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[Jmol-commits] SF.net SVN: jmol:[18111] trunk/Jmol/src/org/jmol
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From: <ha...@us...> - 2013-04-16 02:29:57
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Revision: 18111
http://sourceforge.net/p/jmol/code/18111
Author: hansonr
Date: 2013-04-16 02:29:53 +0000 (Tue, 16 Apr 2013)
Log Message:
-----------
___JmolVersion="13.1.15_dev_2013.04.15a"
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pymol/ModelSettings.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/ModelSettings.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/ModelSettings.java 2013-04-14 23:18:39 UTC (rev 18110)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/ModelSettings.java 2013-04-16 02:29:53 UTC (rev 18111)
@@ -125,6 +125,7 @@
public void createShape(ModelSet m, BS bsCarb) {
ShapeManager sm = m.shapeManager;
int modelIndex = getModelIndex(m);
+ Atom[] atoms;
switch (id) {
case T.movie:
sm.viewer.setMovie((Map<String, Object>) info);
@@ -202,7 +203,7 @@
id = JC.SHAPE_TRACE;
float[] data = new float[bsAtoms.length()];
rd = new RadiusData(data, 0, RadiusData.EnumType.ABSOLUTE, EnumVdw.AUTO);
- Atom[] atoms = sm.viewer.modelSet.atoms;
+ atoms = sm.viewer.modelSet.atoms;
double sum = 0.0,
sumsq = 0.0;
@@ -309,7 +310,7 @@
public void setColors(short[] colixes, float translucency) {
this.colixes = colixes;
- this.colors = new Object[] {colixes, Float.valueOf(translucency) };
+ colors = new Object[] {colixes, Float.valueOf(translucency) };
}
public void setSize(float size) {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java 2013-04-14 23:18:39 UTC (rev 18110)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java 2013-04-16 02:29:53 UTC (rev 18111)
@@ -29,6 +29,7 @@
import java.util.Map;
+import jspecview.util.ArrayUtil;
import jspecview.util.TextFormat;
import org.jmol.adapter.readers.cifpdb.PdbReader;
@@ -89,7 +90,7 @@
private Map<String, int[]> htAtomMap = new Hashtable<String, int[]>();
private Map<String, BS> ssMapSeq = new Hashtable<String, BS>();
private Map<String, BS> ssMapAtom = new Hashtable<String, BS>();
- private JmolList<Integer> colixList = new JmolList<Integer>();
+ private JmolList<Integer> atomColorList = new JmolList<Integer>();
private JmolList<String> labels = new JmolList<String>();
private JmolList<ModelSettings> modelSettings = new JmolList<ModelSettings>();
@@ -586,8 +587,8 @@
BoxInfo.addPointXYZ(x, y, z, xyzMin, xyzMax, 0);
}
}
- processStructures(atomCount0);
- setBranchShapes( BSUtil.newBitSet2(atomCount0, atomCount));
+ processStructures();
+ setBranchShapes();
} else {
ns = 1; // I guess I don't understand what the second set is for in each of these.
lstStates.clear();
@@ -616,8 +617,8 @@
if (bsState != null) {
bsAtoms.or(bsState);
}
- processStructures(atomCount0);
- setBranchShapes(BSUtil.newBitSet2(atomCount0, atomCount));
+ processStructures();
+ setBranchShapes();
}
}
setBonds(bonds);
@@ -892,12 +893,10 @@
//System.out.println(atom.atomName + " " + atom.group3 + " " + Integer.toHexString(atom.flags));
bsNoSurface.set(atomCount);
}
- int colorIndex = getInt(a, 21);
float translucency = getUniqueFloat(atom.uniqueID,
PyMOL.sphere_transparency, sphereTranslucency);
- colixList.addLast(Integer.valueOf(C.getColixTranslucent3(C
- .getColixO(Integer.valueOf(PyMOL.getRGB(colorIndex))),
- translucency > 0, translucency)));
+ int atomColor = getInt(a, 21);
+ atomColorList.addLast(getColix(atomColor, translucency));
bsHidden.setBitTo(atomCount, isHidden);
bsModelAtoms.set(atomCount);
if (bsState != null)
@@ -919,6 +918,12 @@
return true;
}
+ private Integer getColix(int colorIndex, float translucency) {
