Revision: 20251
http://sourceforge.net/p/jmol/code/20251
Author: hansonr
Date: 2015-01-28 16:16:02 +0000 (Wed, 28 Jan 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.01.28"
new feature: MUTATE command
-- replaces one amino acid group with another
-- can read from RCSB or from user-specified file
-- examples:
mutate 33 lys // uses last occurrence of resno=33
mutate @@3 arg // replaces group of atom 3 in current model
mutate @r @g // replaces resno in variable r with group in
variable g
mutate {r} his // same as above; r must be an atom selection
mutate 22 "myfile.cif" // user-defined replacement
new feature: resno is user settable
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/JmolBioResolver.java
trunk/Jmol/src/org/jmol/api/JmolPropertyManager.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/BondCollection.java
trunk/Jmol/src/org/jmol/modelset/Group.java
trunk/Jmol/src/org/jmol/modelset/Model.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java
trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/ScriptExpr.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/NBODialog.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
Modified: trunk/Jmol/src/org/jmol/api/JmolBioResolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolBioResolver.java 2015-01-28 00:19:08 UTC
(rev 20250)
+++ trunk/Jmol/src/org/jmol/api/JmolBioResolver.java 2015-01-28 16:16:02 UTC
(rev 20251)
@@ -55,6 +55,8 @@
Resolver setViewer(Viewer vwr);
public short getGroupID(String g3);
+
+ public boolean mutate(int iatom, String fileName);
}
Modified: trunk/Jmol/src/org/jmol/api/JmolPropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolPropertyManager.java 2015-01-28
00:19:08 UTC (rev 20250)
+++ trunk/Jmol/src/org/jmol/api/JmolPropertyManager.java 2015-01-28
16:16:02 UTC (rev 20251)
@@ -42,5 +42,7 @@
String getModelCml(BS bs, int nAtomsMax, boolean addBonds);
+ String getCoordinateFileData(String atomExpression, String type);
+
}
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2015-01-28 00:19:08 UTC (rev
20250)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2015-01-28 16:16:02 UTC (rev
20251)
@@ -419,7 +419,7 @@
return !Float.isNaN(userDefinedVanDerWaalRadius = (radius > 0 ? radius :
Float.NaN));
}
- public void deleteBonds(BS bsBonds) {
+ public void delete(BS bsBonds) {
valence = -1;
if (bonds != null)
for (int i = bonds.length; --i >= 0; ) {
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-01-28
00:19:08 UTC (rev 20250)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-01-28
16:16:02 UTC (rev 20251)
@@ -88,6 +88,7 @@
String[] atomNames;
String[] atomTypes;
int[] atomSerials;
+ int[] atomResnos;
int[] atomSeqIDs;
public Vibration[] vibrations;
float[] occupancies;
@@ -147,7 +148,8 @@
final public static byte TAINT_VIBRATION = 12;
final public static byte TAINT_ATOMNO = 13;
final public static byte TAINT_SEQID = 14;
- final public static byte TAINT_MAX = 15; // 1 more than last number, above
+ final public static byte TAINT_RESNO = 15;
+ final public static byte TAINT_MAX = 16; // 1 more than last number, above
public static String[] userSettableValues;
@@ -167,7 +169,7 @@
bsClickable = new BS();
// this allows the Google Closure compiler to skip all the TAINTED defs in
Clazz.defineStatics
if (userSettableValues == null)
- userSettableValues = "atomName atomType coord element formalCharge
hydrophobicity ionic occupancy partialCharge temperature valence vanderWaals
vibrationVector atomNo seqID".split(" ");
+ userSettableValues = "atomName atomType coord element formalCharge
hydrophobicity ionic occupancy partialCharge temperature valence vanderWaals
vibrationVector atomNo seqID resNo".split(" ");
}
protected void releaseModelSet() {
@@ -185,6 +187,7 @@
atomNames = null;
atomTypes = null;
+ atomResnos = null;
atomSerials = null;
atomSeqIDs = null;
vibrations = null;
@@ -199,6 +202,7 @@
tainted = mergeModelSet.tainted;
atomNames = mergeModelSet.atomNames;
atomTypes = mergeModelSet.atomTypes;
+ atomResnos = mergeModelSet.atomResnos;
atomSerials = mergeModelSet.atomSerials;
atomSeqIDs = mergeModelSet.atomSeqIDs;
vibrations = mergeModelSet.vibrations;
@@ -655,6 +659,10 @@
if (setBFactor(i, fValue))
taintAtom(i, TAINT_TEMPERATURE);
break;
+ case T.resno:
+ setAtomResno(i, iValue);
+ taintAtom(i, TAINT_RESNO);
+ break;
case T.valence:
atom.setValence(iValue);
taintAtom(i, TAINT_VALENCE);
@@ -796,6 +804,15 @@
return true;
}
+ public boolean setAtomResno(int atomIndex, int resno) {
+ if (atomResnos == null) {
+ atomResnos = new int[at.length];
+ }
+ atomResnos[atomIndex] = resno;
+ at[atomIndex].group.setResno(resno);
+ return true;
+ }
+
public boolean setAtomSeqID(int atomIndex, int seqID) {
if (atomSeqIDs == null) {
atomSeqIDs = new int[at.length];
@@ -903,6 +920,9 @@
case TAINT_ATOMNO:
setAtomNumber(atomIndex, (int) x);
break;
+ case TAINT_RESNO:
+ setAtomResno(atomIndex, (int) x);
+ break;
case TAINT_SEQID:
setAtomSeqID(atomIndex, (int) x);
break;
@@ -2045,7 +2065,7 @@
* @param specInfo
* @return BitSet; or null if we mess up the type
*/
- protected BS getAtomBitsMDa(int tokType, Object specInfo) {
+ public BS getAtomBitsMDa(int tokType, Object specInfo) {
BS bs = new BS() ;
BS bsInfo;
BS bsTemp;
@@ -2619,6 +2639,8 @@
