Revision: 20901
http://sourceforge.net/p/jmol/code/20901
Author: hansonr
Date: 2015-12-23 04:18:04 +0000 (Wed, 23 Dec 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.1_2015.12.22"
bug fix: PyMOL 1.8 PSE files cannot be read
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2015-12-23 04:17:37 UTC (rev 20900)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2015-12-23 04:18:04 UTC (rev 20901)
@@ -272,8 +272,9 @@
pymolVersion, haveScenes, baseAtomIndex, baseModelIndex, doCache,
filePath);
// just log and display some information here
-
- logging = (vwr.getLogFileName().length() > 0);
+ String logFile = vwr.getLogFileName();
+ logging = (logFile.length() > 0);
+ Logger.info(logging ? "PyMOL file data streaming to " + logFile : "To view
raw PyMOL file data, use 'set logFile \"some_filename\" ");
Lst<Object> names = getMapList(map, "names");
for (Map.Entry<String, Object> e : map.entrySet()) {
String name = e.getKey();
@@ -333,6 +334,7 @@
if (!isStateScript && doResize) {
int width = 0, height = 0;
try {
+ // not all PSE files have this
width = intAt(getMapList(map, "main"), 0);
height = intAt(getMapList(map, "main"), 1);
} catch (Exception e) {
@@ -1083,6 +1085,7 @@
int formalCharge = intAt(a, 18);
BS bsReps = getBsReps(listAt(a, 20));
+ int intReps = (bsReps == null ? intAt(a, 20) : 0); // Pymol 1.8
int atomColor = intAt(a, 21);
int serNo = intAt(a, 22);
int cartoonType = intAt(a, 23);
@@ -1116,7 +1119,7 @@
if (isNucleic)
pymolScene.bsNucleic.set(ac);
for (int i = 0; i < PyMOL.REP_MAX; i++)
- if (bsReps.get(i))
+ if (bsReps == null ? ((intReps & (1<<i)) != 0) : bsReps.get(i))
reps[i].set(ac);
if (atom.elementSymbol.equals("H"))
pymolScene.bsHydrogen.set(ac);
@@ -1353,6 +1356,8 @@
}
private static BS getBsReps(Lst<Object> list) {
+ if (list == null)
+ return null;
BS bsReps = new BS();
int n = Math.min(list.size(), PyMOL.REP_MAX);
for (int i = 0; i < n; i++) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-23 04:17:37 UTC
(rev 20900)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-23 04:18:04 UTC
(rev 20901)
@@ -62,8 +62,12 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.1_2015.12.21"
+Jmol.___JmolVersion="14.5.1_2015.12.22"
+bug fix: PyMOL 1.8 PSE files cannot be read
+
+JmolVersion="14.5.1_2015.12.21"
+
bug fix: color [0xffffff] should not be case-sensitive -- [0Xffffff] should be
OK
bug fix: set spin fps ... fails
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