Revision: 18372
http://sourceforge.net/p/jmol/code/18372
Author: hansonr
Date: 2013-06-27 08:48:07 +0000 (Thu, 27 Jun 2013)
Log Message:
-----------
___version=13.0.18
bug fix NOT: pdbAddHydrogens may miss O3' or O5' H atoms at end of DNA strands
bug fix NOT: pdbAddHydrogens may miss H in first group of a chain
bug fix: "ligand" should include all _g=0 (nonPDB atoms)
bug fix: POLYHEDRA with faceCenterOffset not saved in state properly; EDGES
option nonfunctional
bug fix: COMPARE could rotate to less-good fit with SMARTS search
bug fix: draw ARROW ATOM/BOND broken
bug fix: draw ARROW with offset disallows set picking draw adjustments
bug fix: concurrrent loading of two cif files by two different applets fails
bug fix: draw LINEDATA not operative (undocumented, for state; from draw xxx
INTERSECT yyy)
bug fix: jvxl reader ignores jvxlVertexColorData
bug fix: ellipsoid rendering problems
Modified Paths:
--------------
branches/v13_0/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
branches/v13_0/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
branches/v13_0/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
branches/v13_0/Jmol/src/org/jmol/util/ZipUtil.java
branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v13_0/Jmol/src/org/jmol/viewer/JmolConstants.java
Modified:
branches/v13_0/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
===================================================================
---
branches/v13_0/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
2013-06-27 08:28:22 UTC (rev 18371)
+++
branches/v13_0/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
2013-06-27 08:48:07 UTC (rev 18372)
@@ -29,6 +29,7 @@
import java.io.IOException;
import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
@@ -78,6 +79,7 @@
private int stepNumber;
private int moModelSet = -1;
+ private BitSet namedSets = new BitSet();
/**
@@ -216,7 +218,7 @@
energyString = tokens[2] + " " + tokens[3];
// now set the names for the last equivalentAtomSets
atomSetCollection.setAtomSetNames(energyKey + " = " + energyString,
- equivalentAtomSets);
+ equivalentAtomSets, namedSets);
// also set the properties for them
atomSetCollection.setAtomSetPropertyForSets(energyKey, energyString,
equivalentAtomSets);
@@ -242,7 +244,7 @@
String tokens[] = getTokens();
energyKey = "Energy";
energyString = tokens[1];
- atomSetCollection.setAtomSetNames("Energy = "+tokens[1],
equivalentAtomSets);
+ atomSetCollection.setAtomSetNames("Energy = "+tokens[1],
equivalentAtomSets, namedSets);
atomSetCollection.setAtomSetEnergy(energyString, parseFloat(energyString));
}
@@ -280,7 +282,8 @@
// this is needed for the last structure in an optimization
// if energy information is found for this structure the reader
// will overwrite this setting later.
- atomSetCollection.setAtomSetName(energyKey + " = " + energyString);
+ if (energyKey.length() != 0)
+ atomSetCollection.setAtomSetName(energyKey + " = " + energyString);
atomSetCollection.setAtomSetEnergy(energyString, parseFloat(energyString));
// atomSetCollection.setAtomSetName("Last read atomset.");
String path = getTokens()[0]; // path = type of orientation
@@ -626,7 +629,9 @@
continue;
atomSetCollection.cloneLastAtomSet();
// set the properties
- atomSetCollection.setAtomSetFrequency("Calculation " +
calculationNumber, symmetries[i], frequencies[i], null);
+ String name = atomSetCollection.setAtomSetFrequency("Calculation " +
calculationNumber, symmetries[i], frequencies[i], null);
+ appendLoadNote("model " + atomSetCollection.getAtomSetCount() + ": " +
name);
+ namedSets.set(atomSetCollection.getCurrentAtomSetIndex());
atomSetCollection.setAtomSetModelProperty("ReducedMass",
red_masses[i]+" AMU");
atomSetCollection.setAtomSetModelProperty("ForceConstant",
Modified:
branches/v13_0/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
2013-06-27 08:28:22 UTC (rev 18371)
+++ branches/v13_0/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
2013-06-27 08:48:07 UTC (rev 18372)
@@ -218,7 +218,7 @@
atomSetCollection.setAtomSetPropertyForSets(energyKey, energyValue,
equivalentAtomSets);
atomSetCollection.setAtomSetNames(energyKey + " = " + energyValue,
- equivalentAtomSets);
+ equivalentAtomSets, null);
atomSetCollection.setAtomSetEnergy(value, parseFloat(value));
haveEnergy = true;
}
Modified:
branches/v13_0/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-06-27 08:28:22 UTC (rev 18371)