nAtoms);
atomTypes = (String[]) AU.deleteElements(atomTypes, firstAtomIndex,
nAtoms);
+ atomResnos = (int[]) AU.deleteElements(atomResnos, firstAtomIndex,
+ nAtoms);
atomSerials = (int[]) AU.deleteElements(atomSerials, firstAtomIndex,
nAtoms);
atomSeqIDs = (int[]) AU.deleteElements(atomSeqIDs, firstAtomIndex,
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2015-01-28
00:19:08 UTC (rev 20250)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2015-01-28
16:16:02 UTC (rev 20251)
@@ -802,5 +802,43 @@
bo[i].setShapeVisibility(isDisplay);
}
+ public BS getAtomsConnected(float min, float max, int intType, BS bs) {
+ boolean isBonds = bs instanceof BondSet;
+ BS bsResult = (isBonds ? new BondSet() : new BS());
+ int[] nBonded = new int[ac];
+ int i;
+ boolean ishbond = (intType == Edge.BOND_HYDROGEN_MASK);
+ boolean isall = (intType == Edge.BOND_ORDER_ANY);
+ for (int ibond = 0; ibond < bondCount; ibond++) {
+ Bond bond = bo[ibond];
+ if (isall || bond.is(intType) || ishbond && bond.isHydrogen()) {
+ if (isBonds) {
+ bsResult.set(ibond);
+ } else {
+ if (bs.get(bond.atom1.i)) {
+ nBonded[i = bond.atom2.i]++;
+ bsResult.set(i);
+ }
+ if (bs.get(bond.atom2.i)) {
+ nBonded[i = bond.atom1.i]++;
+ bsResult.set(i);
+ }
+ }
+ }
+ }
+ if (isBonds)
+ return bsResult;
+ boolean nonbonded = (min == 0);
+ for (i = ac; --i >= 0;) {
+ int n = nBonded[i];
+ if (n < min || n > max)
+ bsResult.clear(i);
+ else if (nonbonded && n == 0)
+ bsResult.set(i);
+ }
+ return bsResult;
+ }
+
+
}
Modified: trunk/Jmol/src/org/jmol/modelset/Group.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Group.java 2015-01-28 00:19:08 UTC (rev
20250)
+++ trunk/Jmol/src/org/jmol/modelset/Group.java 2015-01-28 16:16:02 UTC (rev
20251)
@@ -110,10 +110,6 @@
return -1;
}
- public Group[] getGroups() {
- return null;
- }
-
public Object getStructure() {
return null;
}
@@ -165,6 +161,10 @@
return (seqcode == Integer.MIN_VALUE ? 0 : seqcode >>
SEQUENCE_NUMBER_SHIFT);
}
+ public void setResno(int i) {
+ seqcode = getSeqcodeFor(i, getInsertionCode());
+ }
+
public final static int getSeqNumberFor(int seqcode) {
return (haveSequenceNumber(seqcode)? seqcode >> SEQUENCE_NUMBER_SHIFT
: Integer.MAX_VALUE);
@@ -204,9 +204,7 @@
}
public char getInsertionCode() {
- if (seqcode == Integer.MIN_VALUE)
- return '\0';
- return (char)(seqcode & INSERTION_CODE_MASK);
+ return (seqcode == Integer.MIN_VALUE ? '\0' :(char)(seqcode &
INSERTION_CODE_MASK));
}
public static int getInsertionCodeFor(int seqcode) {
@@ -246,11 +244,6 @@
|| bsAdded != null && bsAdded.intersects(bs));
}
- boolean isHetero() {
- // just look at the first atom of the group
- return chain.getAtom(firstAtomIndex).isHetero();
- }
-
@Override
public String toString() {
return "[" + getGroup3() + "-" + getSeqcodeString() + "]";
Modified: trunk/Jmol/src/org/jmol/modelset/Model.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Model.java 2015-01-28 00:19:08 UTC (rev
20250)
+++ trunk/Jmol/src/org/jmol/modelset/Model.java 2015-01-28 16:16:02 UTC (rev
20251)
@@ -150,7 +150,7 @@
public int nAltLocs;
int nInsertions;
- int groupCount = -1;
+ public int groupCount = -1;
protected int chainCount = 0;
public Chain[] chains = new Chain[8];
@@ -212,15 +212,6 @@
return chainCount;
}
- public int getGroupCountHetero(boolean isHetero) {
- int n = 0;
- for (int i = chainCount; --i >= 0;)
- for (int j = chains[i].groupCount; --j >= 0;)
- if (chains[i].groups[j].isHetero() == isHetero)
- n++;
- return n;
- }
-
void calcSelectedGroupsCount(BS bsSelected) {
for (int i = chainCount; --i >= 0;)
chains[i].calcSelectedGroupsCount(bsSelected);
@@ -341,8 +332,8 @@
public void setStructureList(Map<STR, float[]> structureList) {
}
- public void getChimeInfo(SB sb, int nHetero) {
- getChimeInfoM(sb, nHetero);
+ public void getChimeInfo(SB sb) {
+ getChimeInfoM(sb, 0);
}
protected void getChimeInfoM(SB sb, int nHetero) {
@@ -360,15 +351,6 @@
//
}
- /**
- * @param bsConformation
- * @param conformationIndex
- * @return true for BioModel
- */
- public boolean getPdbConformation(BS bsConformation, int conformationIndex) {
- return false;
- }
-
public String getFullPDBHeader() {
return null;
}
@@ -529,4 +511,15 @@
// biomodel only
}
+ /**
+ * @param conformationIndex
+ * @param doSet
+ * @param bsAtoms
+ * @param bs
+ */
+ public void getConformation(int conformationIndex, boolean doSet, BS bsAtoms,
+ BS bs) {
+ // biomodel only
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-01-28 00:19:08 UTC
(rev 20250)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-01-28 16:16:02 UTC
(rev 20251)
@@ -984,7 +984,7 @@
*
* @return full array of groups in modelSet
*/
- public Group[] getGroups() {
+ Group[] getGroups() {
int n = 0;
for (int i = 0; i < mc; i++)
n += am[i].getGroupCount();
@@ -1379,28 +1379,11 @@
return bsAtoms;
}
- public BS getConformation(int modelIndex, int conformationIndex, boolean
doSet) {
+ public BS getConformation(int modelIndex, int conformationIndex, boolean
doSet, BS bsAtoms) {
BS bs = new BS();
for (int i = mc; --i >= 0;)
- if (i == modelIndex || modelIndex < 0) {
- String altLocs = getAltLocListInModel(i);
- int nAltLocs = getAltLocCountInModel(i);
- if (conformationIndex > 0 && conformationIndex >= nAltLocs)
- continue;
