Revision: 18492
http://sourceforge.net/p/jmol/code/18492
Author: hansonr
Date: 2013-07-26 11:46:53 +0000 (Fri, 26 Jul 2013)
Log Message:
-----------
___JmolVersion="13.3.3_dev_2013.07.26"
bug fix: PDB header don't do trim();
bug fix: isosuface ID @x ... becomes isosurface ID "@x"
bug fix: color chain broken
bug fix: rockets with color chain
bug fix: filter ":X" broken
bug fix: O not 2- in PDB adding hydrogens
bug fix: NWChem reader error
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlXsdReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/minimize/MinPosition.java
trunk/Jmol/src/org/jmol/minimize/Minimizer.java
trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java
trunk/Jmol/src/org/jmol/minimize/forcefield/ForceField.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
trunk/Jmol/src/org/jmol/renderbio/RocketsRenderer.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/shapespecial/Dots.java
trunk/Jmol/src/org/jmol/util/Measure.java
trunk/Jmol/src/org/jmol/viewer/ColorManager.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/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-07-24 11:28:50 UTC (rev 18491)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-07-26 11:46:53 UTC (rev 18492)
@@ -786,7 +786,7 @@
ch = chain < 256 ? (char) chain : 0;
if (chainAtomCounts != null)
chainAtomCounts[ch]++;
- atom.chainID = ch;
+ setChainID(atom, ch);
atom.sequenceNumber = seqNo;
atom.insertionCode = JmolAdapter.canonizeInsertionCode(insCode);
atom.isHetero = isHetero;
@@ -898,7 +898,7 @@
String msg = " atom [" + atom.group3 + "]"
+ atom.sequenceNumber
+ (atom.insertionCode == '\0' ? "" : "^" +
atom.insertionCode)
- + (atom.chainID == '\0' ? "" : ":" + atom.chainID)
+ + (atom.chainID == 0 ? "" : ":" +
viewer.getChainIDStr(atom.chainID))
+ "." + atom.atomName
+ "%" + atom.alternateLocationID + "\n";
if (conformationIndex >= 0 && atom.alternateLocationID != lastAltLoc) {
@@ -1695,8 +1695,8 @@
for (int j = ranges.size(); --j >= 0;) {
String chains = (String) ranges.get(j).get("chains");
int[] residues = (int[]) ranges.get(j).get("residues");
- char chain0 = chains.charAt(0);
- char chain1 = chains.charAt(1);
+ int chain0 = 0 + chains.charAt(0);
+ int chain1 = 0 + chains.charAt(1);
int res0 = residues[0];
int res1 = residues[1];
int index1 = findAtomForRange(index0, indexMax, chain0, res0, false);
@@ -1732,13 +1732,13 @@
atomSetCollection.setTensors();
}
- private int findAtomForRange(int atom1, int atom2, char chain, int resno,
+ private int findAtomForRange(int atom1, int atom2, int chain, int resno,
boolean isLast) {
int iAtom = findAtom(atom1, atom2, chain, resno, true);
return (isLast && iAtom >= 0 ? findAtom(iAtom, atom2, chain, resno, false)
: iAtom);
}
- private int findAtom(int atom1, int atom2, char chain, int resno, boolean
isTrue) {
+ private int findAtom(int atom1, int atom2, int chain, int resno, boolean
isTrue) {
Atom[] atoms = atomSetCollection.getAtoms();
for (int i = atom1; i < atom2; i++) {
Atom atom = atoms[i];
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
2013-07-24 11:28:50 UTC (rev 18491)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
2013-07-26 11:46:53 UTC (rev 18492)
@@ -184,7 +184,7 @@
chainID++;
}
lastSequenceNumber = atom.sequenceNumber;
- atom.chainID = chainID;
+ setChainID(atom, (char) chainID);
}
if (tokens.length > 7)
atom.group3 = tokens[7];
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-07-24 11:28:50 UTC (rev 18491)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-07-26 11:46:53 UTC (rev 18492)
@@ -1144,7 +1144,7 @@
int thisModel = -1;
for (int i = atomCount0; i < n; i++) {
if (i == atomCount) {
- thischain = '\0';
+ thischain = 0;
} else {
seqNo = atoms[i].sequenceNumber;
thischain = atoms[i].chainID;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlXsdReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlXsdReader.java
2013-07-24 11:28:50 UTC (rev 18491)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlXsdReader.java
2013-07-26 11:46:53 UTC (rev 18492)
@@ -89,7 +89,7 @@
atom.atomName = atts.get("ID");
