Revision: 18611
http://sourceforge.net/p/jmol/code/18611
Author: hansonr
Date: 2013-08-21 14:46:32 +0000 (Wed, 21 Aug 2013)
Log Message:
-----------
___JmolVersion="13.3.4_dev_2013.08.21"
bug fix: JANA2006 reader not processing occupancies
-- read now forced to "PACKED" in order to calculate site multiplicity
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/util/Modulation.java
trunk/Jmol/src/org/jmol/util/ModulationSet.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-21
09:56:53 UTC (rev 18610)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-21
14:46:32 UTC (rev 18611)
@@ -349,7 +349,6 @@
// no atom-centered rotation axes, and no mirror or glide planes.
if (isPDB)
atomSetCollection.setCheckSpecial(false);
-
boolean doCheck = doCheckUnitCell && !isPDB;
SymmetryInterface sym = applySymTrajASCR();
if (auditBlockCode != null && auditBlockCode.contains("REFRNCE") && sym !=
null) {
@@ -1037,8 +1036,8 @@
break;
case OCCUPANCY:
float floatOccupancy = parseFloatStr(field);
- if (!Float.isNaN(floatOccupancy))
- atom.occupancy = (int) (floatOccupancy * 100);
+ if (Float.isNaN(floatOccupancy))
+ atom.foccupancy = floatOccupancy;
break;
case B_ISO:
atom.bfactor = parseFloatStr(field) * (isPDB ? 1 : 100f);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-21 09:56:53 UTC (rev 18610)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-21 14:46:32 UTC (rev 18611)
@@ -117,12 +117,12 @@
}
protected void addModulation(Map<String, P3> map, String id, P3 pt, int
iModel) {
- if (modType != null)
- switch (id.charAt(0)) {
+ char ch = id.charAt(0);
+ switch (ch) {
case 'O':
case 'D':
case 'U':
- if (modType.indexOf(id.charAt(0)) < 0 || modSelected > 0
+ if (modType != null && modType.indexOf(ch) < 0 || modSelected > 0
&& modSelected != 1)
return;
break;
@@ -344,7 +344,7 @@
if (Logger.debuggingHigh)
Logger.debug("\nsetModulation: i=" + a.index + " " + a.atomName + " xyz="
- + a + " occ=" + a.occupancy);
+ + a + " occ=" + a.foccupancy);
if (iop != iopLast) {
//System.out.println("mdim=" + mdim + " op=" + (iop + 1) + " " +
symmetry.getSpaceGroupOperation(iop) + " " + symmetry.getSpaceGroupXyz(iop,
false));
iopLast = iop;
@@ -356,21 +356,24 @@
Logger.debug("setModulation iop = " + iop + " "
+ symmetry.getSpaceGroupXyz(iop, false) + " " + a.bsSymmetry);
}
-
- float vocc0 = a.occupancy / 100f;
+
ModulationSet ms = new ModulationSet(a.index + " " + a.atomName,
- P3.newP(a), vocc0, modDim, list, gammaE, gammaIS, q123, qlen);
+ P3.newP(a), a.foccupancy / 10000f, modDim, list, gammaE, gammaIS,
q123, qlen);
a.vib = ms;
ms.calculate();
- if (!Float.isNaN(ms.vocc)) {
- if (modVib && !Float.isNaN(vocc0)) {
- a.occupancy = (int) ((vocc0 + ms.vocc) * 100);
- } else if (ms.vocc < 0.5f) {
- a.occupancy = 0;
+ float occ = ms.vOcc;
+ if (!Float.isNaN(occ)) {
+ if (modVib && !Float.isNaN(ms.vOcc0)) {
+ a.foccupancy = Math.min(1, Math.max(0, ms.vOcc0 + occ));
+ if (a.foccupancy < 0)
+ a.foccupancy = 0;
+
+ } else if (occ < 0.5f) {
+ a.foccupancy = 0;
if (bsAtoms != null)
bsAtoms.clear(a.index);
- } else if (ms.vocc >= 0.5f) {
- a.occupancy = 100;
+ } else if (occ >= 0.5f) {
+ a.foccupancy = 1;
}
}
if (ms.htUij != null) {
@@ -398,7 +401,7 @@
// set property_modT to be Math.floor (q.r/|q|) -- really only for d=1