- BS bsConformation = vwr.getModelUndeletedAtomsBitSet(i);
- if (conformationIndex >= 0) {
- if (am[i].getPdbConformation(bsConformation, conformationIndex))
- for (int c = nAltLocs; --c >= 0;)
- if (c != conformationIndex)
- bsConformation.andNot(getAtomBitsMDa(T.spec_alternate,
- altLocs.substring(c, c + 1)));
- }
- if (bsConformation.nextSetBit(0) >= 0) {
- bs.or(bsConformation);
- if (doSet)
- am[i].setConformation(bsConformation);
- }
- }
+ if (i == modelIndex || modelIndex < 0)
+ am[i].getConformation(conformationIndex, doSet, bsAtoms, bs);
return bs;
}
@@ -2979,42 +2962,6 @@
return sb.toString();
}
- public BS getAtomsConnected(float min, float max, int intType, BS bs) {
- boolean isBonds = bs instanceof BondSet;
- BS bsResult = (isBonds ? new BondSet() : new BS());
- int[] nBonded = new int[ac];
- int i;
- boolean ishbond = (intType == Edge.BOND_HYDROGEN_MASK);
- boolean isall = (intType == Edge.BOND_ORDER_ANY);
- for (int ibond = 0; ibond < bondCount; ibond++) {
- Bond bond = bo[ibond];
- if (isall || bond.is(intType) || ishbond && bond.isHydrogen()) {
- if (isBonds) {
- bsResult.set(ibond);
- } else {
- if (bs.get(bond.atom1.i)) {
- nBonded[i = bond.atom2.i]++;
- bsResult.set(i);
- }
- if (bs.get(bond.atom2.i)) {
- nBonded[i = bond.atom1.i]++;
- bsResult.set(i);
- }
- }
- }
- }
- if (isBonds)
- return bsResult;
- boolean nonbonded = (min == 0);
- for (i = ac; --i >= 0;) {
- int n = nBonded[i];
- if (n < min || n > max)
- bsResult.clear(i);
- else if (nonbonded && n == 0)
- bsResult.set(i);
- }
- return bsResult;
- }
public SymmetryInterface getSymTemp(boolean forceNew) {
return (symTemp == null || forceNew ? (symTemp =
Interface.getSymmetry(vwr, "ms")) : symTemp);
}
@@ -3198,7 +3145,7 @@
BS bsBonds = new BS();
for (int i = bs.nextSetBit(0); i >= 0 && i < ac; i = bs
.nextSetBit(i + 1))
- at[i].deleteBonds(bsBonds);
+ at[i].delete(bsBonds);
for (int i = 0; i < mc; i++) {
am[i].bsAtomsDeleted.or(bs);
am[i].bsAtomsDeleted.and(am[i].bsAtoms);
@@ -3223,15 +3170,6 @@
if (vibrations != null)
for (int i = i0; i < ac; i++)
vibrations[i] = vibrations[map[i]];
- if (occupancies != null)
- for (int i = i0; i < ac; i++)
- occupancies[i] = occupancies[map[i]];
- if (bfactor100s != null)
- for (int i = i0; i < ac; i++)
- bfactor100s[i] = bfactor100s[map[i]];
- if (partialCharges != null)
- for (int i = i0; i < ac; i++)
- partialCharges[i] = partialCharges[map[i]];
if (atomTensorList != null) {
for (int i = i0; i < ac; i++) {
Object[] list = atomTensorList[i] = atomTensorList[map[i]];
@@ -3250,12 +3188,27 @@
if (atomTypes != null)
for (int i = i0; i < ac; i++)
atomTypes[i] = atomTypes[map[i]];
+
+ if (atomResnos != null)
+ for (int i = i0; i < ac; i++)
+ atomResnos[i] = atomResnos[map[i]];
if (atomSerials != null)
for (int i = i0; i < ac; i++)
atomSerials[i] = atomSerials[map[i]];
if (atomSeqIDs != null)
for (int i = i0; i < ac; i++)
atomSeqIDs[i] = atomSeqIDs[map[i]];
+
+ if (bfactor100s != null)
+ for (int i = i0; i < ac; i++)
+ bfactor100s[i] = bfactor100s[map[i]];
+
+ if (occupancies != null)
+ for (int i = i0; i < ac; i++)
+ occupancies[i] = occupancies[map[i]];
+ if (partialCharges != null)
+ for (int i = i0; i < ac; i++)
+ partialCharges[i] = partialCharges[map[i]];
}
protected void growAtomArrays(int newLength) {
@@ -3275,6 +3228,8 @@
atomNames = AU.arrayCopyS(atomNames, newLength);
if (atomTypes != null)
atomTypes = AU.arrayCopyS(atomTypes, newLength);
+ if (atomResnos != null)
+ atomResnos = AU.arrayCopyI(atomResnos, newLength);
if (atomSerials != null)
atomSerials = AU.arrayCopyI(atomSerials, newLength);
if (atomSeqIDs != null)
@@ -4067,16 +4022,20 @@
if (!setStructure)
return calculateStructuresAllExcept(bsModelsExcluded, asDSSP, doReport,
dsspIgnoreHydrogen, false, false);
- for (int i = 0; i < mc; i++)
- if (!bsModelsExcluded.get(i))
- am[i].clearBioPolymers();
- calculatePolymers(null, 0, 0, bsModelsExcluded);
+ recalculatePolymers(bsModelsExcluded);
String ret = calculateStructuresAllExcept(bsModelsExcluded, asDSSP,
doReport,
dsspIgnoreHydrogen, true, false);
vwr.shm.resetBioshapes(bsAllAtoms);
setStructureIndexes();
return ret;
}
+
+ public void recalculatePolymers(BS bsModelsExcluded) {
+ for (int i = 0; i < mc; i++)
+ if (!bsModelsExcluded.get(i))
+ am[i].clearBioPolymers();
+ calculatePolymers(getGroups(), -1, 0, bsModelsExcluded);
+ }
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-01-28 00:19:08 UTC
(rev 20250)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-01-28 16:16:02 UTC
(rev 20251)
@@ -135,7 +135,6 @@
else if (bioPolymers[i] instanceof AminoPolymer)
haveProt = true;
}
-
String s = "";
if (haveProt)
s += ((DSSPInterface) Interface.getOption("dssx.DSSP", ms.vwr, "ms"))
@@ -153,12 +152,36 @@
bioPolymers[i].setConformation(bsConformation);
}
+ /**
+ * @param conformationIndex
+ * @param bs
+ * @param bsSelected
+ */
@Override
- public boolean getPdbConformation(BS bsConformation, int conformationIndex) {
- if (nAltLocs > 0)
- for (int i = bioPolymerCount; --i >= 0;)
- bioPolymers[i].getConformation(bsConformation, conformationIndex);
- return true;
+ public void getConformation(int conformationIndex, boolean doSet, BS
bsSelected, BS bs) {
+ String altLocs = ms.getAltLocListInModel(modelIndex);
