Revision: 20307
http://sourceforge.net/p/jmol/code/20307
Author: hansonr
Date: 2015-02-18 22:57:53 +0000 (Wed, 18 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.12_2015.02.18b"
bug fix: CML reader does not show proper atom names for crystal structures
bug fix: POV-Ray renderer does not show proper backbone width (since forever)
bug fix: POV-Ray renderer with a translucent surface shows bonds that should be
hidden (since 13.1)
bug fix: unitcell info for PDB file biomolecule does not show "biomolecule 1"
Modified Paths:
--------------
branches/v14_2/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
branches/v14_2/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_2/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
2015-02-18 22:57:06 UTC (rev 20306)
+++ branches/v14_2/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
2015-02-18 22:57:53 UTC (rev 20307)
@@ -138,6 +138,7 @@
* the current state
*/
protected int state = START;
+ private int atomIndex0;
/*
* added 2/2007 Bob Hanson:
@@ -603,10 +604,11 @@
return;
String s;
Atom[] atoms = asc.atoms;
- for (int i = 0; i < ac; i++)
+ for (int i = atomIndex0; i < asc.ac; i++)
if ((s = atomIdNames.getProperty(atoms[i].atomName)) != null)
atoms[i].atomName = s;
atomIdNames = null;
+ atomIndex0 = asc.ac;
}
private void addNewBond(String a1, String a2, int order) {
Modified: branches/v14_2/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
2015-02-18 22:57:06 UTC (rev 20306)
+++ branches/v14_2/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
2015-02-18 22:57:53 UTC (rev 20307)
@@ -992,7 +992,7 @@
//symmetry.setUnitCell(null);
addSpaceGroupOperation("x,y,z", false);
String name = (String) thisBiomolecule.get("name");
- setAtomSetSpaceGroupName(name);
+ setAtomSetSpaceGroupName(acr.sgName = name);
int len = biomts.size();
this.applySymmetryToBonds = applySymmetryToBonds;
bondCount0 = asc.bondCount;
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-18
22:57:06 UTC (rev 20306)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-18
22:57:53 UTC (rev 20307)
@@ -5,10 +5,12 @@
# THIS IS THE RELEASE BRANCH
# BUG FIXES ONLY, PLEASE
-Jmol.___JmolVersion="14.2.12_2015.02.18b"
+Jmol.___JmolVersion="14.3.12_2015.02.18b"
bug fix: POV-Ray renderer does not show proper backbone
bug fix: POV-Ray renderer with a translucent surface shows bonds that should
be hidden
+bug fix: CML reader does not show proper atom names for crystal structures
+bug fix: unitcell info for PDB file biomolecule does not show "biomolecule 1"
JmolVersion="14.2.12_2015.02.16"
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