Revision: 18312
http://sourceforge.net/p/jmol/code/18312
Author: hansonr
Date: 2013-06-07 21:12:44 +0000 (Fri, 07 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.17_dev_2013.06.07"
TODO: PyMOL uniqueAtomSettings for selected atom settings
TODO: selective molecular surface translucency
-- color isosurface {xxxx} red translucent 0.5 ??
bug fix: ellipsoid rendering problems
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
trunk/Jmol/src/org/jmol/adapter/readers/molxyz/XyzReader.java
trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
trunk/Jmol/src/org/jmol/adapter/readers/more/MdTopReader.java
trunk/Jmol/src/org/jmol/adapter/readers/more/P2nReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanSmolReader.java
trunk/Jmol/src/org/jmol/adapter/readers/quantum/WebMOReader.java
trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlChem3dReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlMagResReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlQEReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlVaspReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlXsdReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/AimsReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/GulpReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -243,7 +243,7 @@
atomSetCollection.applySymmetryBio(vBiomts, notionalUnitCell,
applySymmetryToBonds, filter);
}
}
- super.finalizeReader();
+ finalizeReaderASCR();
String header = tokenizer.getFileHeader();
if (header.length() > 0)
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("fileHeader",
@@ -293,7 +293,7 @@
// no atom-centered rotation axes, and no mirror or glide planes.
atomSetCollection.setCheckSpecial(!isPDB);
boolean doCheck = doCheckUnitCell && !isPDB;
- super.applySymmetryAndSetTrajectory();
+ applySymTrajASCR();
if (doCheck && (bondTypes.size() > 0 || isMolecular))
setBondingAndMolecules();
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -339,6 +339,10 @@
@Override
protected void finalizeReader() throws Exception {
+ finalizeReaderPDB();
+ }
+
+ protected void finalizeReaderPDB() throws Exception {
checkNotPDB();
atomSetCollection.connectAll(maxSerial, isConnectStateBug);
if (atomSetCollection.getStructureCount() > 0)
@@ -373,7 +377,7 @@
appendLoadNote(sbTlsErrors.toString());
}
- super.finalizeReader();
+ finalizeReaderASCR();
if (vCompnds != null)
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("compoundSource",
vCompnds);
if (htSites != null) { // && atomSetCollection.getAtomSetCount() == 1)
@@ -387,7 +391,7 @@
Logger.info(sbIgnored.toString());
}
}
-
+
private void checkForResidualBFactors(SymmetryInterface symmetry) {
Atom[] atoms = atomSetCollection.getAtoms();
boolean isResidual = false;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -131,12 +131,17 @@
}
}
}
+
@Override
public void finalizeReader() throws Exception {
+ finalizeReaderMR();
+ }
+
+ protected void finalizeReaderMR() throws Exception {
if (is2D)
set2D();
isTrajectory = false;
- super.finalizeReader();
+ finalizeReaderASCR();
}
void processMolSdHeader() throws Exception {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/molxyz/XyzReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/molxyz/XyzReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/molxyz/XyzReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -85,7 +85,7 @@
@Override
protected void finalizeReader() throws Exception {
isTrajectory = false;
- super.finalizeReader();
+ finalizeReaderASCR();
}
private void skipAtomSet(int modelAtomCount) throws Exception {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -159,7 +159,7 @@
@Override
public void finalizeReader() throws Exception {
processPeakData();
- super.finalizeReader();
+ finalizeReaderMR();
}
private int findModelById(String modelID) {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/MdTopReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/MdTopReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/MdTopReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -87,7 +87,7 @@
@Override
protected void finalizeReader() throws Exception {
- super.finalizeReader();
+ finalizeReaderASCR();
Atom[] atoms = atomSetCollection.getAtoms();
Atom atom;
for (int i = 0; i < atomCount; i++) {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/P2nReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/P2nReader.java 2013-06-07
20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/P2nReader.java 2013-06-07
21:12:44 UTC (rev 18312)
@@ -55,7 +55,7 @@
@Override
protected void finalizeReader() throws Exception {
- super.finalizeReader();
+ finalizeReaderPDB();
if (!useAltNames)
atomSetCollection.setAtomSetAuxiliaryInfo("altName", altNames
.toArray(new String[altNames.size()]));
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -170,6 +170,11 @@
// override PDBReader settings
}
+ @Override
+ protected void finalizeReader() throws Exception {
+ finalizeReaderPDB();
+ atomSetCollection.setEllipsoids();
+ }
/**
* At the end of the day, we need to finalize all the JmolObjects, set the
* trajectories, and, if filtered with DOCACHE, cache a streamlined binary
@@ -1032,7 +1037,7 @@
atom.vectorX = uniqueID;