atom.atomSerial = ++iAtom;
if (iChain >= 0)
- atom.chainID = (iChain - 1)%26 + 'A';
+ setChainID(atom, (char) ((iChain - 1)%26 + 'A'));
atom.group3 = "UNK";
if (iGroup == 0)
iGroup = 1;
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-07-24 11:28:50 UTC
(rev 18491)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-07-26 11:46:53 UTC
(rev 18492)
@@ -47,7 +47,8 @@
public float radius = Float.NaN;
public boolean isHetero;
public int atomSerial = Integer.MIN_VALUE;
- public int chainID;
+ public int chainID; // not public -- set using
AtomSetCollectionReader.setChainID
+
public char alternateLocationID = '\0';
public String group3;
public int sequenceNumber = Integer.MIN_VALUE;
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-07-24 11:28:50 UTC (rev 18491)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-07-26 11:46:53 UTC (rev 18492)
@@ -922,8 +922,8 @@
|| atom.atomName.toUpperCase().indexOf("\0" + filterAtomTypeStr)
>= 0)
&& (!filterElement || atom.elementSymbol == null || !filterReject(f,
"_",
atom.elementSymbol.toUpperCase() + ";"))
- && (!filterChain || atom.chainID == '\0' || !filterReject(f, ":", ""
- + atom.chainID))
+ && (!filterChain || atom.chainID == 0 || !filterReject(f, ":", ""
+ + viewer.getChainIDStr(atom.chainID)))
&& (!filterAltLoc || atom.alternateLocationID == '\0' || !filterReject(
f, "%", "" + atom.alternateLocationID))
&& (!filterHetero || !filterReject(f, "HETATM",
@@ -1615,4 +1615,7 @@
// PyMOL reader only
}
+ public void setChainID(Atom atom, char ch) {
+ atom.chainID = viewer.getChainID("" + ch);
+ }
}
Modified: trunk/Jmol/src/org/jmol/minimize/MinPosition.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/MinPosition.java 2013-07-24 11:28:50 UTC
(rev 18491)
+++ trunk/Jmol/src/org/jmol/minimize/MinPosition.java 2013-07-26 11:46:53 UTC
(rev 18492)
@@ -1,5 +1,8 @@
package org.jmol.minimize;
+/**
+ * not implemented -- would be a force toward a given position in space
+ */
public class MinPosition extends MinObject {
MinPosition(int[] data, double[] ddata) {
this.data = data;
Modified: trunk/Jmol/src/org/jmol/minimize/Minimizer.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/Minimizer.java 2013-07-24 11:28:50 UTC
(rev 18491)
+++ trunk/Jmol/src/org/jmol/minimize/Minimizer.java 2013-07-26 11:46:53 UTC
(rev 18492)
@@ -59,6 +59,8 @@
public MinBond[] minBonds;
public MinAngle[] minAngles;
public MinTorsion[] minTorsions;
+ public MinPosition[] minPositions;
+
public BS bsMinFixed;
private int atomCount;
private int bondCount;
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java
2013-07-24 11:28:50 UTC (rev 18491)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java
2013-07-26 11:46:53 UTC (rev 18492)
@@ -34,7 +34,6 @@
import org.jmol.minimize.MinObject;
import org.jmol.minimize.MinPosition;
import org.jmol.minimize.MinTorsion;
-import org.jmol.minimize.forcefield.CalculationsUFF.PositionCalc;
import org.jmol.util.TextFormat;
/**
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/ForceField.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/ForceField.java 2013-07-24
11:28:50 UTC (rev 18491)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/ForceField.java 2013-07-26
11:46:53 UTC (rev 18492)
@@ -103,6 +103,7 @@
this.minBonds = minimizer.minBonds;
this.minAngles = minimizer.minAngles;
this.minTorsions = minimizer.minTorsions;
+ this.minPositions = minimizer.minPositions; // not implemented
this.bsFixed = minimizer.bsMinFixed;
minAtomCount = minAtoms.length;
minBondCount = minBonds.length;
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-07-24
11:28:50 UTC (rev 18491)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-07-26
11:46:53 UTC (rev 18492)
@@ -1390,7 +1390,8 @@
Atom a = atoms[i];
int nH = getImplicitHydrogenCount(a, true);
if (nH != 0) {
- int c0 = a.getFormalCharge();
+
+ int c0 = a.getFormalCharge();
int c = c0 - nH;
a.setFormalCharge(c);
taintAtom(i, TAINT_FORMALCHARGE);
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-07-24
11:28:50 UTC (rev 18491)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-07-26
11:46:53 UTC (rev 18492)
