Revision: 20248
http://sourceforge.net/p/jmol/code/20248
Author: hansonr
Date: 2015-01-27 22:09:31 +0000 (Tue, 27 Jan 2015)
Log Message:
-----------
atom cleanup; singleton group fix
Modified Paths:
--------------
trunk/Jmol/examples/basic/org/jmol/Export.java
trunk/Jmol/src/org/jmol/api/JmolScriptEvaluator.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/Chain.java
trunk/Jmol/src/org/jmol/modelset/LabelToken.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/ScriptExpr.java
trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/ColorManager.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/examples/basic/org/jmol/Export.java
===================================================================
--- trunk/Jmol/examples/basic/org/jmol/Export.java 2015-01-27 14:21:02 UTC
(rev 20247)
+++ trunk/Jmol/examples/basic/org/jmol/Export.java 2015-01-27 22:09:31 UTC
(rev 20248)
@@ -85,6 +85,7 @@
case HOVER:
case MEASURE:
case MINIMIZATION:
+ case SERVICE:
case RESIZE:
case SYNC:
case STRUCTUREMODIFIED:
Modified: trunk/Jmol/src/org/jmol/api/JmolScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolScriptEvaluator.java 2015-01-27
14:21:02 UTC (rev 20247)
+++ trunk/Jmol/src/org/jmol/api/JmolScriptEvaluator.java 2015-01-27
22:09:31 UTC (rev 20248)
@@ -89,8 +89,6 @@
boolean historyDisabled, boolean listCommands,
SB outputBuffer, boolean allowThreads);
- Map<String, Object> getDefinedAtomSets();
-
String setObjectPropSafe(String id, int tokCommand);
void stopScriptThreads();
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2015-01-27 14:21:02 UTC (rev
20247)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2015-01-27 22:09:31 UTC (rev
20248)
@@ -38,7 +38,6 @@
import org.jmol.atomdata.RadiusData;
import org.jmol.atomdata.RadiusData.EnumType;
import org.jmol.c.PAL;
-import org.jmol.c.STR;
import org.jmol.c.VDW;
import org.jmol.java.BS;
import org.jmol.script.T;
@@ -437,9 +436,8 @@
}
public void setValence(int nBonds) {
- if (isDeleted()) // no resurrection
- return;
- valence = (byte) (nBonds < 0 ? 0 : nBonds < 0xEF ? nBonds : 0xEF);
+ if (!isDeleted()) // no resurrection
+ valence = (byte) (nBonds < 0 ? 0 : nBonds < 0xEF ? nBonds : 0xEF);
}
@Override
@@ -571,10 +569,6 @@
return atomSite;
}
- void setGroup(Group group) {
- this.group = group;
- }
-
@Override
public void getGroupBits(BS bs) {
group.selectAtoms(bs);
@@ -886,7 +880,7 @@
info.append("[");
info.append(group3);
info.append("]");
- String seqcodeString = getSeqcodeString();
+ String seqcodeString = group.getSeqcodeString();
if (seqcodeString != null)
info.append(seqcodeString);
int chainID = getChainID();
@@ -969,10 +963,6 @@
return group.isPyrimidine();
}
- int getSeqcode() {
- return group.seqcode;
- }
-
@Override
public int getResno() {
return group.getResno();
@@ -1031,10 +1021,6 @@
return group.isLeadAtom(i);
}
- public float getGroupParameter(int tok) {
- return group.getGroupParameter(tok);
- }
-
@Override
public int getChainID() {
return group.chain.chainID;
@@ -1065,38 +1051,10 @@
return group.chain.model.ms.getModulationCoord(i, ch);
}
- public int getPolymerLength() {
- return group.getBioPolymerLength();
- }
-
- public int getPolymerIndexInModel() {
- return group.getBioPolymerIndexInModel();
- }
-
- public int getMonomerIndex() {
- return group.getMonomerIndex();
- }
-
- public int getSelectedGroupCountWithinChain() {
- return group.chain.selectedGroupCount;
- }
-
- public int getSelectedGroupIndexWithinChain() {
+ public int getSelectedGroupIndex() {
return group.getSelectedGroupIndex();
}
- public int getSelectedMonomerCountWithinPolymer() {
- return group.getSelectedMonomerCount();
- }
-
- public int getSelectedMonomerIndexWithinPolymer() {
- return group.getSelectedMonomerIndex();
- }
-
- public Chain getChain() {
- return group.chain;
- }
-
public String getModelNumberForLabel() {
return group.chain.model.ms.getModelNumberForAtomLabel(mi);
}
@@ -1107,41 +1065,9 @@
@Override
public String getBioStructureTypeName() {
- return getProteinStructureType().getBioStructureTypeName(true);
+ return group.getProteinStructureType().getBioStructureTypeName(true);
}
- public STR getProteinStructureType() {
- return group.getProteinStructureType();
- }
-
- public STR getProteinStructureSubType() {
- return group.getProteinStructureSubType();
- }
-
- public int getStrucNo() {
- return group.getStrucNo();
- }
-
- public String getStructureId() {
- return group.getStructureId();
- }
-
- public String getProteinStructureTag() {
- return group.getProteinStructureTag();
- }
-
- public short getGroupID() {