+ int nAltLocs = ms.getAltLocCountInModel(modelIndex);
+ if (conformationIndex > 0 && conformationIndex >= nAltLocs)
+ return;
+ BS bsConformation = ms.vwr.getModelUndeletedAtomsBitSet(modelIndex);
+ if (bsSelected != null)
+ bsConformation.and(bsSelected);
+ if (bsConformation.nextSetBit(0) < 0)
+ return;
+ if (conformationIndex >= 0) {
+ if (nAltLocs > 0)
+ for (int i = bioPolymerCount; --i >= 0;)
+ bioPolymers[i].getConformation(bsConformation, conformationIndex);
+ for (int c = nAltLocs; --c >= 0;)
+ if (c != conformationIndex)
+ bsConformation.andNot(ms.getAtomBitsMDa(T.spec_alternate,
+ altLocs.substring(c, c + 1)));
+ }
+ if (bsConformation.nextSetBit(0) >= 0) {
+ bs.or(bsConformation);
+ if (doSet)
+ setConformation(bsConformation);
+ }
}
@Override
@@ -283,55 +306,60 @@
@SuppressWarnings("incomplete-switch")
@Override
- public void getChimeInfo(SB sb, int nHetero) {
+ public void getChimeInfo(SB sb) {
int n = 0;
Model[] models = ms.am;
int modelCount = ms.mc;
int ac = ms.ac;
Atom[] atoms = ms.at;
- sb.append("\nMolecule name ....... "
- + ms.getInfoM("COMPND"));
+ sb.append("\nMolecule name ....... " + ms.getInfoM("COMPND"));
sb.append("\nSecondary Structure . PDB Data Records");
sb.append("\nBrookhaven Code ..... " + ms.modelSetName);
for (int i = modelCount; --i >= 0;)
n += models[i].getChainCount(false);
sb.append("\nNumber of Chains .... " + n);
- n = 0;
- for (int i = modelCount; --i >= 0;)
- n += models[i].getGroupCountHetero(false);
- nHetero = 0;
- for (int i = modelCount; --i >= 0;)
- nHetero += models[i].getGroupCountHetero(true);
- sb.append("\nNumber of Groups .... " + n);
- if (nHetero > 0)
- sb.append(" (" + nHetero + ")");
- for (int i = ac; --i >= 0;)
- if (atoms[i].isHetero())
- nHetero++;
- getChimeInfoM(sb, nHetero);
+ int ng = 0;
+ int ngHetero = 0;
+ int nHetero = 0;
+ Map<Group, Boolean> map = new Hashtable<Group, Boolean>();
int nH = 0;
int nS = 0;
int nT = 0;
int id;
int lastid = -1;
- for (int i = 0; i < ac; i++) {
- if (atoms[i].mi != 0)
- break;
- if ((id = atoms[i].group.getStrucNo()) != lastid && id != 0) {
- lastid = id;
- switch (atoms[i].group.getProteinStructureType()) {
- case HELIX:
- nH++;
- break;
- case SHEET:
- nS++;
- break;
- case TURN:
- nT++;
- break;
+ for (int i = ac; --i >= 0;) {
+ boolean isHetero = atoms[i].isHetero();
+ if (isHetero)
+ nHetero++;
+ Group g = atoms[i].group;
+ if (!map.containsKey(g)) {
+ map.put(g, Boolean.TRUE);
+ if (isHetero)
+ ngHetero++;
+ else
+ ng++;
+ }
+ if (atoms[i].mi == 0) {
+ if ((id = g.getStrucNo()) != lastid && id != 0) {
+ lastid = id;
+ switch (g.getProteinStructureType()) {
+ case HELIX:
+ nH++;
+ break;
+ case SHEET:
+ nS++;
+ break;
+ case TURN:
+ nT++;
+ break;
+ }
}
}
}
+ sb.append("\nNumber of Groups .... " + ng);
+ if (ngHetero > 0)
+ sb.append(" (" + ngHetero + ")");
+ getChimeInfoM(sb, nHetero);
sb.append("\nNumber of Helices ... " + nH);
sb.append("\nNumber of Strands ... " + nS);
sb.append("\nNumber of Turns ..... " + nT);
@@ -755,10 +783,8 @@
int groupCount, int baseGroupIndex,
BS modelsExcluded) {
boolean checkConnections = !ms.vwr.getBoolean(T.pdbsequential);
- if (groups == null) {
- groups = ms.getGroups();
+ if (groupCount < 0)
groupCount = groups.length;
- }
if (modelsExcluded != null)
for (int j = 0; j < groupCount; ++j) {
Group group = groups[j];
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2015-01-28 00:19:08 UTC
(rev 20250)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2015-01-28 16:16:02 UTC
(rev 20251)
@@ -164,8 +164,34 @@
public void getConformation(BS bsConformation, int conformationIndex) {
Atom[] atoms = model.getModelSet().at;
- for (int i = monomerCount; --i >= 0;)
- monomers[i].getConformation(atoms, bsConformation, conformationIndex);
+ for (int j = monomerCount; --j >= 0;) {
+ Monomer m = monomers[j];
+ //clear out bits that are not associated with the nth conformation
+ // counting for each residue from the beginning of the file listing
+
+ // A A
+ // A B
+ // A A
+ // B or B
+ // B A
+ // B B
+
+ char ch = '\0';
+ for (int i = m.firstAtomIndex, n = m.lastAtomIndex; i <= n; i++) {
+ Atom atom = atoms[i];
+ char altloc = atom.altloc;
+ // ignore atoms that have no designation
+ if (altloc == '\0')
+ continue;
+ // count down until we get the desired index into the list
+ if (conformationIndex >= 0 && altloc != ch) {
+ ch = altloc;
+ conformationIndex--;
+ }
+ if (conformationIndex < 0 && altloc != ch)
+ bsConformation.clear(i);
+ }
+ }
recalculateLeadMidpointsAndWingVectors();
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java 2015-01-28 00:19:08 UTC
(rev 20250)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java 2015-01-28 16:16:02 UTC
(rev 20251)
@@ -78,11 +78,6 @@
int monomerIndex;
- @Override
- public Group[] getGroups() {
- return bioPolymer.monomers;
- }
-
void setBioPolymer(BioPolymer polymer, int index) {
this.bioPolymer = polymer;
monomerIndex = index;
@@ -110,7 +105,7 @@
@Override
public int getAtomIndex(String name, int offset) {
- Group[] groups = getGroups();
+ Group[] groups = bioPolymer.monomers;
int ipt = monomerIndex + offset;
if (ipt >= 0 && ipt < groups.length) {
Group m = groups[ipt];
@@ -335,41 +330,6 @@
return (structure instanceof ProteinStructure ?
