Revision: 18297
http://sourceforge.net/p/jmol/code/18297
Author: hansonr
Date: 2013-06-06 13:21:29 +0000 (Thu, 06 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.17"
bug fix: write command doesn't accept parameter sequence IMAGE PNGJ ... (broken
in 13.1.14)
bug fix: load APPEND with PDB file loses structure (broken in 13.1.15)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-06-06 05:47:43 UTC
(rev 18296)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-06-06 13:21:29 UTC
(rev 18297)
@@ -1003,8 +1003,12 @@
String id = iterStructure.getStructureID();
int serID = iterStructure.getSerialID();
int count = iterStructure.getStrandCount();
- int istart = iterStructure.getStartIndex() + baseAtomIndex;
- int iend = iterStructure.getEndIndex() + baseAtomIndex;
+ int istart = iterStructure.getStartIndex();
+ if (istart >= 0)
+ istart += baseAtomIndex;
+ int iend = iterStructure.getEndIndex();
+ if (iend >= 0)
+ iend += baseAtomIndex;
if (bsAssigned == null)
bsAssigned = new BS();
iterStructure.getSerialID();
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2013-06-06 05:47:43 UTC
(rev 18296)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2013-06-06 13:21:29 UTC
(rev 18297)
@@ -94,6 +94,7 @@
String structureID, int serialID, int strandCount,
char startChainID, int startSeqcode,
char endChainID, int endSeqcode, int istart, int
iend, BS bsAssigned) {
+ System.out.println("biomodel " + type + " " + structureID + " " +
serialID + " " + istart + " " + iend);
for (int i = bioPolymerCount; --i >= 0; )
bioPolymers[i].addStructure(type, structureID, serialID, strandCount,
startChainID, startSeqcode,
endChainID, endSeqcode, istart, iend,
bsAssigned);
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-06 05:47:43 UTC
(rev 18296)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-06 13:21:29 UTC
(rev 18297)
@@ -14493,7 +14493,7 @@
throw new ScriptInterruption(this, "restore" + type, 1);
return;
}
- checkLength(2);
+ checkLength23();
switch (tok) {
case T.bonds:
if (!chk)
@@ -14682,13 +14682,14 @@
}
break;
default:
- case T.string:
+ tok = T.image;
+ break;
+ }
+ if (tok == T.image) {
T t = T.getTokenFromName(SV.sValue(args[pt])
.toLowerCase());
- if (t != null) {
- tok = t.tok;
+ if (t != null)
type = SV.sValue(t).toUpperCase();
- }
if (Parser.isOneOf(type, driverList.toUpperCase())) {
// povray, maya, vrml, idtf
pt++;
@@ -14697,7 +14698,7 @@
// Povray, Maya, Vrml, Idtf
isExport = true;
if (isCommand)
- fileName = "Jmol." + type;
+ fileName = "Jmol." + type.toLowerCase();
} else if (type.equals("ZIP")) {
pt++;
} else if (type.equals("ZIPALL")) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-06 05:47:43 UTC
(rev 18296)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-06 13:21:29 UTC
(rev 18297)
@@ -9,8 +9,10 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.17_dev"
+___JmolVersion="13.1.17"
+bug fix: write command doesn't accept parameter sequence IMAGE PNGJ ...
(broken in 13.1.14)
+bug fix: load APPEND with PDB file loses structure (broken in 13.1.15)
=============================================================================
JmolVersion="13.1.16"
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