atom.vectorY = cartoonType;
if (a.size() > 46) {
- float[] data = PyMOLScene.floatsAt(a, 41, new float[7], 6);
+ float[] data = PyMOLScene.floatsAt(a, 41, new float[8], 6);
atomSetCollection.setAnisoBorU(atom, data, 12);
}
//if (uniqueID > 0)
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -983,13 +983,13 @@
private boolean purging;
@Override
public String readLine() throws Exception {
- super.readLine();
+ RL();
if (!purging && line != null && line.startsWith("--")) {
purging = true;
discardLinesUntilStartsWith("*");
readLine();
purging = false;
- super.readLine();
+ RL();
}
return line;
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanSmolReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanSmolReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanSmolReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -137,7 +137,7 @@
@Override
protected void finalizeReader() throws Exception {
- super.finalizeReader();
+ finalizeReaderASCR();
// info out of order -- still a chance, at least for first model
if (atomCount > 0 && spartanArchive != null
&& atomSetCollection.getBondCount() == 0 && bondData != null)
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/WebMOReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/WebMOReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/WebMOReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -95,7 +95,7 @@
@Override
protected void finalizeReader() throws Exception {
- super.finalizeReader();
+ finalizeReaderASCR();
if (nOrbitals > 0)
setMOs("eV");
if (Logger.debugging)
Modified: trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -239,7 +239,7 @@
for (int i = firstLine; i < lineBuffer.size(); i++)
if ((tokens = lineBuffer.get(i)).length > 0)
getAtom();
- super.finalizeReader();
+ finalizeReaderASCR();
}
private void getSymbolic() {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlChem3dReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlChem3dReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlChem3dReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -60,7 +60,7 @@
@Override
protected void processXml(XmlReader parent,
Object saxReader) throws Exception {
- super.processXml(parent, saxReader);
+ PX(parent, saxReader);
finalizeMOData(moData);
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlMagResReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlMagResReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlMagResReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -49,7 +49,7 @@
protected void processXml(XmlReader parent,
Object saxReader) throws Exception {
parent.doProcessLines = true;
- super.processXml(parent, saxReader);
+ PX(parent, saxReader);
}
@Override
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlQEReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlQEReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlQEReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -58,7 +58,7 @@
protected void processXml(XmlReader parent,
Object saxReader) throws Exception {
parent.doProcessLines = true;
- super.processXml(parent, saxReader);
+ PX(parent, saxReader);
}
@Override
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java 2013-06-07
20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java 2013-06-07
21:12:44 UTC (rev 18312)
@@ -166,6 +166,10 @@
*/
protected void processXml(XmlReader parent, Object saxReader)
throws Exception {
+ PX(parent, saxReader);
+ }
+
+ protected void PX(XmlReader parent, Object saxReader) throws Exception {
this.parent = parent;
atomSetCollection = parent.atomSetCollection;
reader = parent.reader;
@@ -199,12 +203,11 @@
saxHandler.parseXML(this, saxReader, reader);
}
}
-
@Override
public void applySymmetryAndSetTrajectory() {
try {
if (parent == null)
- super.applySymmetryAndSetTrajectory();
+ applySymTrajASCR();
else
parent.applySymmetryAndSetTrajectory();
} catch (Exception e) {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlVaspReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlVaspReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlVaspReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -64,7 +64,7 @@
protected void processXml(XmlReader parent,
Object saxReader) throws Exception {
parent.doProcessLines = true;
- super.processXml(parent, saxReader);
+ PX(parent, saxReader);
}
@Override
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlXsdReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlXsdReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlXsdReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -59,7 +59,7 @@
protected void processXml(XmlReader parent,
Object saxReader) throws Exception {
parent.htParams.put("backboneAtoms", bsBackbone);
- super.processXml(parent, saxReader);
+ PX(parent, saxReader);
atomSetCollection.clearSymbolicMap();
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/AimsReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/AimsReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/AimsReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -93,7 +93,7 @@
+ "(which is currently neither supported by FHI-aims");
// note: Jmol DOES support both polymer and slab symmetry.