- if (modVib || a.occupancy != 0) {
+ if (modVib || a.foccupancy != 0) {
float t = q1Norm.dot(a);
if (Math.abs(t - (int) t) > 0.001f)
t = (int) Math.floor(t);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java 2013-08-21
09:56:53 UTC (rev 18610)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java 2013-08-21
14:46:32 UTC (rev 18611)
@@ -955,8 +955,7 @@
}
- atom.occupancy = (Float.isNaN(floatOccupancy) ? 100
- : (int) (floatOccupancy * 100));
+ atom.foccupancy = (Float.isNaN(floatOccupancy) ? 1 : floatOccupancy);
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-08-21 09:56:53 UTC (rev 18610)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-08-21 14:46:32 UTC (rev 18611)
@@ -1051,7 +1051,7 @@
bs.set(seqNo - MIN_RESNO);
}
atom.bfactor = floatAt(a, 14);
- atom.occupancy = (int) (floatAt(a, 15) * 100);
+ atom.foccupancy = floatAt(a, 15);
atom.radius = floatAt(a, 16);
if (atom.radius == 0)
atom.radius = 1;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-21 09:56:53 UTC (rev 18610)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-21 14:46:32 UTC (rev 18611)
@@ -29,6 +29,7 @@
import org.jmol.adapter.readers.cif.ModulationReader;
import org.jmol.adapter.smarter.Atom;
import org.jmol.io.JmolBinary;
+import org.jmol.util.BS;
import org.jmol.util.JmolList;
import org.jmol.util.Logger;
import org.jmol.util.P3;
@@ -48,6 +49,7 @@
setFractionalCoordinates(true);
initializeModulation();
atomSetCollection.newAtomSet();
+ forcePacked = true; // need site occupancies anyway
}
final static String records = "tit cell ndim qi lat sym spg end";
@@ -122,6 +124,7 @@
if (lattvecs != null)
atomSetCollection.getSymmetry().addLatticeVectors(lattvecs);
applySymmetryAndSetTrajectory();
+ adjustM40Occupancies();
setModulation();
finalizeModulation();
finalizeReaderASCR();
@@ -236,6 +239,7 @@
atom.atomName = line.substring(0, 9).trim();
if (!filterAtom(atom, 0))
continue;
+ atom.foccupancy = floats[2];
setAtomCoordXYZ(atom, floats[3], floats[4], floats[5]);
atomSetCollection.addAtom(atom);
if (!incommensurate)
@@ -247,7 +251,6 @@
int nOcc = getInt(65, 68);
int nDisp = getInt(68, 71);
int nUij = getInt(71, 74);
-
// read anisotropies
readM40Floats(r);
boolean isIso = true;
@@ -398,4 +401,19 @@
return data;
}
+ /**
+ * M40 occupancies are divided by the site multiplicity
+ */
+ private void adjustM40Occupancies() {
+ int nOps = atomSetCollection.getSymmetry().getSpaceGroupOperationCount();
+ BS bsSite = new BS();
+ Atom[] atoms = atomSetCollection.getAtoms();
+ for (int i = atomSetCollection.getAtomCount(); --i >= 0;) {
+ Atom a = atoms[i];
+ bsSite.clearAll();
+ bsSite.setBits(0, nOps);
+ bsSite.and(a.bsSymmetry);
+ a.foccupancy *= bsSite.cardinality();
+ }
+ }
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-08-21 09:56:53 UTC
(rev 18610)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-08-21 14:46:32 UTC
(rev 18611)
@@ -43,7 +43,7 @@
public float partialCharge = Float.NaN;
public V3 vib;
public float bfactor = Float.NaN;
- public int occupancy = 100;
+ public float foccupancy = 1;
public float radius = Float.NaN;
public boolean isHetero;
public int atomSerial = Integer.MIN_VALUE;
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java 2013-08-21