- return group.groupID;
- }
-
- public String getSeqcodeString() {
- return group.getSeqcodeString();
- }
-
- public char getInsertionCode() {
- return group.getInsertionCode();
- }
-
@Override
public boolean equals(Object obj) {
return (this == obj);
@@ -1202,7 +1128,7 @@
case T.formalcharge:
return getFormalCharge();
case T.groupid:
- return getGroupID(); //-1 if no group
+ return group.groupID; //-1 if no group
case T.groupindex:
return group.groupIndex;
case T.model:
@@ -1221,7 +1147,7 @@
case T.polymer:
return group.getBioPolymerIndexInModel() + 1;
case T.polymerlength:
- return getPolymerLength();
+ return group.getBioPolymerLength();
case T.radius:
// the comparator uses rasmol radius, unfortunately, for integers
return getRasMolRadius();
@@ -1230,11 +1156,11 @@
case T.site:
return getAtomSite();
case T.structure:
- return getProteinStructureType().getId();
+ return group.getProteinStructureType().getId();
case T.substructure:
- return getProteinStructureSubType().getId();
+ return group.getProteinStructureSubType().getId();
case T.strucno:
- return getStrucNo();
+ return group.getStrucNo();
case T.symop:
return getSymOp();
case T.valence:
@@ -1296,7 +1222,7 @@
case T.eta:
case T.theta:
case T.straightness:
- return getGroupParameter(tokWhat);
+ return group.getGroupParameter(tokWhat);
case T.fracx:
return getFractionalCoord(!vwr.g.legacyJavaFloat, 'X', true, ptTemp);
case T.fracy:
@@ -1339,7 +1265,7 @@
}
}
}
- return getGroupParameter(tokWhat);
+ return group.getGroupParameter(tokWhat);
case T.radius:
case T.spacefill:
return getRadius();
@@ -1430,7 +1356,7 @@
case T.identify:
return getIdentity(true);
case T.insertion:
- ch = getInsertionCode();
+ ch = group.getInsertionCode();
return (ch == '\0' ? "" : "" + ch);
case T.label:
case T.format:
@@ -1439,11 +1365,11 @@
s = "";
return s;
case T.structure:
- return getProteinStructureType().getBioStructureTypeName(false);
+ return group.getProteinStructureType().getBioStructureTypeName(false);
case T.substructure:
- return getProteinStructureSubType().getBioStructureTypeName(false);
+ return group.getProteinStructureSubType().getBioStructureTypeName(false);
case T.strucid:
- return getStructureId();
+ return group.getStructureId();
case T.shape:
return vwr.getHybridizationAndAxes(i, null, null, "d");
case T.symbol:
@@ -1482,10 +1408,6 @@
return null;
}
- boolean isWithinStructure(STR type) {
- return group.isWithinStructure(type);
- }
-
@Override
public int getOffsetResidueAtom(String name, int offset) {
return group.getAtomIndex(name, offset);
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-01-27
14:21:02 UTC (rev 20247)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-01-27
22:09:31 UTC (rev 20248)
@@ -857,7 +857,7 @@
if (hydrophobicities == null) {
hydrophobicities = new float[at.length];
for (int i = 0; i < at.length; i++)
- hydrophobicities[i] = Elements.getHydrophobicity(at[i].getGroupID());
+ hydrophobicities[i] = Elements.getHydrophobicity(at[i].group.groupID);
}
hydrophobicities[atomIndex] = value;
return true;
@@ -2073,6 +2073,11 @@
if (at[i].getAtomNumber() == iSpec)
bs.set(i);
break;
+ case T.bonded:
+ for (i = ac; --i >= 0;)
+ if (at[i].getCovalentBondCount() > 0)
+ bs.set(i);
+ break;
case T.atomname:
String names = "," + specInfo + ",";
for (i = ac; --i >= 0;) {
@@ -2093,7 +2098,7 @@
break;
case T.spec_resid:
for (i = ac; --i >= 0;)
- if (at[i].getGroupID() == iSpec)
+ if (at[i].group.groupID == iSpec)
bs.set(i);
break;
case T.spec_chain:
@@ -2130,7 +2135,7 @@
STR type = (tokType == T.helix ? STR.HELIX
: STR.SHEET);
for (i = ac; --i >= 0;)
- if (at[i].isWithinStructure(type))
+ if (at[i].group.isWithinStructure(type))
bs.set(i);
break;
case T.nucleic:
@@ -2240,7 +2245,7 @@
case T.chain:
bsInfo = BSUtil.copy((BS) specInfo);
for (i = bsInfo.nextSetBit(0); i >= 0; i = bsInfo.nextSetBit(i + 1)) {
- Chain chain = at[i].getChain();
+ Chain chain = at[i].group.chain;
chain.setAtomBitSet(bs);
bsInfo.andNot(bs);
}
@@ -2249,15 +2254,15 @@
for (i = i0; i >= 0; i = bsInfo.nextSetBit(i+1)) {
if (bs.get(i))
continue;
- iPolymer = at[i].getPolymerIndexInModel();
+ iPolymer = at[i].group.getBioPolymerIndexInModel();
bs.set(i);
for (int j = i; --j >= 0;)
- if (at[j].getPolymerIndexInModel() == iPolymer)
+ if (at[j].group.getBioPolymerIndexInModel() == iPolymer)
bs.set(j);
else
break;
for (; ++i < ac;)
- if (at[i].getPolymerIndexInModel() == iPolymer)
+ if (at[i].group.getBioPolymerIndexInModel() == iPolymer)
bs.set(i);
else
break;
@@ -2298,7 +2303,7 @@
int[] hs = new int[2];