@@ -3259,6 +3259,13 @@
return BSUtil.deleteBits(bs, bs1);
}
+ /**
+ *
+ * @param iFirst
+ * 0 from ModelLoader.freeze; -1 from Viewer.assignAtom
+ * @param baseAtomIndex
+ * @param mergeSet
+ */
public void setAtomNamesAndNumbers(int iFirst, int baseAtomIndex,
AtomCollection mergeSet) {
// first, validate that all atomSerials are NaN
@@ -3281,10 +3288,14 @@
// 1) do not change numbers assigned by adapter
// 2) do not change the number already assigned when merging
// 3) restart numbering with new atoms, not a continuation of old
- if (atomSerials[i] == 0 || baseAtomIndex < 0)
- atomSerials[i] = (i < baseAtomIndex ? mergeSet.atomSerials[i] :
atomNo);
- if (atomNames[i] == null || baseAtomIndex < 0)
- atomNames[i] = (atom.getElementSymbol() + atomSerials[i]).intern();
+ if (i >= -baseAtomIndex) {
+ if (atomSerials[i] == 0 || baseAtomIndex < 0)
+ atomSerials[i] = (i < baseAtomIndex ? mergeSet.atomSerials[i]
+ : atomNo);
+ if (atomNames[i] == null || baseAtomIndex < 0)
+ atomNames[i] = (atom.getElementSymbol() + atomSerials[i]).intern();
+ }
+
if (!models[lastModelIndex].isModelKit || atom.getElementNumber() > 0
&& !atom.isDeleted())
atomNo++;
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-07-24 11:28:50 UTC
(rev 18491)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-07-26 11:46:53 UTC
(rev 18492)
@@ -248,7 +248,7 @@
public int baseModelIndex = 0;
private int baseModelCount = 0;
- private int baseAtomIndex = 0;
+ public int baseAtomIndex = 0;
private int baseGroupIndex = 0;
private int baseTrajectoryCount = 0;
Modified: trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2013-07-24 11:28:50 UTC
(rev 18491)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2013-07-26 11:46:53 UTC
(rev 18492)
@@ -40,6 +40,7 @@
import org.jmol.modelset.ModelLoader;
import org.jmol.modelset.ModelSet;
import org.jmol.util.BS;
+import org.jmol.util.BSUtil;
import org.jmol.util.JmolEdge;
import org.jmol.util.Logger;
import org.jmol.util.Measure;
@@ -206,12 +207,9 @@
public void addImplicitHydrogenAtoms(JmolAdapter adapter, int iGroup, int
nH) {
String group3 = modelLoader.getGroup3(iGroup);
- if (group3 != null && group3.equals("FS4"))
- System.out.println("hest");
int nH1;
if (haveHsAlready || group3 == null
- || (nH1 = JC.getStandardPdbHydrogenCount(Group
- .lookupGroupID(group3))) == 0)
+ || (nH1 = JC.getStandardPdbHydrogenCount(Group.lookupGroupID(group3)))
== 0)
return;
nH = (nH1 < 0 ? -1 : nH1 + nH);
Object model = null;
@@ -351,7 +349,6 @@
modelSet.viewer.getLigandModel(null);
finalizePdbMultipleBonds();
addHydrogens();
- modelSet.fixFormalCharges(bsAtomsForHs);
}
private void addHydrogens() {
@@ -453,6 +450,7 @@
}
}
deleteUnneededAtoms();
+ modelSet.fixFormalCharges(BSUtil.newBitSet2(modelLoader.baseAtomIndex,
modelLoader.modelSet.atomCount));
}
/**
Modified: trunk/Jmol/src/org/jmol/renderbio/RocketsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/RocketsRenderer.java 2013-07-24
11:28:50 UTC (rev 18491)
+++ trunk/Jmol/src/org/jmol/renderbio/RocketsRenderer.java 2013-07-26
11:46:53 UTC (rev 18492)
@@ -171,8 +171,8 @@
viewer.transformPt3f(pointEnd, screenB);
int zMid = (int) Math.floor((screenA.z + screenB.z) / 2f);
int diameter = (int) viewer.scaleToScreen(zMid, mad);
- g3d.fillCylinderBits(GData.ENDCAPS_FLAT, diameter, screenA, screenB);
if (g3d.setColix(colix)) {
+ g3d.fillCylinderBits(GData.ENDCAPS_FLAT, diameter, screenA, screenB);
if (tEnd && renderArrowHeads) {
vtemp.sub2(pointEnd, pointStart);
vtemp.normalize();
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2013-07-24 11:28:50 UTC
(rev 18491)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2013-07-26 11:46:53 UTC
(rev 18492)
@@ -2348,7 +2348,7 @@
ichT = ptLastChar + 1;
else if (ptSpace > 0)
ichT = ptSpace;
- if (isVariable && ptSpace < 0 && parenpt <= 0 && ichT - ichToken > 1) {
+ if (isVariable && (!allowSpace || ptSpace < 0 && parenpt <= 0 && ichT -
ichToken > 1)) {
// if we have @xxx then this is not an implied string
return false;
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-24