09:56:53 UTC (rev 18610)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java 2013-08-21
14:46:32 UTC (rev 18611)
@@ -123,7 +123,7 @@
public int getOccupancy() {
- return atom.occupancy;
+ return (int) (atom.foccupancy * 100);
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-08-21 09:56:53 UTC (rev 18610)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-08-21 14:46:32 UTC (rev 18611)
@@ -55,6 +55,8 @@
@SuppressWarnings("unchecked")
public class AtomSetCollection {
+ public BS bsAtoms; // required for CIF reader
+
private String fileTypeName;
public String getFileTypeName() {
@@ -80,8 +82,6 @@
return atomSetCollectionAuxiliaryInfo;
}
- public BS bsAtoms; // required for CIF reader
-
private final static String[] globalBooleans =
{"someModelsHaveFractionalCoordinates",
"someModelsHaveSymmetry", "someModelsHaveUnitcells",
"someModelsHaveCONECT", "isPDB"};
@@ -1509,7 +1509,7 @@
haveMappedSerials = false;
}
- boolean haveMappedSerials;
+ private boolean haveMappedSerials;
private void mapMostRecentAtomSerialNumber() {
if (atomCount == 0)
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-08-21 09:56:53 UTC (rev 18610)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-08-21 14:46:32 UTC (rev 18611)
@@ -183,6 +183,7 @@
protected String strSupercell;
protected P3 ptSupercell;
protected boolean mustFinalizeModelSet;
+ protected boolean forcePacked;
// private state variables
@@ -514,27 +515,7 @@
symmetryRange = (htParams.containsKey("symmetryRange") ? ((Float) htParams
.get("symmetryRange")).floatValue() : 0);
- latticeCells = new int[3];
- if (htParams.containsKey("lattice")) {
- P3 pt = ((P3) htParams.get("lattice"));
- latticeCells[0] = (int) pt.x;
- latticeCells[1] = (int) pt.y;
- latticeCells[2] = (int) pt.z;
- doCentroidUnitCell = (htParams.containsKey("centroid"));
- if (doCentroidUnitCell && (latticeCells[2] == -1 || latticeCells[2] ==
0))
- latticeCells[2] = 1;
- centroidPacked = doCentroidUnitCell && htParams.containsKey("packed");
- doPackUnitCell = !doCentroidUnitCell && (htParams.containsKey("packed")
|| latticeCells[2] < 0);
-
- }
- doApplySymmetry = (latticeCells[0] > 0 && latticeCells[1] > 0);
- //allows for {1 1 1} or {1 1 -1} or {555 555 0|1|-1} (-1 being "packed")
- if (!doApplySymmetry) {
- latticeCells[0] = 0;
- latticeCells[1] = 0;
- latticeCells[2] = 0;
- }
-
+ initializeSymmetryOptions();
//this flag FORCES symmetry -- generally if coordinates are not fractional,
//we may note the unit cell, but we do not apply symmetry
//with this flag, we convert any nonfractional coordinates to fractional
@@ -581,6 +562,31 @@
}
}
+ protected void initializeSymmetryOptions() {
+ latticeCells = new int[3];
+ P3 pt = ((P3) htParams.get("lattice"));
+ if (forcePacked && pt == null)
+ pt = P3.new3(1, 1, 1);
+ if (pt != null) {
+ latticeCells[0] = (int) pt.x;
+ latticeCells[1] = (int) pt.y;
+ latticeCells[2] = (int) pt.z;
+ doCentroidUnitCell = (htParams.containsKey("centroid"));
+ if (doCentroidUnitCell && (latticeCells[2] == -1 || latticeCells[2] ==
0))
+ latticeCells[2] = 1;
+ boolean isPacked = forcePacked || htParams.containsKey("packed");
+ centroidPacked = doCentroidUnitCell && isPacked;
+ doPackUnitCell = !doCentroidUnitCell && (isPacked || latticeCells[2] <