+ return Integer.valueOf(C.getColixTranslucent3(C
+ .getColixO(Integer.valueOf(PyMOL.getRGB(colorIndex))),
+ translucency > 0, translucency));
+ }
+
private BS getBsReps(JmolList<Object> list) {
BS bsReps = new BS();
for (int i = 0; i < PyMOL.REP_MAX; i++)
@@ -935,20 +940,20 @@
protected void setAdditionalAtomParameters(Atom atom) {
}
- private void processStructures(int i0) {
+ private void processStructures() {
if (atomSetCollection.bsStructuredModels == null)
atomSetCollection.bsStructuredModels = new BS();
atomSetCollection.bsStructuredModels.set(Math.max(atomSetCollection
.getCurrentAtomSetIndex(), 0));
- processSS(i0, "H", ssMapAtom.get("H"), EnumStructure.HELIX, 0);
- processSS(i0, "S", ssMapAtom.get("S"), EnumStructure.SHEET, 1);
- processSS(i0, "L", ssMapAtom.get("L"), EnumStructure.TURN, 0);
- processSS(i0, " ", ssMapAtom.get(" "), EnumStructure.NONE, 0);
+ processSS("H", ssMapAtom.get("H"), EnumStructure.HELIX, 0);
+ processSS("S", ssMapAtom.get("S"), EnumStructure.SHEET, 1);
+ processSS("L", ssMapAtom.get("L"), EnumStructure.TURN, 0);
+ processSS(" ", ssMapAtom.get(" "), EnumStructure.NONE, 0);
ssMapSeq = new Hashtable<String, BS>();
}
- private void processSS(int atomCount0, String ssType, BS bsAtom,
+ private void processSS(String ssType, BS bsAtom,
EnumStructure type, int strandCount) {
if (ssMapSeq.get(ssType) == null)
return;
@@ -1086,13 +1091,12 @@
private final static int REP_JMOL_STARS = 15;
private final static int REP_JMOL_MAX = 16;
- private void setBranchShapes(BS bs) {
+ private void setBranchShapes() {
if (isStateScript)
return;
+ BS bs = BSUtil.newBitSet2(atomCount0, atomCount);
ModelSettings ms = new ModelSettings(JC.SHAPE_BALLS, bs, null);
- colixes = new short[colixList.size()];
- for (int i = colixes.length; --i >= 0;)
- colixes[i] = (short) colixList.get(i).intValue();
+ colixes = setColors(colixes, atomColorList);
ms.setSize(0);
ms.setColors(colixes, 0);
modelSettings.addLast(ms);
@@ -1104,14 +1108,24 @@
reps[REP_JMOL_TRACE].and(reps[PyMOL.REP_CARTOON]);
reps[PyMOL.REP_CARTOON].andNot(reps[REP_JMOL_TRACE]);
//reps[REP_JMOL_PUTTY].and(reps[REP_CARTOON]);
- // reps[REP_CARTOON].andNot(reps[REP_JMOL_PUTTY]);
+ // reps[REP_CARTOON].andNot(reps[REP_JMOL_PUTTY]);
for (int i = 0; i < REP_JMOL_MAX; i++)
setShape(i);
setSurface();
ssMapAtom = new Hashtable<String, BS>();
}
+
+ private short[] setColors(short[] colixes,
+ JmolList<Integer> colorList) {
+ if (colixes == null)
+ colixes = new short[atomCount];
+ else
+ colixes = ArrayUtil.ensureLength(colixes, atomCount);
+ for (int i = atomCount; --i >= atomCount0;)
+ colixes[i] = (short) colorList.get(i).intValue();
+ return colixes;
+ }
-
private void setShape(int shapeID) {
// add more to implement
BS bs = reps[shapeID];
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2013-04-14 23:18:39 UTC (rev 18110)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2013-04-16 02:29:53 UTC (rev 18111)
@@ -449,7 +449,8 @@
}
void finish(ModelSet modelSet, int baseModelIndex, int baseAtomIndex) {
- reader.finalizeModelSet(modelSet, baseModelIndex, baseAtomIndex);
+ if (reader != null)
+ reader.finalizeModelSet(modelSet, baseModelIndex, baseAtomIndex);
atoms = null;
atomSetAtomCounts = new int[16];
atomSetAuxiliaryInfo = new Hashtable[16];
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-14 23:18:39 UTC (rev 18110)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-16 02:29:53 UTC (rev 18111)
@@ -9,7 +9,7 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.15_dev_2013.04.14a"
+___JmolVersion="13.1.15_dev_2013.04.15a"
TODO: PyMOL movies, electron density, CGO
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