Revision: 18451
http://sourceforge.net/p/jmol/code/18451
Author: hansonr
Date: 2013-07-18 08:23:36 +0000 (Thu, 18 Jul 2013)
Log Message:
-----------
___JmolVersion="13.1.19_dev_2013.07.18"
bug fix: JSmol menu not disappearing upon touch outside menu
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/jvxl/readers/PyMOLMeshReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/PyMOLMeshReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/PyMOLMeshReader.java 2013-07-17
03:53:50 UTC (rev 18450)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/PyMOLMeshReader.java 2013-07-18
08:23:36 UTC (rev 18451)
@@ -32,8 +32,26 @@
import org.jmol.util.SB;
+/**
+ * A reader for PyMOL PSE file ObjectMap data
+ *
+ * From PyMOL/layer2/ObjectMap.h: in order to achieve better backwards
compatibility
+ * with session files, future map source should be either:
+ * cMapSourceCrystallographic or cMapSourceGeneralPurpose
+ */
class PyMOLMeshReader extends MapFileReader {
+ final static int cMapSourceCrystallographic = 1;
+ final static int cMapSourceCCP4 = 2;
+ final static int cMapSourceGeneralPurpose = 3;
+ final static int cMapSourceDesc = 4;
+ final static int cMapSourceFLD = 5;
+ final static int cMapSourceBRIX = 6;
+ final static int cMapSourceGRD = 7;
+ final static int cMapSourceChempyBrick = 8;
+ final static int cMapSourceVMDPlugin = 9;
+ final static int cMapSourceObsolete = 10;
+
private Hashtable<String, JmolList<Object>> map;
private JmolList<Object> data;
private JmolList<Object> surfaceList;
@@ -42,6 +60,7 @@
private int pymolType;
private boolean isMesh;
//private float cutoff = Float.NaN;
+ private int pymolState; // not nec. 0, but assuming that here.
/*
* PyMOL surface/mesh reader.
@@ -87,64 +106,81 @@
@Override
protected void readParameters() throws Exception {
-
+
JmolList<Object> t;
jvxlFileHeaderBuffer = new SB();
jvxlFileHeaderBuffer.append("PyMOL surface reader\n");
- jvxlFileHeaderBuffer.append(surfaceName + " (" + params.calculationType +
")\n");
+ jvxlFileHeaderBuffer.append(surfaceName + " (" + params.calculationType
+ + ")\n");
+ // extentMin
+ t = getList(surfaceList, 7);
+ origin.set(getFloat(t, 0), getFloat(t, 1), getFloat(t, 2));
+
+
+ // extentMax
+ t = getList(surfaceList, 8);
+ a = getFloat(t, 0) - origin.x;
+ b = getFloat(t, 1) - origin.y;
+ c = getFloat(t, 2) - origin.z;
+
// cell parameters
JmolList<Object> s = getList(surfaceList, 1);
t = getList(s, 0);
// change in format between PyMOL versions
- if (t.size() < 3)
- t = getList(s = getList(s, 0), 0);
- a = getFloat(t, 0);
- b = getFloat(t, 1);
- c = getFloat(t, 2);
- t = getList(s, 1);
- alpha = getFloat(t, 0);
- beta = getFloat(t, 1);
- gamma = getFloat(t, 2);
+ // with PyMOL 1.6 allowing multiple crystal defs??
+
+ if (t == null) {
+ alpha = 1;
+ } else {
+ try {
+ getFloat(t, 0);
+ } catch (Exception e) {
+ // just pick up first crystal data
+ t = getList(s = getList(s, 0), 0);
+ }
+ // these seem to be irrelevant
+ //a = getFloat(t, 0);
+ //b = getFloat(t, 1);
+ //c = getFloat(t, 2);
+ t = getList(s, 1);
+ alpha = getFloat(t, 0);
+ beta = getFloat(t, 1);
+ gamma = getFloat(t, 2);
+ }
+ if (alpha == 1)
+ alpha = beta = gamma = 90;
+
+
+ // ignoring I->Div for now
- // origin
- t = getList(surfaceList, 7);
- origin.set(getFloat(t, 0), getFloat(t, 1), getFloat(t, 2));
-
- // unit cell vectors in grid counts
- t = getList(surfaceList, 10);
- na = (int) getFloat(t, 0);
- nb = (int) getFloat(t, 1);
- nc = (int) getFloat(t, 2);
+// t = getList(surfaceList, 10); // I->Div
+// ?? = (int) getFloat(t, 0);
+// ?? = (int) getFloat(t, 1);
+// ?? = (int) getFloat(t, 2);
+
// data block start and extents in grid units
- t = getList(surfaceList, 11);
+ t = getList(surfaceList, 11); // I->Min
nxyzStart[0] = (int) getFloat(t, 0);
nxyzStart[1] = (int) getFloat(t, 1);
nxyzStart[2] = (int) getFloat(t, 2);
-
+
// number of grid points
// will end up with xyz, but we use zyx because of the storage
- t = getList(surfaceList, 13);
+ t = getList(surfaceList, 13); // I->FDim
nz = (int) getFloat(t, 0);
ny = (int) getFloat(t, 1);
nx = (int) getFloat(t, 2);
- if (na < 0 || nb < 0 || nc < 0) {
- na = nz - 1;
- nb = ny - 1;
- nc = nx - 1;
- t = getList(surfaceList, 8);
- a = getFloat(t, 0) - origin.x;
- b = getFloat(t, 1) - origin.y;
- c = getFloat(t, 2) - origin.z;
- }
-
-
+ na = nz - 1;
+ nb = ny - 1;
+ nc = nx - 1;
+
mapc = 3; // fastest
mapr = 2;
maps = 1; // slowest
-
+
getVectorsAndOrigin();
setCutoffAutomatic();
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-17 03:53:50 UTC
(rev 18450)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-18 08:23:36 UTC
(rev 18451)
@@ -9,8 +9,11 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.19_dev_2013.07.16"
+___JmolVersion="13.1.19_dev_2013.07.18"
+bug fix: JSmol menu not disappearing upon touch outside menu
+bug fix: PyMOL surface map reading error
+
new feature: set exportScale x.x
-- adjusts export scale
-- only implemented for VRML and X3D exporters
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