((ProteinStructure)structure).type.getBioStructureTypeName(false) : "");
}
- /**
- * clear out bits that are not associated with the nth conformation
- * counting for each residue from the beginning of the file listing
- *
- *
- * @param atoms
- * @param bsConformation
- * @param conformationIndex will be >= 0
- */
- void getConformation(Atom[] atoms, BS bsConformation, int conformationIndex)
{
-
- // A A
- // A B
- // A A
- // B or B
- // B A
- // B B
-
- char ch = '\0';
- for (int i = firstAtomIndex; i <= lastAtomIndex; i++) {
- Atom atom = atoms[i];
- char altloc = atom.altloc;
- // ignore atoms that have no designation
- if (altloc == '\0')
- continue;
- // count down until we get the desired index into the list
- if (conformationIndex >= 0 && altloc != ch) {
- ch = altloc;
- conformationIndex--;
- }
- if (conformationIndex < 0 && altloc != ch)
- bsConformation.clear(i);
- }
- }
-
final void updateOffsetsForAlternativeLocations(Atom[] atoms, BS bsSelected)
{
for (int offsetIndex = offsets.length; --offsetIndex >= 0;) {
int offset = offsets[offsetIndex] & 0xFF;
Modified: trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-01-28 00:19:08 UTC
(rev 20250)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-01-28 16:16:02 UTC
(rev 20251)
@@ -41,6 +41,7 @@
import org.jmol.modelset.ModelLoader;
import org.jmol.modelset.ModelSet;
import org.jmol.script.SV;
+import org.jmol.script.ScriptException;
import org.jmol.script.T;
import org.jmol.util.BSUtil;
import org.jmol.util.Edge;
@@ -282,7 +283,7 @@
for (int i = 0; i < nH; i++)
ms.addAtom(a.mi, a.group, 1, "H", null, 0, a.getSeqID(), 0, xyz,
Float.NaN, null, 0, 0, 1, 0, null, isHetero, (byte) 0, null)
- .deleteBonds(null);
+ .delete(null);
}
private void getBondInfo(JmolAdapter adapter, String group3, Object model) {
@@ -539,7 +540,7 @@
Atom atomO = bonds1[j].getOtherAtom(atom1);
if (atomO.getElementNumber() == 8) {
bsAddedHydrogens.set(atomH.i);
- atomH.deleteBonds(bsBondsDeleted);
+ atomH.delete(bsBondsDeleted);
break;
}
}
@@ -1733,6 +1734,88 @@
return (groupID == -1 ? addGroup3Name(group3) : groupID);
}
+ @Override
+ public boolean mutate(int iatom, String fileName) {
+ boolean b = vwr.getBoolean(T.appendnew);
+ Group g = vwr.ms.at[iatom].group;
+ //try {
+ // get the initial group -- protein for now
+ if (!(g instanceof AminoMonomer))
+ return false;
+ AminoMonomer res0 = (AminoMonomer) g;
+ int ac = vwr.ms.ac;
+ BS bsRes0 = new BS();
+ res0.selectAtoms(bsRes0);
+ int r = g.getResno();
+ // just use a script -- it is much easier!
+
+ String script = "try{var atoms0 = {*}\n"
+ + "var res0 = " + BS.escape(bsRes0,'(',')') + "\n"
+ + "set appendNew false\n"
+ + "load append \""+fileName+"\"\n"
+ + "set appendNew " + b + "\n"
+ + "var res1 = {!atoms0};var r1 = res1[1];var r0 = res1[0]\n"
+ + "if ({r1 & within(group, r0)}){"
+ + "var haveHs = ({_H and connected(res0)} != 0)\n"
+ + "if (!haveHs) {delete _H and res1}\n"
+ + "var sm = '[*.N][*.CA][*.C][*.O]'\n"
+ + "var keyatoms = res1.find(sm)\n"
+ + "var x = compare(res1,res0,sm,'BONDS')\n"
+ + "if(x){\n"
+ + "rotate branch @x 1\n"
+ + "compare res1 res0 SMARTS @sm rotate translate 0\n"
+ + "var N2 = {*.N and !res0 && connected(res0)}\n"
+ + "var C0 = {*.C and !res0 && connected(res0)}\n"
+ + "delete res0\n"
+ + "if (N2) {\n"
+ + "delete *.OXT and res1\n"
+ + "connect {N2} {res1 & *.C}\n"
+ + "}\n"
+ + "if (C0) {\n"
+ + "connect {C0} {res1 & *.N}\n"
+ + "}\n"
+ + "}\n"
+ + "}}catch(e){print e}\n";
+ try {
+ vwr.eval.runScript(script);
+ } catch (ScriptException e) {
+ // TODO
+ }
+ if (vwr.ms.ac == ac)
+ return false;
+ // check for protein monomer
+ g = vwr.ms.at[vwr.ms.ac - 1].group;
+ if (g != vwr.ms.at[ac + 1].group || !(g instanceof AminoMonomer)) {
+ BS bsAtoms = new BS();
+ g.selectAtoms(bsAtoms);
+ vwr.deleteAtoms(bsAtoms, false);
+ return false;
+ }
+ AminoMonomer res1 = (AminoMonomer) g;
+
+ // must get new group into old chain
+
+ Group[] groups = res0.chain.groups;
+ for (int i = groups.length; --i >= 0;)
+ if (groups[i] == res0) {
+ groups[i] = res1;
+ break;
+ }
+ res1.setResno(r);
+ res1.chain.groupCount = 0;
+ res1.chain = res0.chain;
+ BS bsExclude = BSUtil.newBitSet2(0, vwr.ms.mc);
+ bsExclude.clear(res1.chain.model.modelIndex);
+ res1.chain.model.groupCount = -1;
+ vwr.ms.recalculatePolymers(bsExclude);
+ //} catch (Exception e) {
+ // System.out.println("" + e);
+ // }
+ vwr.setBooleanProperty("appendNew", b);
+ return true;
+
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-01-28 00:19:08 UTC
(rev 20250)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-01-28 16:16:02 UTC
(rev 20251)
@@ -2518,6 +2518,7 @@
case T.mapproperty:
case T.minimize:
case T.modulation:
+ case T.mutate:
case T.data:
case T.navigate:
case T.plot:
Modified: trunk/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-01-28 00:19:08 UTC
(rev 20250)
+++ trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-01-28 16:16:02 UTC
(rev 20251)
@@ -1295,8 +1295,7 @@
case T.opGT:
return BSUtil.newBitSet2(ival + 1, ac);
case T.opEQ:
- return (ival < ac ? BSUtil.newBitSet2(
- ival, ival + 1) : new BS());
+ return (ival < ac ? BSUtil.newBitSet2(ival, ival + 1) : new BS());
case T.opNE:
default:
bs = BSUtil.setAll(ac);
@@ -1319,8 +1318,7 @@
case T.subsystem:
case T.configuration:
// these are all-inclusive; no need to do a by-atom comparison