}
- super.finalizeReader();
+ finalizeReaderASCR();
}
/*
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -373,20 +373,18 @@
protected void finalizeReader() throws Exception {
if (isPhonon || isOutput) {
isTrajectory = false;
- super.finalizeReader();
- return;
+ } else {
+ doApplySymmetry = true;
+ setLatticeVectors();
+ int nAtoms = atomSetCollection.getAtomCount();
+ /*
+ * this needs to be run either way (i.e. even if coordinates are already
+ * fractional) - to satisfy the logic in AtomSetCollectionReader()
+ */
+ for (int i = 0; i < nAtoms; i++)
+ setAtomCoord(atomSetCollection.getAtom(i));
}
-
- doApplySymmetry = true;
- setLatticeVectors();
- int nAtoms = atomSetCollection.getAtomCount();
- /*
- * this needs to be run either way (i.e. even if coordinates are already
- * fractional) - to satisfy the logic in AtomSetCollectionReader()
- */
- for (int i = 0; i < nAtoms; i++)
- setAtomCoord(atomSetCollection.getAtom(i));
- super.finalizeReader();
+ finalizeReaderASCR();
}
private void setLatticeVectors() {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -293,7 +293,7 @@
processInputCoords();
if (energy != null)
setEnergy();
- super.finalizeReader();
+ finalizeReaderASCR();
}
/*
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/GulpReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/GulpReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/GulpReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -320,7 +320,7 @@
}
setModelParameters(false);
}
- super.applySymmetryAndSetTrajectory();
+ applySymTrajASCR();
}
/* Fractional coordinates of asymmetric unit :
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-06-07 20:32:43 UTC (rev 18311)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-06-07 21:12:44 UTC (rev 18312)
@@ -236,7 +236,7 @@
} else {
processBinaryDocument(doc);
}
- finalizeReader();
+ finalizeReader(); // upstairs
} catch (Throwable e) {
Logger.info("Reader error: " + e);
if (!viewer.isApplet())
@@ -328,7 +328,15 @@
htParams.put("trajectorySteps", trajectorySteps = new JmolList<P3[]>());
}
+ /**
+ * optional reader-specific method run first.
+ * @throws Exception
+ */
protected void finalizeReader() throws Exception {
+ finalizeReaderASCR();
+ }
+
+ protected void finalizeReaderASCR() throws Exception {
applySymmetryAndSetTrajectory();
setLoadNote();
if (doCentralize)
@@ -994,6 +1002,10 @@
}
public void applySymmetryAndSetTrajectory() throws Exception {
+ applySymTrajASCR();
+ }
+
+ public void applySymTrajASCR() throws Exception {
if (iHaveUnitCell && doCheckUnitCell) {
atomSetCollection.setCoordinatesAreFractional(iHaveFractionalCoordinates);
atomSetCollection.setNotionalUnitCell(notionalUnitCell,
@@ -1351,6 +1363,10 @@
}
public String readLine() throws Exception {
+ return RL();
+ }
+
+ public String RL() throws Exception {
prevline = line;
line = reader.readLine();
if (os != null && line != null) {
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