public class BioExt
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private static java.lang.String |
aaPlus |
private static java.lang.String |
aaSp2 |
private static java.lang.String |
aaSp21 |
private ModelSet |
ms |
private static java.lang.String |
naNoH |
private static java.lang.String[] |
pdbRecords |
private static java.lang.String[] |
qColor |
private Viewer |
vwr |
Constructor and Description |
---|
BioExt() |
Modifier and Type | Method and Description |
---|---|
(package private) int |
calculateAllstruts(Viewer vwr,
ModelSet ms,
BS bs1,
BS bs2) |
(package private) void |
calculateStraightnessAll() |
private static javajs.util.Lst<Atom[]> |
calculateStruts(ModelSet modelSet,
BS bs1,
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).
|
(package private) static java.lang.String |
drawQuat(javajs.util.Quat q,
java.lang.String prefix,
java.lang.String id,
javajs.util.P3 ptCenter,
float scale) |
private static float |
get3DStraightness(java.lang.String id,
javajs.util.Quat dq,
javajs.util.Quat dqnext) |
(package private) void |
getAllPolymerInfo(BS bs,
java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> fullInfo) |
(package private) boolean |
getAminoAcidValenceAndCharge(java.lang.String res,
java.lang.String name,
int[] ret)
returns an array if we have special hybridization or charge
|
private void |
getData(int m0,
int mStep,
BioPolymer p,
char ctype,
char qtype,
int derivType,
BS bsAtoms,
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,
BS bsWritten,
javajs.util.P3 ptTemp) |
(package private) java.lang.String |
getFullPDBHeader(java.util.Map<java.lang.String,java.lang.Object> auxiliaryInfo) |
private static Atom[] |
getMutationBackbone(AminoMonomer res1,
Atom[] backbone) |
private void |
getPdbData(BioPolymer bp,
char ctype,
char qtype,
int mStep,
int derivType,
BS bsAtoms,
BS bsSelected,
boolean bothEnds,
boolean isDraw,
boolean addHeader,
LabelToken[] tokens,
javajs.util.OC pdbATOM,
javajs.util.SB pdbCONECT,
BS bsWritten,
javajs.util.P3 ptTemp) |
(package private) void |
getPdbDataM(BioModel m,
Viewer vwr,
java.lang.String type,
char ctype,
boolean isDraw,
BS bsSelected,
javajs.util.OC out,
LabelToken[] tokens,
javajs.util.SB pdbCONECT,
BS bsWritten) |
private static java.lang.String |
getQInfo(javajs.util.Quat q) |
private static float |
getQuaternionStraightness(java.lang.String id,
javajs.util.Quat dq,
javajs.util.Quat dqnext) |
private static float |
getStraightness(float cosHalfTheta) |
(package private) boolean |
mutate(Viewer vwr,
BS bs,
java.lang.String group,
java.lang.String[] sequence) |
private static boolean |
mutateAtom(Viewer vwr,
int iatom,
java.lang.String fileName) |
private static void |
replaceMutatedMonomer(Viewer vwr,
AminoMonomer res0,
AminoMonomer res1) |
(package private) BioExt |
set(Viewer vwr,
ModelSet ms) |
private static void |
setStrut(int i,
int j,
int n,
javajs.util.Lst<Atom> vCA,
BS bs1,
BS bs2,
javajs.util.Lst<Atom[]> vStruts,
BS bsStruts,
BS bsNotAvailable,
BS bsNearbyResidues,
int delta) |
private static int |
strutPoint(int i,
int j,
int n) |
private Viewer vwr
private ModelSet ms
private static final java.lang.String[] qColor
private static final java.lang.String[] pdbRecords
private static final java.lang.String naNoH
private static final java.lang.String aaSp2
private static final java.lang.String aaSp21
private static final java.lang.String aaPlus
void getAllPolymerInfo(BS bs, java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> fullInfo)
void calculateStraightnessAll()
private void getPdbData(BioPolymer bp, char ctype, char qtype, int mStep, int derivType, BS bsAtoms, BS bsSelected, boolean bothEnds, boolean isDraw, boolean addHeader, LabelToken[] tokens, javajs.util.OC pdbATOM, javajs.util.SB pdbCONECT, BS bsWritten, javajs.util.P3 ptTemp)
private void getData(int m0, int mStep, BioPolymer p, char ctype, char qtype, int derivType, BS bsAtoms, 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, BS bsWritten, javajs.util.P3 ptTemp)
m0
- mStep
- p
- ctype
- qtype
- derivType
- bsAtoms
- bsSelected
- isDraw
- isRamachandran
- calcRamachandranStraightness
- useQuaternionStraightness
- writeRamachandranStraightness
- quaternionStraightness
- NOT USEDfactor
- isAmino
- isRelativeAlias
- tokens
- pdbATOM
- pdbCONECT
- bsWritten
- ptTemp
- private static java.lang.String getQInfo(javajs.util.Quat q)
static java.lang.String drawQuat(javajs.util.Quat q, java.lang.String prefix, java.lang.String id, javajs.util.P3 ptCenter, float scale)
private static float get3DStraightness(java.lang.String id, javajs.util.Quat dq, javajs.util.Quat dqnext)
id
- for debugging onlydq
- dqnext
- private static float getQuaternionStraightness(java.lang.String id, javajs.util.Quat dq, javajs.util.Quat dqnext)
id
- for debugging onlydq
- dqnext
- private static float getStraightness(float cosHalfTheta)
void getPdbDataM(BioModel m, Viewer vwr, java.lang.String type, char ctype, boolean isDraw, BS bsSelected, javajs.util.OC out, LabelToken[] tokens, javajs.util.SB pdbCONECT, BS bsWritten)
private static javajs.util.Lst<Atom[]> calculateStruts(ModelSet modelSet, BS bs1, BS bs2, javajs.util.Lst<Atom> vCA, float thresh, int delta, boolean allowMultiple)
modelSet
- bs1
- bs2
- vCA
- thresh
- delta
- allowMultiple
- private static int strutPoint(int i, int j, int n)
private static void setStrut(int i, int j, int n, javajs.util.Lst<Atom> vCA, BS bs1, BS bs2, javajs.util.Lst<Atom[]> vStruts, BS bsStruts, BS bsNotAvailable, BS bsNearbyResidues, int delta)
private static boolean mutateAtom(Viewer vwr, int iatom, java.lang.String fileName)
private static void replaceMutatedMonomer(Viewer vwr, AminoMonomer res0, AminoMonomer res1)
private static Atom[] getMutationBackbone(AminoMonomer res1, Atom[] backbone)
res1
- backbone
- java.lang.String getFullPDBHeader(java.util.Map<java.lang.String,java.lang.Object> auxiliaryInfo)
boolean getAminoAcidValenceAndCharge(java.lang.String res, java.lang.String name, int[] ret)
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