Atom a;
for (int i = ac; --i >= 0;) {
- int g = at[i].getGroupID();
+ int g = at[i].group.groupID;
if (g >= JC.GROUPID_WATER && g < JC.GROUPID_SOLVENT_MIN) {
bs.set(i);
} else if ((a = at[i]).getElementNumber() == 8 &&
a.getCovalentBondCount() == 2) {
@@ -2463,7 +2468,7 @@
switch (insCode) {
case '?':
for (int i = ac; --i >= 0;) {
- int atomSeqcode = at[i].getSeqcode();
+ int atomSeqcode = at[i].group.seqcode;
if (!haveSeqNumber
|| seqNum == Group.getSeqNumberFor(atomSeqcode)
&& Group.getInsertionCodeFor(atomSeqcode) != 0) {
@@ -2474,7 +2479,7 @@
break;
default:
for (int i = ac; --i >= 0;) {
- int atomSeqcode = at[i].getSeqcode();
+ int atomSeqcode = at[i].group.seqcode;
if (seqcode == atomSeqcode ||
!haveSeqNumber && seqcode ==
Group.getInsertionCodeFor(atomSeqcode)
|| insCode == '*' && seqNum == Group.getSeqNumberFor(atomSeqcode))
{
@@ -2494,7 +2499,7 @@
BS bsDone = BS.newN(ac);
int id;
for (int i = bsDone.nextClearBit(0); i < ac; i = bsDone.nextClearBit(i +
1)) {
- Chain chain = at[i].getChain();
+ Chain chain = at[i].group.chain;
if (chainID == (id = chain.chainID) || !caseSensitive
&& id >= 0 && id < 300 && chainID == chainToUpper(id)) {
chain.setAtomBitSet(bs);
@@ -2795,6 +2800,15 @@
//{*}.vxyz = {*}.vxyz.all.mul(3.0/{*}.vxyz.all.max)
}
+ public BS getAtomsFromAtomNumberInFrame(int atomNumber) {
+ BS bs = vwr.getFrameAtoms();
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ if (at[i].getAtomNumber() != atomNumber)
+ bs.clear(i);
+ return bs;
+ }
+
+
}
Modified: trunk/Jmol/src/org/jmol/modelset/Chain.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Chain.java 2015-01-27 14:21:02 UTC (rev
20247)
+++ trunk/Jmol/src/org/jmol/modelset/Chain.java 2015-01-27 22:09:31 UTC (rev
20248)
@@ -34,7 +34,7 @@
public int groupCount;
public Group[] groups;
- int selectedGroupCount;
+ public int selectedGroupCount;
public Atom getAtom(int index) {
return model.ms.at[index];
Modified: trunk/Jmol/src/org/jmol/modelset/LabelToken.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/LabelToken.java 2015-01-27 14:21:02 UTC
(rev 20247)
+++ trunk/Jmol/src/org/jmol/modelset/LabelToken.java 2015-01-27 22:09:31 UTC
(rev 20248)
@@ -549,7 +549,7 @@
: formalCharge < 0 ? "" + -formalCharge + "-" : "");
break;
case 'g':
- strT = "" + atom.getSelectedGroupIndexWithinChain();
+ strT = "" + atom.getSelectedGroupIndex();
break;
case T.model:
strT = atom.getModelNumberForLabel();
@@ -567,17 +567,17 @@
floatT = atom.atomPropertyFloat(vwr, t.tok, ptTemp);
break;
case 'r':
- strT = atom.getSeqcodeString();
+ strT = atom.group.getSeqcodeString();
break;
case T.strucid:
- strT = atom.getStructureId();
+ strT = atom.group.getStructureId();
break;
case T.strucno:
- int id = atom.getStrucNo();
+ int id = atom.group.getStrucNo();
strT = (id <= 0 ? "" : "" + id);
break;
case T.straightness:
- if (Float.isNaN(floatT = atom.getGroupParameter(T.straightness)))
+ if (Float.isNaN(floatT = atom.group.getGroupParameter(T.straightness)))
strT = "null";
break;
case T.vibx:
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-01-27 14:21:02 UTC
(rev 20247)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-01-27 22:09:31 UTC
(rev 20248)
@@ -1228,8 +1228,8 @@
groups[groupIndex] = group;
group.groupIndex = groupIndex;
- for (int i = lastAtomIndex; --i >= firstAtomIndex;)
- ms.at[i].setGroup(group);
+ for (int i = lastAtomIndex + 1; --i >= firstAtomIndex;)
+ ms.at[i].group = group;
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-01-27 14:21:02 UTC
(rev 20247)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-01-27 22:09:31 UTC
(rev 20248)
@@ -1342,7 +1342,7 @@
i = am[modelIndex].firstAtomIndex + am[modelIndex].ac;
continue;
}
- iLast = at[i].getStrucNo();
+ iLast = at[i].group.getStrucNo();
if (iLast < 1000 && iLast > lastStrucNo[modelIndex])
lastStrucNo[modelIndex] = iLast;
i = at[i].group.lastAtomIndex + 1;
@@ -1353,7 +1353,7 @@
i = am[modelIndex].firstAtomIndex + am[modelIndex].ac;
continue;
}
- if (at[i].getStrucNo() > 1000)
+ if (at[i].group.getStrucNo() > 1000)
at[i].group.setStrucNo(++lastStrucNo[modelIndex]);
i = at[i].group.lastAtomIndex + 1;
}
@@ -2929,7 +2929,7 @@
lastmodel = imodel;
lastid = -1;
}
- if ((id = at[i].getStrucNo()) != lastid && id != 0) {
+ if ((id = at[i].group.getStrucNo()) != lastid && id != 0) {
at[i].group.setStrucNo(++idnew);
lastid = idnew;
}
@@ -4079,21 +4079,5 @@
return ret;
}
- public BS getAtomsFromAtomNumberInFrame(int atomNumber) {
- BS bs = new BS();
- BS bsModels = vwr.getVisibleFramesBitSet();
- for (int i = ac; --i >= 0;) {
- Atom atom = at[i];