- return BSUtil.copy(vwr.ms.getConformation(-1, ival - 1,
- false));
+ return BSUtil.copy(vwr.ms.getConformation(-1, ival - 1, false, null));
case T.symop:
propertyBitSet = atom.atomSymmetry;
if (propertyBitSet == null)
@@ -1360,8 +1358,7 @@
}
bitsetComparator = T.none;
if (symop < 0)
- ia = atom.getCellTranslation(ival, cellRange,
- nOps);
+ ia = atom.getCellTranslation(ival, cellRange, nOps);
else
ia = atom.getSymmetryTranslation(symop, cellRange, nOps);
} else if (nOps > 0) {
@@ -1370,8 +1367,7 @@
continue;
}
if (bitsetComparator == T.opNE) {
- if (ival > 0 && ival <= nOps
- && !propertyBitSet.get(ival)) {
+ if (ival > 0 && ival <= nOps && !propertyBitSet.get(ival)) {
bs.set(i);
}
continue;
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2015-01-28 00:19:08 UTC (rev
20250)
+++ trunk/Jmol/src/org/jmol/script/T.java 2015-01-28 16:16:02 UTC (rev
20251)
@@ -334,8 +334,9 @@
//public final static int model see mathfunc
//public final static int measure see mathfunc
public final static int move = scriptCommand | 32;
- public final static int moveto = scriptCommand | 34;
- public final static int navigate = scriptCommand | 35;
+ public final static int moveto = scriptCommand | 33;
+ public final static int mutate = scriptCommand | 34;
+ public final static int navigate = scriptCommand | 35;
//public final static int quaternion see mathfunc
public final static int parallel = flowCommand | 36;
public final static int plot = scriptCommand | 37;
@@ -604,7 +605,7 @@
public final static int molecule = intproperty | 16;
public final static int polymer = intproperty | 17;
public final static int polymerlength = intproperty | 18;
- public final static int resno = intproperty | 19;
+ public final static int resno = intproperty | 19 | settable;
public final static int seqid = intproperty | 20;
public final static int site = intproperty | 21;
public final static int strucno = intproperty | 22;
@@ -1756,6 +1757,7 @@
"modulation",
"move",
"moveTo",
+ "mutate",
"navigate",
"navigation",
"nbo",
@@ -2779,6 +2781,7 @@
modulation, // "modulation"
move, // "move"
moveto, // "moveTo"
+ mutate, // "mutate"
navigate, // "navigate"
-1, // "navigation"
nbo, // "nbo"
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-01-28 00:19:08 UTC
(rev 20250)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-01-28 16:16:02 UTC
(rev 20251)
@@ -158,6 +158,9 @@
case T.modulation:
modulation();
break;
+ case T.mutate:
+ mutate();
+ break;
case T.navigate:
navigate();
break;
@@ -934,22 +937,30 @@
private void configuration() throws ScriptException {
// if (!chk && vwr.getDisplayModelIndex() <= -2)
// error(ERROR_backgroundModelError, "\"CONFIGURATION\"");
- BS bsAtoms;
+ BS bsAtoms = null;
BS bsSelected = vwr.bsA();
if (slen == 1) {
+ // configuration
bsAtoms = vwr.ms.setConformation(bsSelected);
- vwr.ms.addStateScript("select", null, bsSelected, null,
- "configuration", true, false);
- } else {
- int n = intParameter(e.checkLast(1));
+ vwr.ms.addStateScript("select", null, bsSelected, null, "configuration",
+ true, false);
if (chk)
return;
- bsAtoms = vwr.ms.getConformation(vwr.am.cmi, n - 1,
- true);
- vwr.addStateScript("configuration " + n + ";", true, false);
+ } else {
+ int n;
+ if (isFloatParameter(1)) {
+ n = intParameter(e.checkLast(1));
+ if (chk)
+ return;
+ bsAtoms = vwr.ms.getConformation(vwr.am.cmi, n - 1, true, null);
+ vwr.addStateScript("configuration " + n + ";", true, false);
+ } else {
+ bsAtoms = atomExpressionAt(1);
+ n = intParameter(e.checkLast(e.iToken + 1));
+ vwr.addStateScript("configuration " + bsAtoms + " " + n + ";", true,
false);
+ bsAtoms = vwr.ms.getConformation(vwr.am.cmi, n - 1, true, bsAtoms);
+ }
}
- if (chk)
- return;
setShapeProperty(JC.SHAPE_STICKS, "type",
Integer.valueOf(Edge.BOND_HYDROGEN_MASK));
e.setShapeSizeBs(JC.SHAPE_STICKS, 0, bsAtoms);
@@ -1567,7 +1578,7 @@
}
}
- public void data() throws ScriptException {
+ private void data() throws ScriptException {
ScriptEval eval = e;
String dataString = null;
String dataLabel = null;
@@ -2175,7 +2186,25 @@
}
}
- public void navigate() throws ScriptException {
+ private void mutate() throws ScriptException {
+ // mutate {resno} "LYS" or "file identifier"
+ if (tokAt(1) == T.integer)
+ st[1] =T.o(T.string, "" + st[1].value); // allows @x
+ int iatom = atomExpressionAt(1).length() - 1;
+
+ // check for last model
+ if (iatom < 0 || vwr.ms.mc != vwr.ms.at[iatom].mi + 1)
+ return;
+ int i = ++e.iToken;
+ String group = e.optParameterAsString(e.checkLast(i));
+ if (chk)
+ return;
+ if (tokAt(i) != T.string)
+ group = "==" + group;
+ vwr.getJBR().mutate(iatom, group);
+ }
+
+ private void navigate() throws ScriptException {
/*
* navigation on/off navigation depth p # would be as a depth value, like
* slab, in percent, but could be negative navigation nSec translate X Y #
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-28 00:19:08 UTC
(rev 20250)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-28 16:16:02 UTC
(rev 20251)
@@ -12,13 +12,25 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-TODO: design and implement sidechain mutation -- MUTATE command ?
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
TODO: add 2D graphics panel for Ramachandran and NBO-style 2D graphics -- send
to browser as data uri?
