Revision: 20312
http://sourceforge.net/p/jmol/code/20312
Author: hansonr
Date: 2015-02-22 17:59:57 +0000 (Sun, 22 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.12_2015.02.22"
bug fix: WRITE PDB broken
bug fix: minimizer treats hydrogen bonds as covalent single bonds
Modified Paths:
--------------
branches/v14_2/Jmol/src/org/jmol/minimize/Minimizer.java
branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
Modified: branches/v14_2/Jmol/src/org/jmol/minimize/Minimizer.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/minimize/Minimizer.java 2015-02-22
06:59:02 UTC (rev 20311)
+++ branches/v14_2/Jmol/src/org/jmol/minimize/Minimizer.java 2015-02-22
17:59:57 UTC (rev 20312)
@@ -364,6 +364,9 @@
}
int bondOrder = bond.getCovalentOrder();
switch (bondOrder) {
+ case 0:
+ // hydrogen bond
+ continue;
case 1:
case 2:
case 3:
Modified: branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-22
06:59:02 UTC (rev 20311)
+++ branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-22
17:59:57 UTC (rev 20312)
@@ -3085,7 +3085,7 @@
tok = T.image;
break;
}
- if (tok == T.image) {
+ if (tok == T.image && pt < args.length) {
T t = T.getTokenFromName(SV.sValue(args[pt]).toLowerCase());
if (t != null) {
type = SV.sValue(t).toUpperCase();
@@ -3165,6 +3165,9 @@
break;
case T.clipboard:
break;
+ case T.opIf:
+ fileName = (type.equals("IMAGE") || type.equals("(image)") ?
"?jmol.png" : "?jmol." + type.toLowerCase());
+ break;
case T.identifier:
case T.string:
fileName = SV.sValue(tokenAt(pt, args));
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-22
06:59:02 UTC (rev 20311)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-22
17:59:57 UTC (rev 20312)
@@ -5,8 +5,13 @@
# THIS IS THE RELEASE BRANCH
# BUG FIXES ONLY, PLEASE
-Jmol.___JmolVersion="14.3.12_2015.02.18b"
+Jmol.___JmolVersion="14.2.12_2015.02.22"
+bug fix: WRITE PDB broken
+bug fix: minimizer treats hydrogen bonds as covalent single bonds
+
+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
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
2015-02-22 06:59:02 UTC (rev 20311)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
2015-02-22 17:59:57 UTC (rev 20312)
@@ -1715,8 +1715,6 @@
"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();
- if (isBiomodel && doConnect)
- PT.leftJustify(sbATOMS, " ", "" + a.getPolymerIndexInModel());
sbATOMS
.append(
LabelToken.formatLabelAtomArray(vwr, a, tokens, '\0', null,
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