_FILE_SIZE
40L
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
"http://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"