- if (!bsModels.get(atom.mi)) {
- i = am[atom.mi].firstAtomIndex;
- continue;
- }
- if (atom.getAtomNumber() == atomNumber)
- bs.set(i);
- }
- return bs;
- }
-
-
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java 2015-01-27
14:21:02 UTC (rev 20247)
+++ trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java 2015-01-27
22:09:31 UTC (rev 20248)
@@ -220,8 +220,8 @@
int[][] biopolymerStartsEnds = new int[nBiopolymers][nEndMin * 2];
for (int i = 0; i < n; i++) {
a1 = vCA.get(i);
- int polymerIndex = a1.getPolymerIndexInModel();
- int monomerIndex = a1.getMonomerIndex();
+ int polymerIndex = a1.group.getBioPolymerIndexInModel();
+ int monomerIndex = a1.group.getMonomerIndex();
int bpt = monomerIndex;
if (bpt < nEndMin)
biopolymerStartsEnds[polymerIndex][bpt] = i + 1;
@@ -244,9 +244,9 @@
int ipt = strutPoint(i, j, n);
a2 = vCA.get(j);
int resno1 = a1.getResno();
- int polymerIndex1 = a1.getPolymerIndexInModel();
+ int polymerIndex1 = a1.group.getBioPolymerIndexInModel();
int resno2 = a2.getResno();
- int polymerIndex2 = a2.getPolymerIndexInModel();
+ int polymerIndex2 = a2.group.getBioPolymerIndexInModel();
if (polymerIndex1 == polymerIndex2 && Math.abs(resno2 - resno1) <
delta)
bsNearbyResidues.set(ipt);
float d = d2[ipt] = a1.distanceSquared(a2);
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-01-27 14:21:02 UTC
(rev 20247)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-01-27 22:09:31 UTC
(rev 20248)
@@ -317,9 +317,9 @@
for (int i = 0; i < ac; i++) {
if (atoms[i].mi != 0)
break;
- if ((id = atoms[i].getStrucNo()) != lastid && id != 0) {
+ if ((id = atoms[i].group.getStrucNo()) != lastid && id != 0) {
lastid = id;
- switch (atoms[i].getProteinStructureType()) {
+ switch (atoms[i].group.getProteinStructureType()) {
case HELIX:
nH++;
break;
@@ -615,7 +615,7 @@
if (taintedOnly && !bsTainted.get(i))
continue;
id = 0;
- if (i == ac || (id = atoms[i].getStrucNo()) != lastId) {
+ if (i == ac || (id = atoms[i].group.getStrucNo()) != lastId) {
if (bs != null) {
switch (type) {
case HELIX:
@@ -711,8 +711,8 @@
if (id == 0
|| bsAtoms != null
&& needPhiPsi
- && (Float.isNaN(atoms[i].getGroupParameter(T.phi)) || Float
- .isNaN(atoms[i].getGroupParameter(T.psi))))
+ && (Float.isNaN(atoms[i].group.getGroupParameter(T.phi)) || Float
+ .isNaN(atoms[i].group.getGroupParameter(T.psi))))
continue;
}
String ch = atoms[i].getChainIDStr();
@@ -722,9 +722,9 @@
group1 = atoms[i].getGroup3(false);
chain1 = ch;
}
- type = atoms[i].getProteinStructureType();
- subtype = atoms[i].getProteinStructureSubType();
- sid = atoms[i].getProteinStructureTag();
+ type = atoms[i].group.getProteinStructureType();
+ subtype = atoms[i].group.getProteinStructureSubType();
+ sid = atoms[i].group.getProteinStructureTag();
bs.set(i);
lastId = id;
res2 = atoms[i].getResno();
@@ -850,7 +850,7 @@
for (int i = bsCheck.nextSetBit(0); i >= 0; i = bsCheck.nextSetBit(i + 1))
if (atoms[i].checkVisible()
&& atoms[i].atomID == JC.ATOMID_ALPHA_CARBON
- && atoms[i].getGroupID() != JC.GROUPID_CYSTEINE)
+ && atoms[i].group.groupID != JC.GROUPID_CYSTEINE)
vCA.addLast((a1 = atoms[i]));
if (vCA.size() == 0)
return 0;
@@ -858,7 +858,7 @@
short mad = (short) (vwr.getFloat(T.strutdefaultradius) * 2000);
int delta = vwr.getInt(T.strutspacing);
boolean strutsMultiple = vwr.getBoolean(T.strutsmultiple);
- Lst<Atom[]> struts = ((BioModel)
m).getBioPolymer(a1.getPolymerIndexInModel())
+ Lst<Atom[]> struts = ((BioModel)
m).getBioPolymer(a1.group.getBioPolymerIndexInModel())
.calculateStruts(ms, bs1, bs2, vCA, thresh, delta, strutsMultiple);
for (int i = 0; i < struts.size(); i++) {
Atom[] o = struts.get(i);
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2015-01-27 14:21:02 UTC
(rev 20247)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2015-01-27 22:09:31 UTC
(rev 20248)
@@ -901,7 +901,7 @@
new float[] { x * factor, y * factor, z * factor,
w * factor } }));
if (atomLast != null
- && atomLast.getPolymerIndexInModel() ==
a.getPolymerIndexInModel()) {
+ && atomLast.group.getBioPolymerIndexInModel() ==
a.group.getBioPolymerIndexInModel()) {
pdbCONECT.append("CONECT").append(
PT.formatStringI("%5i", "i", atomLast.getAtomNumber()))
.append(PT.formatStringI("%5i", "i", a.getAtomNumber()))
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-01-27 14:21:02 UTC
(rev 20247)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-01-27 22:09:31 UTC
(rev 20248)
@@ -1306,7 +1306,7 @@
&& theTok != T.defaultcmd && lastToken.tok != T.switchcmd)
return ERROR(ERROR_badContext, ident);