+Jmol.___JmolVersion="14.3.12_2015.01.28"
-Jmol.___JmolVersion="14.3.12_2015.01.27"
+new feature: MUTATE command
+ -- replaces one amino acid group with another
+ -- can read from RCSB or from user-specified file
+ -- examples:
+ mutate 33 lys // uses last occurrence of resno=33
+ mutate @@3 arg // replaces group of atom 3 in current model
+ mutate @r @g // replaces resno in variable r with group in
variable g
+ mutate {r} his // same as above; r must be an atom selection
+ mutate 22 "myfile.cif" // user-defined replacement
+
+new feature: resno is user settable
+JmolVersion="14.3.12_2015.01.27"
+
bug fix: select thisModel does not select all atoms in visible frame set
new feature: @@3 for "atomno=3 and thisModel"
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-01-28 00:19:08 UTC
(rev 20250)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-01-28 16:16:02 UTC
(rev 20251)
@@ -41,6 +41,7 @@
import java.util.Arrays;
import java.util.Calendar;
+import java.util.Comparator;
import java.util.Date;
import java.util.Enumeration;
import java.util.Hashtable;
@@ -82,7 +83,7 @@
@J2SIgnoreImport({ javajs.util.XmlUtil.class })
-public class PropertyManager implements JmolPropertyManager {
+public class PropertyManager implements JmolPropertyManager,
Comparator<String> {
public PropertyManager() {
// required for reflection
@@ -1209,7 +1210,7 @@
return getChimeInfoA(vwr.ms.at, tok, bs);
}
SB sb = new SB();
- vwr.ms.am[0].getChimeInfo(sb, 0);
+ vwr.ms.am[0].getChimeInfo(sb);
return sb.appendC('\n').toString().substring(1);
}
@@ -1657,6 +1658,7 @@
int iModel = atoms[bs.nextSetBit(0)].mi;
int iModelLast = -1;
boolean isPQR = "PQR".equals(out.getType());
+ boolean isBiomodel = false;
String occTemp = "%6.2Q%6.2b ";
if (isPQR) {
occTemp = "%8.4P%7.4V ";
@@ -1675,21 +1677,23 @@
int lastAtomIndex = bs.length() - 1;
boolean showModels = (iModel != atoms[lastAtomIndex].mi);
SB sbCONECT = (showModels ? null : new SB());
+ SB sbATOMS = new SB();
boolean isMultipleBondPDB = models[iModel].isPdbWithMultipleBonds;
LabelToken[] tokens;
P3 ptTemp = new P3();
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
Atom a = atoms[i];
+ isBiomodel = models[a.mi].isBioModel;
if (showModels && a.mi != iModelLast) {
if (iModelLast != -1)
out.append("ENDMDL\n");
iModelLast = a.mi;
out.append("MODEL " + (iModelLast + 1) + "\n");
+ sbATOMS = new SB();
}
String sa = a.getAtomName();
boolean leftJustify = (a.getElementSymbol().length() == 2
|| sa.length() >= 4 || PT.isDigit(sa.charAt(0)));
- boolean isBiomodel = models[a.mi].isBioModel;
boolean isHetero = a.isHetero();
if (!isBiomodel)
tokens = (leftJustify ? LabelToken.compile(vwr,
@@ -1713,38 +1717,52 @@
"ATOM %5.-5i %-3.3a%1A%3.-3n %1c%4.-4R%1E %8.3x%8.3y%8.3z"
+ occTemp, '\0', null));
String XX = a.getElementSymbolIso(false).toUpperCase();
- out.append(LabelToken.formatLabelAtomArray(vwr, a, tokens, '\0', null,
ptTemp))
+ sbATOMS
+ .append(
+ LabelToken.formatLabelAtomArray(vwr, a, tokens, '\0', null,
+ ptTemp))
.append(XX.length() == 1 ? " " + XX : XX.substring(0, 2))
.append(" \n");
- if (!showModels && (!isBiomodel || isHetero || isMultipleBondPDB)) {
- Bond[] bonds = a.bonds;
- if (bonds != null)
- for (int j = 0; j < bonds.length; j++) {
- int iThis = a.getAtomNumber();
- Atom a2 = bonds[j].getOtherAtom(a);
- if (!bs.get(a2.i))
- continue;
- int n = bonds[j].getCovalentOrder();
- if (n == 1 && isMultipleBondPDB && !isHetero)
- continue;
- int iOther = a2.getAtomNumber();
- switch (n) {
- case 2:
- case 3:
- if (iOther < iThis)
- continue; // only one entry in this case -- pseudo-PDB style
- //$FALL-THROUGH$
- case 1:
- sbCONECT.append("CONECT").append(
- PT.formatStringI("%5i", "i", iThis));
- for (int k = 0; k < n; k++)
- sbCONECT.append(PT.formatStringI("%5i", "i", iOther));
- sbCONECT.appendC('\n');
- break;
+ }
+ boolean doConnect = (!showModels && isBiomodel);
+ Map<Integer, Integer> map = (doConnect ? new Hashtable<Integer, Integer>()
: null);
+ String sAtoms = fixPDBFormat(sbATOMS.toString(), map);
+ if (doConnect) {
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ Atom a = atoms[i];
+ boolean isHetero = a.isHetero();
+ if (isHetero || isMultipleBondPDB) {
+ Bond[] bonds = a.bonds;
+ if (bonds != null)
+ for (int j = 0; j < bonds.length; j++) {
+ int iThis = a.getAtomNumber();
+ Atom a2 = bonds[j].getOtherAtom(a);
+ if (!bs.get(a2.i))
+ continue;
+ int n = bonds[j].getCovalentOrder();
+ if (n == 1 && isMultipleBondPDB && !isHetero)
+ continue;
+ int iOther = a2.getAtomNumber();
+ switch (n) {
+ case 2:
+ case 3:
+ if (iOther < iThis)
+ continue; // only one entry in this case -- pseudo-PDB style
+ //$FALL-THROUGH$
+ case 1:
+ sbCONECT.append("CONECT").append(
+ PT.formatStringI("%5i", "i",
map.get(Integer.valueOf(iThis)).intValue()));
+ String s = PT.formatStringI("%5i", "i",
map.get(Integer.valueOf(iOther)).intValue());
+ for (int k = 0; k < n; k++)
+ sbCONECT.append(s);
+ sbCONECT.appendC('\n');
+ break;
+ }
}
- }
+ }
}
}
+ out.append(sAtoms);
if (showModels)
out.append("ENDMDL\n");
else
@@ -1752,6 +1770,38 @@
return out.toString();
}
+ /**
+ * must re-order by resno and then renumber atoms
+ * @param s
+ * @param map
+ * @return fixed string
+ */
+ private String fixPDBFormat(String s, Map<Integer, Integer> map) {
+ String[] lines = PT.split(s, "\n");
+ Arrays.sort(lines, this);
+ SB sb = new SB();
+ for (int i = 0; i < lines.length; i++) {
+ s = lines[i];
+ int p = PT.parseInt(lines[i].substring(6, 12));
+ if (map != null)
+ map.put(Integer.valueOf(p), Integer.valueOf(i));
+ String si = " " + (i + 1);
+ sb.append(s.substring(0, 6))
+ .append(si.substring(si.length() - 5))
+ .append(s.substring(11)).append("\n");
+ }
+ return sb.toString();
+ }