+++ branches/v13_0/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-06-27 08:48:07 UTC (rev 18372)
@@ -1710,10 +1710,12 @@
* The name
* @param n
* The number of last AtomSets that needs these set
+ * @param namedSets to ignore
*/
- public void setAtomSetNames(String atomSetName, int n) {
- for (int idx = currentAtomSetIndex; --n >= 0 && idx >= 0; --idx)
- setAtomSetAuxiliaryInfo("name", atomSetName, idx);
+ public void setAtomSetNames(String atomSetName, int n, BitSet namedSets) {
+ for (int i = currentAtomSetIndex; --n >= 0 && i >= 0; --i)
+ if (namedSets == null || !namedSets.get(i))
+ setAtomSetAuxiliaryInfo("name", atomSetName, i);
}
/**
@@ -1910,15 +1912,17 @@
setAtomSetModelProperty("Energy", "" + value);
}
- public void setAtomSetFrequency(String pathKey, String label, String freq,
String units) {
+ public String setAtomSetFrequency(String pathKey, String label, String freq,
String units) {
freq += " " + (units == null ? "cm^-1" : units);
- setAtomSetName((label == null ? "" : label + " ") + freq);
+ String name = (label == null ? "" : label + " ") + freq;
+ setAtomSetName(name);
setAtomSetModelProperty("Frequency", freq);
if (label != null)
setAtomSetModelProperty("FrequencyLabel", label);
setAtomSetModelProperty(SmarterJmolAdapter.PATH_KEY, (pathKey == null ? ""
: pathKey + SmarterJmolAdapter.PATH_SEPARATOR + "Frequencies")
+ "Frequencies");
+ return name;
}
void toCartesian(SymmetryInterface symmetry) {
Modified: branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
2013-06-27 08:28:22 UTC (rev 18371)
+++ branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
2013-06-27 08:48:07 UTC (rev 18372)
@@ -10671,17 +10671,15 @@
}
private void delete() throws ScriptException {
- if (statementLength == 1) {
- zap(true);
- return;
- }
if (tokAt(1) == Token.dollarsign) {
setObjectProperty();
return;
}
- BitSet bs = atomExpression(statement, 1, 0, true, false, true, false);
+ BitSet bs = (statementLength == 1 ? null : atomExpression(statement, 1, 0,
true, false, true, false));
if (isSyntaxCheck)
return;
+ if (bs == null)
+ bs = viewer.getModelUndeletedAtomsBitSet(-1);
int nDeleted = viewer.deleteAtoms(bs, false);
if (!(tQuiet || scriptLevel > scriptReportingLevel))
scriptStatusOrBuffer(GT._("{0} atoms deleted", nDeleted));
Modified: branches/v13_0/Jmol/src/org/jmol/util/ZipUtil.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/util/ZipUtil.java 2013-06-27 08:28:22 UTC
(rev 18371)
+++ branches/v13_0/Jmol/src/org/jmol/util/ZipUtil.java 2013-06-27 08:48:07 UTC
(rev 18372)
@@ -543,7 +543,7 @@
return null;
}
Logger.info("ZipUtil cached " + n + " bytes from " + fileName);
- return listing.toString();
+ return (listing.length() == 0 ? null : listing.toString());
}
/**
Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-27
08:28:22 UTC (rev 18371)
+++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-27
08:48:07 UTC (rev 18372)
@@ -9,8 +9,11 @@
# Don't use ___ in your text, as that is the key for stripping out
# the information saved in the JAR version of this file.
-___version=13.0.17_dev_2013.06.16b
+___version=13.0.18
+bug fix NOT: pdbAddHydrogens may miss O3' or O5' H atoms at end of DNA strands
+bug fix NOT: pdbAddHydrogens may miss H in first group of a chain
+bug fix: "ligand" should include all _g=0 (nonPDB atoms)
bug fix: POLYHEDRA with faceCenterOffset not saved in state properly; EDGES
option nonfunctional
bug fix: COMPARE could rotate to less-good fit with SMARTS search
bug fix: draw ARROW ATOM/BOND broken
Modified: branches/v13_0/Jmol/src/org/jmol/viewer/JmolConstants.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/viewer/JmolConstants.java 2013-06-27
08:28:22 UTC (rev 18371)
+++ branches/v13_0/Jmol/src/org/jmol/viewer/JmolConstants.java 2013-06-27
08:48:07 UTC (rev 18372)
@@ -766,6 +766,7 @@
"UREA",// 45 urea, a cosolvent
"PO4", // 46 phosphate ions -- from here on is "ligand"
"SO4", // 47 sulphate ions
+ "UNL",
};
@@ -1186,7 +1187,7 @@
"@water _g>=" + GROUPID_WATER + " & _g<" + GROUPID_SOLVENT_MIN
+ ", oxygen & connected(2) & connected(2, hydrogen), (hydrogen) &
connected(oxygen & connected(2) & connected(2, hydrogen))",
"@solvent water, (_g>=" + GROUPID_SOLVENT_MIN + " & _g<" + GROUPID_ION_MAX
+ ")", // water, other solvent or ions
- "@ligand !(_g<"+ GROUPID_ION_MIN + ",protein,nucleic,water)",
+ "@ligand _g=0|!(_g<"+ GROUPID_ION_MIN + ",protein,nucleic,water)",
// structure
"@turn structure=1",
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