0);
+ }
+ doApplySymmetry = (latticeCells[0] > 0 && latticeCells[1] > 0);
+ //allows for {1 1 1} or {1 1 -1} or {555 555 0|1|-1} (-1 being "packed")
+ if (!doApplySymmetry) {
+ latticeCells[0] = 0;
+ latticeCells[1] = 0;
+ latticeCells[2] = 0;
+ }
+ }
+
public boolean haveModel;
public boolean doGetModel(int modelNumber, String title) {
@@ -1051,6 +1057,8 @@
}
public SymmetryInterface applySymTrajASCR() throws Exception {
+ if (forcePacked)
+ initializeSymmetryOptions();
SymmetryInterface sym = null;
if (iHaveUnitCell && doCheckUnitCell) {
atomSetCollection.setCoordinatesAreFractional(iHaveFractionalCoordinates);
Modified: trunk/Jmol/src/org/jmol/util/Modulation.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-21 09:56:53 UTC
(rev 18610)
+++ trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-21 14:46:32 UTC
(rev 18611)
@@ -153,8 +153,8 @@
// p(x4)=0 if x4 is outside the interval [c-w/2,c+w/2],
x -= Math.floor(x);
- ms.vocc = (range(x) ? 1 : 0);
- ms.vocc0 = Float.NaN; // don't add this in
+ ms.vOcc = (range(x) ? 1 : 0);
+ ms.vOcc0 = Float.NaN; // don't add this in
//System.out.println("MOD " + ms.r + " " + ms.delta + " " + ms.epsilon
+ " " + ms.id + " " + ms.v + " l=" + left + " x=" + x4 + " r=" + right);
return;
case TYPE_DISP_SAWTOOTH:
@@ -249,9 +249,9 @@
ms.addUTens(utens, (float) v);
break;
default:
- if (Float.isNaN(ms.vocc))
- ms.vocc = 0;
- ms.vocc += (float) v;
+ if (Float.isNaN(ms.vOcc))
+ ms.vOcc = 0;
+ ms.vOcc += (float) v;
}
}
Modified: trunk/Jmol/src/org/jmol/util/ModulationSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-21 09:56:53 UTC
(rev 18610)
+++ trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-21 14:46:32 UTC
(rev 18611)
@@ -13,13 +13,13 @@
public class ModulationSet extends Vibration {
- public float vocc = Float.NaN;
+ public float vOcc = Float.NaN;
public Map<String, Float> htUij;
public boolean enabled = false;
public String id;
public V3 prevSetting;
- float vocc0 = Float.NaN;
+ public float vOcc0;
private JmolList<Modulation> mods;
private Matrix3f gammaE;
@@ -48,7 +48,7 @@
public ModulationSet(String id, P3 r, float vocc0, int modDim,
JmolList<Modulation> mods, Matrix3f gammaE, Matrix4f
gammaIS, P3[] q123, double[] qlen) {
this.id = id;
- this.vocc0 = vocc0;
+ this.vOcc0 = vocc0;
this.modDim = modDim;
this.mods = mods;
@@ -76,7 +76,7 @@
public void calculate() {
x = y = z = 0;
htUij = null;
- vocc = Float.NaN;
+ vOcc = Float.NaN;
double offset = (t == Integer.MAX_VALUE ? 0 : qlen[0] * t);
for (int i = mods.size(); --i >= 0;)
mods.get(i).apply(this, offset);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-21 09:56:53 UTC
(rev 18610)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-21 14:46:32 UTC
(rev 18611)
@@ -11,8 +11,10 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.3.4_dev_2013.08.20c"
+___JmolVersion="13.3.4_dev_2013.08.21"
+bug fix: JANA2006 reader not processing occupancies
+ -- read now forced to "PACKED" in order to calculate site multiplicity
bug fix: CIF reader not reading _CCDC_GEOM_BOND_TYPE record
bug fix: File dialog problems with paths having space
bug fix: GAMESS reader not reading energies
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