if (lastToken.tok == T.define && theTok != T.leftbrace && nTokens != 1) {
- addTokenToPrefix(T.o(T.string, ident));
+ addTokenToPrefix(theTok == T.define ? lastToken : T.o(T.string, ident));
return CONTINUE;
}
switch (theTok) {
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-01-27 14:21:02 UTC
(rev 20247)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-01-27 22:09:31 UTC
(rev 20248)
@@ -287,13 +287,7 @@
private Thread currentThread;
public ScriptCompiler compiler;
- public Map<String, Object> definedAtomSets;
- @Override
- public Map<String, Object> getDefinedAtomSets() {
- return definedAtomSets;
- }
-
public SB outputBuffer;
private String contextPath = "";
@@ -355,7 +349,6 @@
this.compiler = (compiler == null ? (ScriptCompiler) vwr.compiler
: compiler);
isJS = vwr.isSingleThreaded;
- definedAtomSets = vwr.definedAtomSets;
return this;
}
@@ -1192,7 +1185,7 @@
@Override
public void clearDefinedVariableAtomSets() {
- definedAtomSets.remove("# variable");
+ vwr.definedAtomSets.remove("# variable");
}
/**
@@ -1200,12 +1193,12 @@
*
*/
private void defineSets() {
- if (!definedAtomSets.containsKey("# static")) {
+ if (!vwr.definedAtomSets.containsKey("# static")) {
for (int i = 0; i < JC.predefinedStatic.length; i++)
defineAtomSet(JC.predefinedStatic[i]);
defineAtomSet("# static");
}
- if (definedAtomSets.containsKey("# variable"))
+ if (vwr.definedAtomSets.containsKey("# variable"))
return;
for (int i = 0; i < JC.predefinedVariable.length; i++)
defineAtomSet(JC.predefinedVariable[i]);
@@ -1258,7 +1251,7 @@
private void defineAtomSet(String script) {
if (script.indexOf("#") == 0) {
- definedAtomSets.put(script, Boolean.TRUE);
+ vwr.definedAtomSets.put(script, Boolean.TRUE);
return;
}
ScriptContext sc = compiler.compile("#predefine", script, true, false,
@@ -1291,7 +1284,7 @@
String name = ((String) statement[1].value).toLowerCase();
if (name.startsWith("dynamic_"))
name = "!" + name.substring(8);
- definedAtomSets.put(name, statement);
+ vwr.definedAtomSets.put(name, statement);
}
@Override
@@ -1320,10 +1313,10 @@
}
defineSets();
setName = setName.toLowerCase();
- Object value = definedAtomSets.get(setName);
+ Object value = vwr.definedAtomSets.get(setName);
boolean isDynamic = false;
if (value == null) {
- value = definedAtomSets.get("!" + setName);
+ value = vwr.definedAtomSets.get("!" + setName);
isDynamic = (value != null);
}
if (value instanceof BS)
@@ -1333,13 +1326,13 @@
BS bs = atomExpression((T[]) value, -2, 0, true, false, true, true);
popContext(false, false);
if (!isDynamic)
- definedAtomSets.put(setName, bs);
+ vwr.definedAtomSets.put(setName, bs);
return bs;
}
if (setName.equals("water")) {
BS bs = vwr.ms.getAtoms(T.solvent, null);
if (!isDynamic)
- definedAtomSets.put(setName, bs);
+ vwr.definedAtomSets.put(setName, bs);
return bs;
}
if (plurals)
@@ -1358,7 +1351,7 @@
@Override
public void deleteAtomsInVariables(BS bsDeleted) {
- for (Map.Entry<String, Object> entry : definedAtomSets.entrySet()) {
+ for (Map.Entry<String, Object> entry : vwr.definedAtomSets.entrySet()) {
Object value = entry.getValue();
if (value instanceof BS) {
BSUtil.deleteBits((BS) value, bsDeleted);
@@ -3225,13 +3218,13 @@
T[] code = new T[slen];
for (int i = slen; --i >= 0;)
code[i] = st[i];
- definedAtomSets
+ vwr.definedAtomSets
.put("!" + (isSite ? setName : setName.substring(8)), code);
//if (!isSite)
//vwr.addStateScript(thisCommand, false, true); removed for 12.1.16
} else {
BS bs = atomExpressionAt(2);
- definedAtomSets.put(setName, bs);
+ vwr.definedAtomSets.put(setName, bs);
if (!chk)
vwr.g.setUserVariable("@" + setName, SV.newV(T.bitset, bs));
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-01-27 14:21:02 UTC
(rev 20247)
+++ trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-01-27 22:09:31 UTC
(rev 20248)
@@ -195,14 +195,20 @@
switch (tok) {
case T.define:
- // @{@x} or @{@{x}} or @{@1} -- also userFunction(@1)
- if (tokAt(++i) == T.expressionBegin) {
+ if ((tok = tokAt(++i)) == T.expressionBegin) {
+ // @{@x} or @{@{x}} or @{@1} -- also userFunction(@1)
v = parameterExpressionToken(++i);
i = iToken;
- } else if (tokAt(i) == T.integer) {
+ } else if (tok == T.integer) {
+ // @3
v = vwr.ms.getAtoms(T.atomno, Integer.valueOf(st[i].intValue));
break;
+ } else if (tok == T.define && tokAt(i + 1) == T.integer) {
+ // @@3
+ v = vwr.ms.getAtomsFromAtomNumberInFrame(st[++i].intValue);
+ break;
} else {
+ // @@x
v = getParameter(SV.sValue(st[i]), T.variable, true);
}
v = getParameter(((SV) v).asString(), T.variable, true);
@@ -805,6 +811,7 @@
rpn.addXBs(lookupIdentifierValue("_" + value));
