Constant Field Values

Contents

• org.strbio.*

org.strbio.*

org.strbio.app.BlastProtein

public static final java.lang.String

VERSION

"Version 3.1, 3/27/03"

org.strbio.app.ConvertProtein

public static final java.lang.String

VERSION

"Version 1.5, 3/29/04"

org.strbio.app.Modify2ary

public static final java.lang.String

VERSION

"Version 1.0, 11/22/00"

org.strbio.app.SplitProteins

public static final java.lang.String

VERSION

"Version 1.0, 7/20/1"

org.strbio.local.PDB

public static final java.lang.String

DEFAULT_PDB_PATH

"/lab/db/pdb/all:."

org.strbio.mol.Alignment

public static final double	LONGEST_DISTANCE_CUTOFF	6.0
public static final int	SHORTEST_ALIGNMENT_LENGTH	2

org.strbio.mol.Molecule

public static final int

MAX_NAME_LENGTH

4096

org.strbio.mol.Nucleotide

public static final java.lang.String

oneLetter

"ATGCUN"

org.strbio.mol.PolymerProperties

public static final int	BACKBONE_POTENTIAL	256
public static final int	KNOWN_2ARY	4
public static final int	KNOWN_ATOMS	1
public static final int	KNOWN_ENV	32
public static final int	MULTI_CHAIN	2
public static final int	PRECALC_ALPHATAU	2048
public static final int	PRECALC_CW	512
public static final int	PRECALC_FREQ	1024
public static final int	PRECALC_PHIPSI	16
public static final int	PRED_2ARY	8
public static final int	PSI_BLAST_MATRIX	128
public static final int	VAR_TOM_INFO	64

org.strbio.mol.ProfRes

public static final java.lang.String

oneLetterHSSP

"VLIMFWYGAPSTCHRKQEND"

org.strbio.mol.Residue

public static final java.lang.String	oneLetter	"-ARNDCQEGHILKMFPSTWYV"
public static final java.lang.String	oneLetterBLAST	"-ABCDEFGHIKLMNPQRSTVWXYZU*"
public static final java.lang.String	oneLetterDefay	"-ACDEFGHIKLMNPQRSTVWY"
public static final java.lang.String	threeLetter	"NUL ALA ARG ASN ASP CYS GLN GLU GLY HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL "

org.strbio.mol.lib.BackbonePotential

public static final int	AVG_RESIDUE	1
public static final int	AVG_RESIDUE_SAME_TYPE	2
public static final int	UNIFORM	0

org.strbio.mol.lib.BlastConstants

public static final java.lang.String

oneLetterBLAST

"-ABCDEFGHIKLMNPQRSTVWXYZU*"

org.strbio.mol.lib.Score2ary

public static final double	EQUAL	-1.31
public static final double	NOTEQUAL	0.761

org.strbio.mol.lib.ScoreDefay

public final java.lang.String

defaultTable

"defay.matrix"

org.strbio.mol.lib.ScoreFischer

public static final double	EQUAL	-1.94
public static final double	NOTEQUAL	1.12

org.strbio.mol.lib.ScoreID

public static final double	EQUAL	-1.0
public static final double	NOTEQUAL	0.0

org.strbio.mol.lib.ScoreJDB10

public final java.lang.String

defaultTable

"jdb10.dat"

org.strbio.mol.lib.ScorePhiPsi

public final java.lang.String

defaultFile

"p681.phipsi.separate.gz"

org.strbio.mol.lib.ScorePred2ary

public static final double	EQUAL	-1.28
public static final double	NOTEQUAL	0.779

org.strbio.mol.lib.ScorePredFreq

public static final double	EQUAL	-1.94
public static final double	NOTEQUAL	1.12

org.strbio.mol.lib.ScoreScaledID

public static final double	EQUAL	-3.98
public static final double	NOTEQUAL	0.254

org.strbio.mol.lib.ScoreSippl90

public static final java.lang.String

defaultFile

"sippl90.p681.gz"

org.strbio.mol.lib.ScoreUFSippl90

public final java.lang.String

defaultFile

"sippl90.p681.gz"

org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame

public static final java.lang.String

VERSION

"Version 1.06AP, 6/9/99"

org.strbio.mol.lib.pred2ary.ProfileDisplayArea

public static final int	MAX_NAME_PRINTED	12
protected final int	padX	5
protected final int	padY	2

org.strbio.mol.lib.pred2ary.TPSet

public static final boolean	CLASS_2ARY	true
public static final boolean	CLASS_AA	true
public static final boolean	CLASS_STRONG	true
public static final boolean	USE_LENGTH_INFO	true

org.strbio.raf.RAFResidue

public static final java.lang.String	oneLetter	"IAFCPCNKRCDHCLMCCCIRCWCVRRCDCTYRCWDYADTADVDANDDABSKLAKTCSYLKMLSKSCSIYGYSYHYDHGKYLAHEWWGTAKGCAFSWCFFCRCHKSFYKCHQRHWELYZCGMGDCECAVPKSECEQCCGCGCMTCLAEMACPLHAEAVAFA.."
public static final java.lang.String	threeLetter	"IIL DAL DPN EFC DPR CSO MEN KCX DAR CSP DAS 3AH CSS CLE MET SCH CSW CSX DIL ARG SCS HTR CEA DIV ARM ACL SCY BHD PEC THR IYR HMR CME TPL ASA PTR FLA ASB TPO TPQ ASK MVA ASL TIH ASN ASP ASQ ALA ASX OAS LYM NLE ALM LYS ALO DCY SEL TYB NLN LYZ FME NLP SEP ALY SER SMC SET ILE STY GL3 TYQ DSN TYR NEM TYS DSP NEP NMC TRG TYY DLE MAA MHS CGU TRO TRP MPQ DTH HAC DLY GSC BCS CHG PHE SVA DTR OCS HPQ PHI CY1 HAR CY3 HIC LLP MIS PHL DTY LLY SOC HIP GLN AGM HIS LTR GLU LEU PAQ GLX PR3 GLY CXM GLZ 2AS SHC GMA C5C DNP DVA HYP SHR SAC 5HP CYG DGL DGN CYM CYQ SAR CYS MSA BUC MSE BMT C6C BUG AIB PCA OMT DHA CCS PRO MLE DHI PRR GGL BNN VAL CSD DAH AYA ACE NH2 "

org.strbio.util.DensityPlot

public static final int	FLIP_X	1
public static final int	FLIP_Y	2

org.strbio.util.Hooke

public static final boolean

CompliesWithLicense

true

org.strbio.util.graph.BarPlot

public final double

barWidth

0.9

org.strbio.util.graph.Graph2D

public final int	BOX_ALL	15
public final int	BOX_BOTTOM	8
public final int	BOX_LEFT	1
public final int	BOX_NONE	0
public final int	BOX_RIGHT	2
public final int	BOX_TOP	4
public static final int	FLIP_X	1
public static final int	FLIP_Y	2