11:28:50 UTC (rev 18491)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-26
11:46:53 UTC (rev 18492)
@@ -47,7 +47,6 @@
import org.jmol.util.BS;
import org.jmol.util.BSUtil;
import org.jmol.util.BoxInfo;
-import org.jmol.util.C;
import org.jmol.util.ColorEncoder;
import org.jmol.util.ColorUtil;
import org.jmol.util.Escape;
Modified: trunk/Jmol/src/org/jmol/shapespecial/Dots.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Dots.java 2013-07-24 11:28:50 UTC
(rev 18491)
+++ trunk/Jmol/src/org/jmol/shapespecial/Dots.java 2013-07-26 11:46:53 UTC
(rev 18492)
@@ -30,7 +30,6 @@
import org.jmol.util.BSUtil;
import org.jmol.util.C;
import org.jmol.util.Escape;
-import org.jmol.util.Logger;
import org.jmol.util.Matrix3f;
import org.jmol.util.Matrix4f;
import org.jmol.util.SB;
Modified: trunk/Jmol/src/org/jmol/util/Measure.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Measure.java 2013-07-24 11:28:50 UTC (rev
18491)
+++ trunk/Jmol/src/org/jmol/util/Measure.java 2013-07-26 11:46:53 UTC (rev
18492)
@@ -510,7 +510,7 @@
for (int i = 1; i <= n; i++) {
P3 aij = centerAndPoints[0][i];
P3 bij = centerAndPoints[1][i];
- if (aij instanceof Atom)
+ if (aij instanceof Atom && bij instanceof Atom)
Logger.info(" atom 1 " + ((Atom) aij).getInfo() + "\tatom 2 "
+ ((Atom) bij).getInfo());
else
Modified: trunk/Jmol/src/org/jmol/viewer/ColorManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2013-07-24 11:28:50 UTC
(rev 18491)
+++ trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2013-07-26 11:46:53 UTC
(rev 18492)
@@ -253,6 +253,7 @@
chain = 0;
else if (chain >= 256)
chain -= 256;
+ chain &= 0x1F;
chain = chain % JC.argbsChainAtom.length;
argb = (atom.isHetero() ? JC.argbsChainHetero :
JC.argbsChainAtom)[chain];
break;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-24 11:28:50 UTC
(rev 18491)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-26 11:46:53 UTC
(rev 18492)
@@ -11,11 +11,19 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.3.3_dev_2013.07.23"
+___JmolVersion="13.3.3_dev_2013.07.26"
+
+bug fix: PDB header don't do trim();
+bug fix: isosuface ID @x ... becomes isosurface ID "@x"
+bug fix: color chain broken
+bug fix: rockets with color chain
+bug fix: filter ":X" broken
+bug fix: O not 2- in PDB adding hydrogens
+bug fix: NWChem reader error
-bug fix: NWChem reader error -- unclear what is going on with "OR
+TODO: mouse exit then release doesn't trigger release
TODO: ingenol/jsmetest.htm?
-
+TODO: minimization set position calculation optimization?
TODO: documentation (see below, including % units on measure distance)
TODO: isosurface SLAB TRANSLUCENT 0.x color
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2013-07-24 11:28:50 UTC
(rev 18491)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2013-07-26 11:46:53 UTC
(rev 18492)
@@ -538,10 +538,11 @@
}
String[] lines = TextFormat.split((String) objHeader, '\n');
// this is meant to be for PDB files only
- if (lines.length == 0
- || lines[0].length() < 6
- || lines[0].charAt(6) != ' '
- || !lines[0].substring(0, 6).equals(lines[0].substring(0,
6).toUpperCase())) {
+ if (lines.length == 0
+ || lines[0].length() < 6
+ || lines[0].charAt(6) != ' '
+ || !lines[0].substring(0, 6).equals(
+ lines[0].substring(0, 6).toUpperCase())) {
ht.put("fileHeader", (String) objHeader);
return ht;
}
@@ -569,7 +570,7 @@
keyLast = key;
}
if (!haveType || key.equals(type))
- sb.append(line.substring(10).trim()).appendC('\n');
+ sb.append(line).appendC('\n');
}
if (!haveType) {
ht.put(keyLast, sb.toString());
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-07-24 11:28:50 UTC (rev
18491)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-07-26 11:46:53 UTC (rev
18492)
@@ -9437,8 +9437,10 @@
return;
clearModelDependentObjects();
if (pt == null) {
+ int atomCount = modelSet.getAtomCount();
modelSet.assignAtom(atomIndex, type, true);
- modelSet.setAtomNamesAndNumbers(atomIndex, -1, null);
+ if (!Parser.isOneOf(type,";Mi;Pl;X;"))
+ modelSet.setAtomNamesAndNumbers(atomIndex, -atomCount, null);
refresh(3, "assignAtom");
return;
}
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