}
break;
+ case T.bonded:
case T.carbohydrate:
case T.dna:
case T.hetero:
@@ -819,7 +826,6 @@
case T.spec_alternate:
case T.specialposition:
case T.symmetry:
- case T.nonequivalent:
case T.unitcell:
rpn.addXBs(getAtomBits(instruction.tok, value));
break;
@@ -876,7 +882,7 @@
(int) Math.floor(pt.y * 1000), (int) Math.floor(pt.z * 1000)
}));
break;
case T.thismodel:
- rpn.addXBs(vwr.getModelUndeletedAtomsBitSet(vwr.am.cmi));
+ rpn.addXBs(vwr.am.cmi < 0 ? vwr.getFrameAtoms() :
vwr.getModelUndeletedAtomsBitSet(vwr.am.cmi));
break;
case T.hydrogen:
case T.amino:
@@ -2319,11 +2325,13 @@
boolean isSetAt = (j == 1 && st[0] == T.tokenSetCmd);
if (isClauseDefine) {
SV vt = parameterExpressionToken(++i);
+ v = (vt.tok == T.varray ? vt : SV.oValue(vt));
i = iToken;
- v = (vt.tok == T.varray ? vt : SV.oValue(vt));
} else {
if (tokAt(i) == T.integer) {
- v = vwr.ms.getAtomsFromAtomNumberInFrame(st[i].intValue);
+ v = vwr.ms.getAtoms(T.atomno, Integer.valueOf(st[i].intValue));
+ } else if (tokAt(i) == T.define && tokAt(i + 1) == T.integer) {
+ v = vwr.ms.getAtomsFromAtomNumberInFrame(st[++i].intValue);
} else {
v = getParameter(var, T.nada, true);
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java 2015-01-27
14:21:02 UTC (rev 20247)
+++ trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java 2015-01-27
22:09:31 UTC (rev 20248)
@@ -162,17 +162,19 @@
int tok = tokAt(1);
switch (tokCommand) {
case T.define:
- if (tokAt(1) == T.integer && tokAt(2) == T.per && tokAt(4) == T.opEQ) {
+ int i = (tokAt(1) == T.define ? 2 : 1);
+ if (tokAt(i) == T.integer && tokAt(i + 1) == T.per && tokAt(i + 3) ==
T.opEQ) {
// @2.xxx =
+ // @@2.xxx =
tokCommand = T.set;
isSetBrace = true;
- ptNewSetModifier = 4;
+ ptNewSetModifier = i + 3;
isMathExpressionCommand = true;
isEmbeddedExpression = true;
addTokenToPostfixToken(T.tokenSetProperty);
addTokenToPostfixToken(T.tokenExpressionBegin);
- addNextToken();
- addNextToken();
+ for (int j = 0; j++ <= i;)
+ addNextToken();
addTokenToPostfixToken(T.tokenExpressionEnd);
firstToken = 0;
}
@@ -1011,12 +1013,15 @@
token = T.tokenDefineString;
addTokenToPostfixToken(token);
}
- if (tokPeek() == T.nada)
+ if (tokPeekIs(T.nada))
return error(ERROR_endOfCommandUnexpected);
// we allow @x[1], which compiles as {@x}[1], not @{x[1]}
// otherwise [1] gets read as a general atom name selector
- if (!addSubstituteTokenIf(T.leftbrace, T.tokenExpressionBegin))
+ if (!addSubstituteTokenIf(T.leftbrace, T.tokenExpressionBegin)) {
+ if (tokPeek() == T.define)
+ addNextToken();
return addNextToken() && checkForItemSelector(true);
+ }
while (moreTokens() && !tokPeekIs(T.rightbrace)) {
if (tokPeekIs(T.leftbrace)) {
if (!checkForCoordinate(true))
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2015-01-27 14:21:02 UTC (rev
20247)
+++ trunk/Jmol/src/org/jmol/script/T.java 2015-01-27 22:09:31 UTC (rev
20248)
@@ -431,6 +431,7 @@
public final static int spec_seqcode_range = expression | 39;
public final static int amino = predefinedset | 2;
+ public final static int bonded = predefinedset | 3;
public final static int dna = predefinedset | 4;
public final static int hetero = predefinedset | 6 | deprecatedparam;
public final static int helixalpha = predefinedset | 7; // Jmol
12.1.14
@@ -456,8 +457,7 @@
public final static int hidden = predefinedset | 42;
public final static int specialposition = predefinedset | 44;
public final static int visible = predefinedset | 46;
- public final static int basemodel = predefinedset | 48;
- public final static int nonequivalent = predefinedset | 50;
+ public final static int basemodel = predefinedset | 48; //
specific to JCAMP-MOL files
static int getPrecedence(int tokOperator) {
@@ -1898,6 +1898,7 @@
"best",
"bin",
"bondCount",
+ "bonded",
"bottom",
"branch",
"brillouin",
@@ -2038,7 +2039,6 @@
"inherit",
"normal",
"noContourLines",
- "nonequivalent",
"notFrontOnly",
"noTriangles",
"now",
@@ -2921,6 +2921,7 @@
best, // "best"
bin, // "bin"
bondcount, // "bondCount"
+ bonded, // "bonded"
bottom, // "bottom"
branch, // "branch"
brillouin, // "brillouin"
@@ -3061,7 +3062,6 @@
-1, // "inherit"
normal, // "normal"
nocontourlines, // "noContourLines"
- nonequivalent, // "nonequivalent"
notfrontonly, // "notFrontOnly"
notriangles, // "noTriangles"
now, // "now"
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-01-27 14:21:02 UTC
(rev 20247)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-01-27 22:09:31 UTC
(rev 20248)
@@ -1507,7 +1507,7 @@
int[] result;
if (expression2 > 0) {
BS bs = new BS();