+
+ @Override
+ public int compare(String s1, String s2) {
+ int atA = PT.parseInt(s1.substring(6, 12));
+ int atB = PT.parseInt(s2.substring(6, 12));
+ int resA = PT.parseInt(s1.substring(22, 26));
+ int resB = PT.parseInt(s2.substring(22, 26));
+ return (resA < resB ? -1 : resA > resB ? 1 : atA < atB ? -1
+ : atA > atB ? 1 : 0);
+ }
/* **********************
*
* Jmol Data Frame methods
@@ -1941,4 +1991,35 @@
return sb.toString();
}
+ @Override
+ public String getCoordinateFileData(String atomExpression, String type) {
+ String exp = "";
+ if (type.equalsIgnoreCase("MOL") || type.equalsIgnoreCase("SDF")
+ || type.equalsIgnoreCase("V2000") || type.equalsIgnoreCase("V3000")
+ || type.equalsIgnoreCase("XYZVIB") || type.equalsIgnoreCase("CD") ||
type.equalsIgnoreCase("JSON"))
+ return vwr.getModelExtract(atomExpression, false, false, type);
+ if (type.toLowerCase().indexOf("property_") == 0)
+ exp = "{selected}.label(\"%{" + type + "}\")";
+ else if (type.equalsIgnoreCase("CML"))
+ return getModelCml(vwr.getAtomBitSet(atomExpression), Integer.MAX_VALUE,
true);
+ else if (type.equalsIgnoreCase("PDB"))
+ // very crude - no connections -- not used
+ exp = "{selected and not hetero}.label(\"ATOM %5i %-4a%1A%3.3n
%1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e \").lines"
+ + "+{selected and hetero}.label(\"HETATM%5i %-4a%1A%3.3n
%1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e \").lines";
+ else if (type.equalsIgnoreCase("XYZRN"))
+ exp = "\"\" + {selected}.size + \"\n\n\"+{selected}.label(\"%-2e %8.3x
%8.3y %8.3z %4.2[vdw] 1 [%n]%r.%a#%i\").lines";
+ else if (type.startsWith("USER:"))
+ exp = "{selected}.label(\"" + type.substring(5) + "\").lines";
+ else
+ // if(type.equals("XYZ"))
+ exp = "\"\" + {selected}.size + \"\n\n\"+{selected}.label(\"%-2e %10.5x
%10.5y %10.5z\").lines";
+ if (!atomExpression.equals("selected"))
+ exp = PT.rep(exp, "selected", atomExpression);
+ String s = (String) vwr.evaluateExpression(exp);
+ if (type.equalsIgnoreCase("PDB"))
+ s = fixPDBFormat(s, null);
+ return s;
+ }
+
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-01-28 00:19:08 UTC
(rev 20250)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-01-28 16:16:02 UTC
(rev 20251)
@@ -1539,6 +1539,8 @@
BS[] tainted = vwr.ms.tainted;
if (bs != null)
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ if (atoms[i].isDeleted())
+ continue;
s.appendI(i + 1).append(" ").append(atoms[i].getElementSymbol())
.append(" ").append(atoms[i].getInfo().replace(' ', '_')).append(
" ");
@@ -1551,6 +1553,9 @@
case AtomCollection.TAINT_ATOMNO:
s.appendI(atoms[i].getAtomNumber());
break;
+ case AtomCollection.TAINT_RESNO:
+ s.appendI(atoms[i].group.getResno());
+ break;
case AtomCollection.TAINT_SEQID:
s.appendI(atoms[i].getSeqID());
break;
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-01-28 00:19:08 UTC (rev
20250)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-01-28 16:16:02 UTC (rev
20251)
@@ -7166,29 +7166,7 @@
@Override
public String getData(String atomExpression, String type) {
- String exp = "";
- if (type.equalsIgnoreCase("MOL") || type.equalsIgnoreCase("SDF")
- || type.equalsIgnoreCase("V2000") || type.equalsIgnoreCase("V3000")
- || type.equalsIgnoreCase("XYZVIB") || type.equalsIgnoreCase("CD") ||
type.equalsIgnoreCase("JSON"))
- return getModelExtract(atomExpression, false, false, type);
- if (type.toLowerCase().indexOf("property_") == 0)
- exp = "{selected}.label(\"%{" + type + "}\")";
- else if (type.equalsIgnoreCase("CML"))
- return getModelCml(getAtomBitSet(atomExpression), Integer.MAX_VALUE,
true);
- else if (type.equalsIgnoreCase("PDB"))
- // old crude
- exp = "{selected and not hetero}.label(\"ATOM %5i %-4a%1A%3.3n
%1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e \").lines"
- + "+{selected and hetero}.label(\"HETATM%5i %-4a%1A%3.3n %1c%4R%1E
%8.3x%8.3y%8.3z%6.2Q%6.2b %2e \").lines";
- else if (type.equalsIgnoreCase("XYZRN"))
- exp = "\"\" + {selected}.size + \"\n\n\"+{selected}.label(\"%-2e %8.3x
%8.3y %8.3z %4.2[vdw] 1 [%n]%r.%a#%i\").lines";
- else if (type.startsWith("USER:"))
- exp = "{selected}.label(\"" + type.substring(5) + "\").lines";
- else
- // if(type.equals("XYZ"))
- exp = "\"\" + {selected}.size + \"\n\n\"+{selected}.label(\"%-2e %10.5x
%10.5y %10.5z\").lines";
- if (!atomExpression.equals("selected"))
- exp = PT.rep(exp, "selected", atomExpression);
- return (String) evaluateExpression(exp);
+ return getPropertyManager().getCoordinateFileData(atomExpression, type);
}
public String getModelCml(BS bs, int nAtomsMax, boolean addBonds) {
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/NBODialog.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/NBODialog.java
2015-01-28 00:19:08 UTC (rev 20250)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/NBODialog.java
2015-01-28 16:16:02 UTC (rev 20251)
@@ -326,7 +326,11 @@
public void nboReport(String s) {
nboOutput.setText(s == null ? "" : nboOutput.getText() + s + "\n");
- editPane2.getVerticalScrollBar().setValue(Integer.MAX_VALUE);
+ try {
+ editPane2.getVerticalScrollBar().setValue(Integer.MAX_VALUE);
+ } catch (Exception e) {
+ //
+ }
}
protected void modelCmd() {
Modified:
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
2015-01-28 00:19:08 UTC (rev 20250)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
2015-01-28 16:16:02 UTC (rev 20251)
@@ -877,7 +877,12 @@
pt = caretPosition.getOffset();
consoleTextPane.setCaretPosition(pt);
- vBar.setValue(Integer.MAX_VALUE);
+ try {
+ vBar.setValue(Integer.MAX_VALUE);
+ } catch (Exception e) {
+ //
+ }
+
} catch (Exception e) {
e.printStackTrace();
consoleTextPane.setCaretPosition(getLength());
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