Revision: 21208
http://sourceforge.net/p/jmol/code/21208
Author: hansonr
Date: 2016-08-11 01:43:07 +0000 (Thu, 11 Aug 2016)
Log Message:
-----------
PyMOL reader upgrade -- complete and tested
Modified Paths:
--------------
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
Modified:
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2016-08-10 21:51:12 UTC (rev 21207)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2016-08-11 01:43:07 UTC (rev 21208)
@@ -557,10 +557,8 @@
if (ns > stateCount)
stateCount = ns;
int nAtoms, nBonds;
- Object o = listAt(pymolObject, 6).get(1);
- haveBinaryArrays = AU.isAB(o);
if (haveBinaryArrays) {
- nBonds = ((byte[]) o).length / 20;
+ nBonds = ((byte[]) listAt(pymolObject, 6).get(1)).length / 20;
nAtoms = ((byte[]) listAt(pymolObject, 7).get(1)).length / 120;
n += nAtoms;
} else {
@@ -1803,8 +1801,6 @@
}
static String stringAt(Lst<Object> list, int i) {
- if (!AU.isAB(list.get(i)))
- System.out.println("??");
byte[] a = (byte[]) list.get(i);
return (a.length == 0 ? " " : bytesToString(a));
}
@@ -1812,7 +1808,7 @@
static String bytesToString(Object object) {
try {
return new String((byte[]) object, "UTF-8");
- } catch (UnsupportedEncodingException e) {
+ } catch (Exception e) {
return object.toString();
}
}
Modified: branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2016-08-10 21:51:12 UTC (rev 21207)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2016-08-11 01:43:07 UTC (rev 21208)
@@ -432,6 +432,7 @@
sname = "_!c_" + name + "_";
Lst<Object> colorection = PyMOLReader.listAt(thisScene, 3);
int n = colorection.size();
+ n -= n % 2;
// [color/selEntry,color/selEntry,color/selEntry.....]
// [3, 262, 0, 263, 4, 264, .....]
// see layer3/Selector.c SelectorColorectionApply
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2016-08-10 21:51:12 UTC (rev 21207)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2016-08-11 01:43:07 UTC (rev 21208)
@@ -557,10 +557,8 @@
if (ns > stateCount)
stateCount = ns;
int nAtoms, nBonds;
- Object o = listAt(pymolObject, 6).get(1);
- haveBinaryArrays = AU.isAB(o);
if (haveBinaryArrays) {
- nBonds = ((byte[]) o).length / 20;
+ nBonds = ((byte[]) listAt(pymolObject, 6).get(1)).length / 20;
nAtoms = ((byte[]) listAt(pymolObject, 7).get(1)).length / 120;
n += nAtoms;
} else {
@@ -1803,8 +1801,6 @@
}
static String stringAt(Lst<Object> list, int i) {
- if (!AU.isAB(list.get(i)))
- System.out.println("??");
byte[] a = (byte[]) list.get(i);
return (a.length == 0 ? " " : bytesToString(a));
}
@@ -1812,7 +1808,7 @@
static String bytesToString(Object object) {
try {
return new String((byte[]) object, "UTF-8");
- } catch (UnsupportedEncodingException e) {
+ } catch (Exception e) {
return object.toString();
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2016-08-10 21:51:12 UTC (rev 21207)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2016-08-11 01:43:07 UTC (rev 21208)
@@ -432,6 +432,7 @@
sname = "_!c_" + name + "_";
Lst<Object> colorection = PyMOLReader.listAt(thisScene, 3);
int n = colorection.size();
+ n -= n % 2;
// [color/selEntry,color/selEntry,color/selEntry.....]
// [3, 262, 0, 263, 4, 264, .....]
// see layer3/Selector.c SelectorColorectionApply
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