Package org.jmol.modelsetbio
Class BioExt
java.lang.Object
org.jmol.modelsetbio.BioExt
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate static final String
private static final String
private static final String
(package private) static final Object[]
(package private) static String
private ModelSet
private static String
private static final String
private static final String[]
private static final String[]
private Viewer
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescription(package private) int
calculateAllstruts
(Viewer vwr, ModelSet ms, javajs.util.BS bs1, javajs.util.BS bs2) (package private) void
private static javajs.util.Lst<Atom[]>
calculateStruts
(ModelSet modelSet, javajs.util.BS bs1, javajs.util.BS bs2, javajs.util.Lst<Atom> vCA, float thresh, int delta, boolean allowMultiple) Algorithm of George Phillips phillips@biochem.wisc.edu originally a contribution to pyMol as struts.py; adapted here by Bob Hanson for Jmol 1/2010 Return a vector of support posts for rapid prototyping models along the lines of George Phillips for Pymol except on actual molecular segments (biopolymers), not PDB chains (which may or may not be continuous).private static void
createHelix
(Viewer vwr, int nRes, int[] gly, float[] phipsi, boolean isTurn) (package private) static String
private static void
fixHydrogens
(Viewer vwr, AminoMonomer res1) private static float
get3DStraightness
(String id, javajs.util.Quat dq, javajs.util.Quat dqnext) (package private) void
(package private) boolean
getAminoAcidValenceAndCharge
(String res, String name, int[] ret) returns an array if we have special hybridization or chargeprivate void
getData
(int m0, int mStep, BioPolymer p, char ctype, char qtype, int derivType, javajs.util.BS bsAtoms, javajs.util.BS bsSelected, boolean isDraw, boolean isRamachandran, boolean calcRamachandranStraightness, boolean useQuaternionStraightness, boolean writeRamachandranStraightness, boolean quaternionStraightness, float factor, boolean isAmino, boolean isRelativeAlias, LabelToken[] tokens, javajs.util.OC pdbATOM, javajs.util.SB pdbCONECT, javajs.util.BS bsWritten, javajs.util.P3 ptTemp) (package private) String
getFullPDBHeader
(Map<String, Object> auxiliaryInfo) private static Atom[]
getMutationBackbone
(AminoMonomer res, Atom[] backbone) private void
getPdbData
(BioPolymer bp, char ctype, char qtype, int mStep, int derivType, javajs.util.BS bsAtoms, javajs.util.BS bsSelected, boolean bothEnds, boolean isDraw, boolean addHeader, LabelToken[] tokens, javajs.util.OC pdbATOM, javajs.util.SB pdbCONECT, javajs.util.BS bsWritten, javajs.util.P3 ptTemp) (package private) void
getPdbDataM
(BioModel m, Viewer vwr, String type, char ctype, boolean isDraw, javajs.util.BS bsSelected, javajs.util.OC out, LabelToken[] tokens, javajs.util.SB pdbCONECT, javajs.util.BS bsWritten) float[]
private static String
getQInfo
(javajs.util.Quat q) private static float
getQuaternionStraightness
(String id, javajs.util.Quat dq, javajs.util.Quat dqnext) private static float
getStraightness
(float cosHalfTheta) (package private) boolean
mutate
(Viewer vwr, javajs.util.BS bs, String group, String[] sequence, String helixType, float[] phipsi) mutate the given groupprivate static boolean
mutateAtom
(Viewer vwr, int iatom, String fileName, boolean addH) private static void
replaceMutatedMonomer
(Viewer vwr, AminoMonomer res0, AminoMonomer res1, boolean addH) (package private) BioExt
private static void
setStrut
(int i, int j, int n, javajs.util.Lst<Atom> vCA, javajs.util.BS bs1, javajs.util.BS bs2, javajs.util.Lst<Atom[]> vStruts, javajs.util.BS bsStruts, javajs.util.BS bsNotAvailable, javajs.util.BS bsNearbyResidues, int delta) private static int
strutPoint
(int i, int j, int n)
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Field Details
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vwr
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ms
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qColor
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helixScript
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alphaTypes
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mutateScript
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pdbRecords
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naNoH
- See Also:
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aaSp2
- See Also:
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aaSp21
- See Also:
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aaPlus
- See Also:
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Constructor Details
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BioExt
public BioExt()
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Method Details
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set
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getAllPolymerInfo
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calculateStraightnessAll
void calculateStraightnessAll() -
getPdbData