- eval.definedAtomSets.put("_1", bs);
+ vwr.definedAtomSets.put("_1", bs);
BS bs0 = atomSets[0];
for (int atom1 = bs0.nextSetBit(0); atom1 >= 0; atom1 = bs0
.nextSetBit(atom1 + 1)) {
@@ -3713,7 +3713,7 @@
break;
case T.variables:
if (!chk)
- msg = vwr.getAtomDefs(eval.definedAtomSets) + vwr.g.getVariableList()
+ msg = vwr.getAtomDefs(vwr.definedAtomSets) + vwr.g.getVariableList()
+ getContext(true);
break;
case T.trajectory:
Modified: trunk/Jmol/src/org/jmol/viewer/ColorManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2015-01-27 14:21:02 UTC
(rev 20247)
+++ trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2015-01-27 22:09:31 UTC
(rev 20248)
@@ -172,17 +172,17 @@
atom.getBfactor100(), lo, hi, ColorEncoder.BWR, false);
case PAL.PALETTE_STRAIGHTNESS:
return ce.getColorIndexFromPalette(
- atom.getGroupParameter(T.straightness), -1, 1, ColorEncoder.BWR,
+ atom.group.getGroupParameter(T.straightness), -1, 1,
ColorEncoder.BWR,
false);
case PAL.PALETTE_SURFACE:
hi = vwr.ms.getSurfaceDistanceMax();
return ce.getColorIndexFromPalette(
atom.getSurfaceDistance100(), 0, hi, ColorEncoder.BWR, false);
case PAL.PALETTE_AMINO:
- return ce.getColorIndexFromPalette(atom.getGroupID(),
+ return ce.getColorIndexFromPalette(atom.group.groupID,
0, 0, ColorEncoder.AMINO, false);
case PAL.PALETTE_SHAPELY:
- return ce.getColorIndexFromPalette(atom.getGroupID(),
+ return ce.getColorIndexFromPalette(atom.group.groupID,
0, 0, ColorEncoder.SHAPELY, false);
case PAL.PALETTE_GROUP:
// vwr.calcSelectedGroupsCount() must be called first ...
@@ -192,19 +192,19 @@
// for each atom
// therefore, we call it in Eval.colorObject();
return ce.getColorIndexFromPalette(
- atom.getSelectedGroupIndexWithinChain(), 0,
- atom.getSelectedGroupCountWithinChain() - 1, ColorEncoder.BGYOR,
+ atom.getSelectedGroupIndex(), 0,
+ atom.group.chain.selectedGroupCount - 1, ColorEncoder.BGYOR,
false);
case PAL.PALETTE_POLYMER:
Model m = vwr.ms.am[atom.mi];
return ce.getColorIndexFromPalette(
- atom.getPolymerIndexInModel(), 0, m.getBioPolymerCount() - 1,
+ atom.group.getBioPolymerIndexInModel(), 0, m.getBioPolymerCount() -
1,
ColorEncoder.BGYOR, false);
case PAL.PALETTE_MONOMER:
// vwr.calcSelectedMonomersCount() must be called first ...
return ce.getColorIndexFromPalette(
- atom.getSelectedMonomerIndexWithinPolymer(), 0,
- atom.getSelectedMonomerCountWithinPolymer() - 1, ColorEncoder.BGYOR,
+ atom.group.getSelectedMonomerIndex(), 0,
+ atom.group.getSelectedMonomerCount() - 1, ColorEncoder.BGYOR,
false);
case PAL.PALETTE_MOLECULE:
return ce.getColorIndexFromPalette(
@@ -225,7 +225,7 @@
modelIndex = atom.mi;
return ce.getColorIndexFromPalette(
modelSet.getInsertionCodeIndexInModel(modelIndex,
- atom.getInsertionCode()), 0,
+ atom.group.getInsertionCode()), 0,
modelSet.getInsertionCountInModel(modelIndex), ColorEncoder.ROYGB,
false);
case PAL.PALETTE_JMOL:
@@ -237,7 +237,7 @@
argb = getJmolOrRasmolArgb(id, T.rasmol);
break;
case PAL.PALETTE_STRUCTURE:
- argb = atom.getProteinStructureSubType().getColor();
+ argb = atom.group.getProteinStructureSubType().getColor();
break;
case PAL.PALETTE_CHAIN:
int chain = atom.getChainID();
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-01-27 14:21:02 UTC (rev
20247)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-01-27 22:09:31 UTC (rev
20248)
@@ -519,7 +519,6 @@
"@helix310 substructure=7",
"@helixalpha substructure=8",
"@helixpi substructure=9",
- "@bonded bondcount>0",
};
// these are only updated once per file load or file append
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-27 14:21:02 UTC
(rev 20247)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-27 22:09:31 UTC
(rev 20248)
@@ -19,14 +19,28 @@
Jmol.___JmolVersion="14.3.12_2015.01.26"
+bug fix: select thisModel does not select all atoms in visible frame set
+
+new feature: @@3 for "atomno=3 and thisModel"
+ -- provides a function distinct from @3 when there are multiple models
+ -- includes all atoms in current frame set
+ -- example:
+
+ load "cyclohexane_movie.xyz"
+ select @10
+ 35 atoms selected
+ select @@10
+ 1 atom selected
+ frame [1 2 4 6]
+ select @@10
+ 4 atoms selected
+ @@10.label = "atom 10"
+
+
new feature: frame [1 3 5 6]
-- sets limited number of frames for animation and frame *
-- same as animation frame [1 3 5 6]; frame *
-
-bug fix: @3 for "atomno=3" should not extend to models that are not part of
the current model set
- -- commonly used for shortcut at the console
- -- provides a function distinct from "atomno=3"
-
+
new feature: CGO SCREEN option
-- CGO [SCREEN z ...]
