Constant Field Values

Contents

• org.biojava.*

org.biojava.*

org.biojava.bio.structure.AminoAcid

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

org.biojava.bio.structure.AminoAcidImpl

Modifier and Type	Constant Field	Value
public static final String	type	"amino"

org.biojava.bio.structure.Calc

Modifier and Type	Constant Field	Value
public static final float	degreesPerRadian	57.295780181884766f
public static final float	radiansPerDegree	0.01745329238474369f

org.biojava.bio.structure.GroupType

Modifier and Type	Constant Field	Value
public static final String	AMINOACID	"amino"
public static final String	HETATM	"hetatm"
public static final String	NUCLEOTIDE	"nucleotide"

org.biojava.bio.structure.HetatomImpl

Modifier and Type	Constant Field	Value
public static final String	type	"hetatm"

org.biojava.bio.structure.NucleotideImpl

Modifier and Type	Constant Field	Value
public static final String	type	"nucleotide"

org.biojava.bio.structure.PDBHeader

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

org.biojava.bio.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.bio.structure.StructureException

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

org.biojava.bio.structure.StructureTools

Modifier and Type	Constant Field	Value
public static final String	caAtomName	" CA "
public static final String	cbAtomName	"CB"
public static final String	nAtomName	"N"
public static final String	oAtomName	"O"

org.biojava.bio.structure.align.BioJavaStructureAlignment

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

org.biojava.bio.structure.align.ClusterAltAligs

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

org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor

Modifier and Type	Constant Field	Value
public static final String	PDB_DIR	"PDB_DIR"

org.biojava.bio.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.bio.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.bio.structure.align.ce.CeCPMain

Modifier and Type	Constant Field	Value
public static final String	algorithmName	"jCE Circular Permutation"
public static final int	DEFAULT_MIN_CP_LENGTH	5
public static final String	version	"1.3"

org.biojava.bio.structure.align.ce.CeMain

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

org.biojava.bio.structure.align.ce.CeParameters

Modifier and Type	Constant Field	Value
public static final int	CA_AND_SIDE_CHAIN_ANGLE_SCORING	3
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
public static final int	DEFAULT_SCORING_STRATEGY	0
protected static final double	DISTANCE_INCREMENT	0.5
public static final String	SCORING_STRATEGY	"ScoringStrategy"
public static final int	SEQUENCE_CONSERVATION	4
public static final int	SIDE_CHAIN_ANGLE_SCORING	2
public static final int	SIDE_CHAIN_SCORING	1

org.biojava.bio.structure.align.ce.CeSideChainMain

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

org.biojava.bio.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.bio.structure.align.client.FarmJobParameters

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_BATCH_SIZE	100
public static final boolean	DEFAULT_DIR_SPLIT	true
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.bio.structure.align.fatcat.FatCat

Modifier and Type	Constant Field	Value
public static final float	VERSION	1.0f

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

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

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

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

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

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

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

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

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

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

org.biojava.bio.structure.align.gui.ChooseDirAction

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

org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel

Modifier and Type	Constant Field	Value
public static final String	PDB_DIR	"PDB_DIR"

org.biojava.bio.structure.align.gui.DisplayAFP

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

org.biojava.bio.structure.align.gui.MenuCreator

Modifier and Type	Constant Field	Value
public static final String	ALIGNMENT_PANEL	"Alignment Panel"
public static final String	EQR_COLOR	"Color By EQR"
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	PAIRS_ONLY	"View Aligned Pairs"
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.bio.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.bio.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.bio.structure.align.gui.jmol.StructureAlignmentJmol

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

org.biojava.bio.structure.align.model.AFPChain

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

org.biojava.bio.structure.align.seq.SmithWaterman3Daligner

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

org.biojava.bio.structure.align.util.AtomCache

Modifier and Type	Constant Field	Value
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.bio.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.bio.structure.align.util.UserConfiguration

Modifier and Type	Constant Field	Value
public static final String	MMCIF_FORMAT	"mmCif"
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.bio.structure.domain.RemotePDPProvider

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

org.biojava.bio.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.bio.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.bio.structure.gui.ScaleableMatrixPanel

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

org.biojava.bio.structure.gui.SequenceDisplay

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

org.biojava.bio.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.bio.structure.gui.util.PDBDirPanel

Modifier and Type	Constant Field	Value
public static final String	PDB_DIR	"PDB_DIR"

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

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

org.biojava.bio.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.bio.structure.io.PDBFileParser

Modifier and Type	Constant Field	Value
public static final String	HELIX	"HELIX"
public static final String	PDB_AUTHOR_ASSIGNMENT	"PDB_AUTHOR_ASSIGNMENT"
public static final String	STRAND	"STRAND"
public static final String	TURN	"TURN"

org.biojava.bio.structure.io.PDBFileReader

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

org.biojava.bio.structure.io.PDBParseException

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

org.biojava.bio.structure.io.mmcif.SimpleMMcifParser

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

org.biojava.bio.structure.scop.RemoteScopInstallation

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

org.biojava.bio.structure.scop.ScopInstallation

Modifier and Type	Constant Field	Value
public static final String	claFileName	"dir.cla.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/"

org.biojava.bio.structure.secstruc.BigSqrt

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_MAX_ITERATIONS	50
public static final int	DEFAULT_SCALE	3

org.biojava.bio.structure.server.FlatFileInstallation

Modifier and Type	Constant Field	Value
public static final String	DEFAUL_CHAIN_FILE	"chaininfo.txt"
public static final String	DEFAULT_INDEX_FILE	"pdbinfo.txt"

org.biojava3.*

org.biojava3.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.biojava3.core.sequence.io.IUPACParser

Modifier and Type	Constant Field	Value
public static final String	IUPAC_LOCATION	"org/biojava3/core/sequence/iupac.txt"

org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker<C extends Compound>

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

org.biojava3.core.util.Hashcoder

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

org.biojava3.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.biojava3.core.util.SequenceTools

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

org.biojava3.core.util.SoftHashMap<K,V>

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

org.biojava3.phylo.ResidueProperties

Modifier and Type	Constant Field	Value
public static final double	buriedmax	4.6
public static final double	buriedmin	0.05
public static final double	helixmax	1.51
public static final double	helixmin	0.57
public static final double	hydmax	4.5
public static final double	hydmin	-3.9
public static final double	strandmax	1.7
public static final double	strandmin	0.37
public static final double	turnmax	1.56
public static final double	turnmin	0.47

org.biojava3.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.biojava3.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.biojava3.ws.alignment.RemotePairwiseAlignmentOutputProperties

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

org.biojava3.ws.alignment.RemotePairwiseAlignmentProperties

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

org.biojava3.ws.alignment.qblast.NCBIQBlastService

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