private void getPdbData(BioPolymer bp, char ctype, char qtype, int mStep, int derivType, javajs.util.BS bsAtoms, javajs.util.BS bsSelected, boolean bothEnds, boolean isDraw, boolean addHeader, LabelToken[] tokens, javajs.util.OC pdbATOM, javajs.util.SB pdbCONECT, javajs.util.BS bsWritten, javajs.util.P3 ptTemp) -
getData
private void getData(int m0, int mStep, BioPolymer p, char ctype, char qtype, int derivType, javajs.util.BS bsAtoms, javajs.util.BS bsSelected, boolean isDraw, boolean isRamachandran, boolean calcRamachandranStraightness, boolean useQuaternionStraightness, boolean writeRamachandranStraightness, boolean quaternionStraightness, float factor, boolean isAmino, boolean isRelativeAlias, LabelToken[] tokens, javajs.util.OC pdbATOM, javajs.util.SB pdbCONECT, javajs.util.BS bsWritten, javajs.util.P3 ptTemp) - Parameters:
m0
-mStep
-p
-ctype
-qtype
-derivType
-bsAtoms
-bsSelected
-isDraw
-isRamachandran
-calcRamachandranStraightness
-useQuaternionStraightness
-writeRamachandranStraightness
-quaternionStraightness
- NOT USEDfactor
-isAmino
-isRelativeAlias
-tokens
-pdbATOM
-pdbCONECT
-bsWritten
-ptTemp
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getQInfo
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drawQuat
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get3DStraightness
- Parameters:
id
- for debugging onlydq
-dqnext
-- Returns:
- calculated straightness
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getQuaternionStraightness
private static float getQuaternionStraightness(String id, javajs.util.Quat dq, javajs.util.Quat dqnext) - Parameters:
id
- for debugging onlydq
-dqnext
-- Returns:
- straightness
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getStraightness
private static float getStraightness(float cosHalfTheta) -
getPdbDataM
void getPdbDataM(BioModel m, Viewer vwr, String type, char ctype, boolean isDraw, javajs.util.BS bsSelected, javajs.util.OC out, LabelToken[] tokens, javajs.util.SB pdbCONECT, javajs.util.BS bsWritten) -
calculateAllstruts
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calculateStruts
private static javajs.util.Lst<Atom[]> calculateStruts(ModelSet modelSet, javajs.util.BS bs1, javajs.util.BS bs2, javajs.util.Lst<Atom> vCA, float thresh, int delta, boolean allowMultiple) Algorithm of George Phillips phillips@biochem.wisc.edu originally a contribution to pyMol as struts.py; adapted here by Bob Hanson for Jmol 1/2010 Return a vector of support posts for rapid prototyping models along the lines of George Phillips for Pymol except on actual molecular segments (biopolymers), not PDB chains (which may or may not be continuous). Like George, we go from thresh-4 to thresh in units of 1 Angstrom, but we do not require this threshold to be an integer. In addition, we prevent double-creation of struts by tracking where struts are, and we do not look for any addtional end struts if there is a strut already to an atom at a particular biopolymer end. The three parameters are: set strutDefaultRadius 0.3 set strutSpacingMinimum 6 set strutLengthMaximum 7.0 Struts will be introduced by: calculate struts {atom set A} {atom set B} where the two atom sets are optional and default to the currently selected set. They can be manipulated using the STRUTS command much like any "bond" struts 0.3 color struts opaque pink connect {atomno=3} {atomno=4} strut struts only command- Parameters:
modelSet
-bs1
-bs2
-vCA
-thresh
-delta
-allowMultiple
-- Returns:
- vector of pairs of atoms
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strutPoint
private static int strutPoint(int i, int j, int n) -
setStrut
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mutate
boolean mutate(Viewer vwr, javajs.util.BS bs, String group, String[] sequence, String helixType, float[] phipsi) mutate the given group- Parameters:
vwr
-bs
-group
-sequence
-phipsi
-helixType
-- Returns:
- true if even partially successful
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createHelix
- Parameters:
vwr
-nRes
-gly
-phipsi
-isTurn
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getPhiPsiForHelixType
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mutateAtom
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replaceMutatedMonomer
private static void replaceMutatedMonomer(Viewer vwr, AminoMonomer res0, AminoMonomer res1, boolean addH) -
fixHydrogens
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getMutationBackbone
- Parameters:
res
-backbone
-- Returns:
- [C O CA N H]
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getFullPDBHeader
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getAminoAcidValenceAndCharge
returns an array if we have special hybridization or charge- Parameters:
res
-name
-ret
- [0] (target valence) may be reduced by one for sp2 for C or O only [1] will be set to 1 if positive (lysine or terminal N) or -1 if negative (OXT) [2] will be set to 2 if sp2 [3] is supplied covalent bond count- Returns:
- true for special; false if not
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