-- reads CGO 2D VERTEX records as screen coordinates, installing them at a
depth of z
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-01-27 14:21:02 UTC
(rev 20247)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-01-27 22:09:31 UTC
(rev 20248)
@@ -1246,7 +1246,7 @@
s = PT.esc(s);
switch (tok) {
case T.residue:
- s = "[" + a.getGroup3(false) + "]" + a.getSeqcodeString() + ":" +
s;
+ s = "[" + a.getGroup3(false) + "]" + a.group.getSeqcodeString() +
":" + s;
break;
case T.sequence:
case T.group1:
@@ -1258,10 +1258,10 @@
glast = null;
clast = null;
}
- if (a.getChain() != clast) {
+ if (a.group.chain != clast) {
info.appendC('\n');
n = 0;
- clast = a.getChain();
+ clast = a.group.chain;
info.append("Chain " + s + ":\n");
glast = null;
}
@@ -1355,7 +1355,7 @@
info.put("surfaceDistance", Float.valueOf(d));
if (ms.am[atom.mi].isBioModel) {
info.put("resname", atom.getGroup3(false));
- char insCode = atom.getInsertionCode();
+ char insCode = atom.group.getInsertionCode();
int seqNum = atom.getResno();
if (seqNum > 0)
info.put("resno", Integer.valueOf(seqNum));
@@ -1364,12 +1364,12 @@
info.put("name", ms.at[i].getAtomName());
info.put("chain", atom.getChainIDStr());
info.put("atomID", Integer.valueOf(atom.atomID));
- info.put("groupID", Integer.valueOf(atom.getGroupID()));
+ info.put("groupID", Integer.valueOf(atom.group.groupID));
if (atom.altloc != '\0')
info.put("altLocation", "" + atom.altloc);
- info.put("structure", Integer.valueOf(atom.getProteinStructureType()
+ info.put("structure",
Integer.valueOf(atom.group.getProteinStructureType()
.getId()));
- info.put("polymerLength", Integer.valueOf(atom.getPolymerLength()));
+ info.put("polymerLength",
Integer.valueOf(atom.group.getBioPolymerLength()));
info.put("occupancy", Integer.valueOf(atom.getOccupancy100()));
int temp = atom.getBfactor100();
info.put("temp", Integer.valueOf(temp / 100));
@@ -1510,7 +1510,7 @@
private static void getAtomResidueInfo(SB info, Atom atom) {
info.append("[").append(atom.getGroup3(false)).append("]").append(
- atom.getSeqcodeString()).append(":");
+ atom.group.getSeqcodeString()).append(":");
int id = atom.getChainID();
info.append(id == 0 ? " " : atom.getChainIDStr());
}
@@ -1837,8 +1837,8 @@
new Object[] { a.getElementSymbolIso(false).toUpperCase(),
strExtra, new float[] { x, y, z, 0f } }));
if (atomLast != null
- && atomLast.getPolymerIndexInModel() == a
- .getPolymerIndexInModel())
+ && atomLast.group.getBioPolymerIndexInModel() == a.group
+ .getBioPolymerIndexInModel())
pdbCONECT.append("CONECT")
.append(PT.formatStringI("%5i", "i", atomLast.getAtomNumber()))
.append(PT.formatStringI("%5i", "i", a.getAtomNumber()))
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-01-27 14:21:02 UTC (rev
20247)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-01-27 22:09:31 UTC (rev
20248)
@@ -3039,6 +3039,10 @@
.copy(am.bsVisibleModels));
}
+ public BS getFrameAtoms() {
+ return getModelUndeletedAtomsBitSetBs(getVisibleFramesBitSet());
+ }
+
public void defineAtomSets(Map<String, Object> info) {
definedAtomSets.putAll(info);
}
@@ -8243,7 +8247,7 @@
// We only work on atoms that are in frame
String ff = g.forceField;
- BS bsInFrame = getModelUndeletedAtomsBitSetBs(getVisibleFramesBitSet());
+ BS bsInFrame = getFrameAtoms();
if (bsSelected == null)
bsSelected = getModelUndeletedAtomsBitSet(getVisibleFramesBitSet()
@@ -8591,9 +8595,8 @@
case '{':
if (getScriptManager() != null) {
Map<String, Object> m = (Map<String, Object>) map;
- Map<String, Object> sets = eval.getDefinedAtomSets();
- if (sets != null)
- m.putAll(sets);
+ if (definedAtomSets != null)
+ m.putAll(definedAtomSets);
T.getTokensType(m, T.predefinedset);
}
return;
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