Revision: 18517
http://sourceforge.net/p/jmol/code/18517
Author: hansonr
Date: 2013-08-08 03:06:45 +0000 (Thu, 08 Aug 2013)
Log Message:
-----------
partial commit
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/ModulationReader.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-08-07 19:52:31 UTC (rev 18516)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-08-08 03:06:45 UTC (rev 18517)
@@ -128,6 +128,11 @@
molecularType = "filter \"MOLECULAR\"";
}
initializeMod();
+ readCifData();
+ continuing = false;
+ }
+
+ private void readCifData() throws Exception {
/*
* Modified for 10.9.64 9/23/06 by Bob Hanson to remove as much as possible
@@ -141,7 +146,6 @@
* report if it finds data where a key is supposed to be.
*/
line = "";
- skipping = false;
while ((key = tokenizer.peekToken()) != null)
if (!readAllData())
break;
@@ -152,7 +156,6 @@
if (!readAllData())
break;
}
- continuing = false;
}
public String readNextLine() throws Exception {
@@ -211,18 +214,7 @@
} else if (key.startsWith("_chemical_formula_sum") ||
key.equals("_chem_comp_formula")) {
processChemicalInfo("formula");
} else if (key.equals("_cell_modulation_dimension") && !modAverage) {
- modDim = parseIntStr(data);
- if (modDim > 1) {
- // not ready for dim=2
- appendLoadNote("CIF Reader: Too high modulation dimension (" +
modDim + ") -- reading average structure");
- modDim = 0;
- modAverage = true;
- } else {
- appendLoadNote("CIF Reader: modulation dimension = " + modDim);
- htModulation = new Hashtable<String, P3>();
- //allowRotations = false;
- }
- incommensurate = (modDim > 0);
+ setModDim(data);
} else if (key.startsWith("_cell_")) {
processCellParameter();
} else if (key.startsWith("_symmetry_space_group_name_H-M")
@@ -265,8 +257,7 @@
@Override
protected void finalizeReader() throws Exception {
- if (incommensurate)
-
atomSetCollection.setBaseSymmetryAtomCount(atomSetCollection.getAtomCount());
+ finalizeIncommensurate();
if (atomSetCollection.getAtomCount() == nAtoms)
atomSetCollection.removeCurrentAtomSet();
else
@@ -285,8 +276,7 @@
atomSetCollection.applySymmetryBio(vBiomts, notionalUnitCell,
applySymmetryToBonds, filter);
}
}
- if (incommensurate && htModulation != null)
- setModulation();
+ setModulation();
finalizeReaderASCR();
String header = tokenizer.getFileHeader();
if (header.length() > 0)
@@ -332,8 +322,9 @@
// This speeds up calculation, because no crosschecking
// No special-position atoms in mmCIF files, because there will
// be no center of symmetry, no rotation-inversions,
- // no atom-centered rotation axes, and no mirror or glide planes.
- atomSetCollection.setCheckSpecial(checkSpecial && !isPDB);
+ // no atom-centered rotation axes, and no mirror or glide planes.
+ if (isPDB)
+ atomSetCollection.setCheckSpecial(false);
boolean doCheck = doCheckUnitCell && !isPDB;
applySymTrajASCR();
if (doCheck && (bondTypes.size() > 0 || isMolecular))
@@ -2026,17 +2017,17 @@
if (id.equals("D_S")) {
// saw tooth displacement center/width/Axyz
if (pt.x != 0)
- addModulation(htModulation, "D_Sx;" + atomLabel, P3.new3(c, w,
pt.x));
+ addModulation(null, "D_Sx;" + atomLabel, P3.new3(c, w, pt.x));
if (pt.y != 0)
- addModulation(htModulation, "D_Sy;" + atomLabel, P3.new3(c, w,
pt.y));
+ addModulation(null, "D_Sy;" + atomLabel, P3.new3(c, w, pt.y));
if (pt.z != 0)
- addModulation(htModulation, "D_Sz;" + atomLabel, P3.new3(c, w,
pt.z));
+ addModulation(null, "D_Sz;" + atomLabel, P3.new3(c, w, pt.z));
continue;
}
id += axis + ";" + atomLabel;
break;
}
- addModulation(htModulation, id, pt);
+ addModulation(null, id, pt);
}
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/ModulationReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/ModulationReader.java
2013-08-07 19:52:31 UTC (rev 18516)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/ModulationReader.java
2013-08-08 03:06:45 UTC (rev 18517)
@@ -53,11 +53,11 @@
protected String modAxes;
protected boolean modAverage;
protected boolean checkSpecial = true;
- protected boolean modCentered;
- protected boolean modOffset;
protected int modDim;
+ //protected boolean modCentered;
+ //protected boolean modOffset;
protected boolean incommensurate;
- protected Map<String, P3> htModulation;
+ private Map<String, P3> htModulation;
protected Atom[] atoms;
protected void initializeMod() throws Exception {
@@ -65,18 +65,63 @@
modVib = checkFilterKey("MODVIB");
modAverage = checkFilterKey("MODAVE");
checkSpecial = !checkFilterKey("NOSPECIAL");
- modOffset = !checkFilterKey("NOMODOFFSET");
- modCentered = !checkFilterKey("NOMODCENT");
+ atomSetCollection.setCheckSpecial(checkSpecial);
allowRotations = !checkFilterKey("NOSYM");
- if (!modCentered) {
- if (doCentralize && filter.indexOf("CENTER") ==
filter.lastIndexOf("CENTER"))
- doCentralize = false;
- appendLoadNote("CIF reader not using delta to recenter modulation.");
+ //modOffset = !checkFilterKey("NOMODOFFSET");
+ //modCentered = !checkFilterKey("NOMODCENT");
+ //if (!modCentered) {
+ // if (doCentralize && filter.indexOf("CENTER") ==
filter.lastIndexOf("CENTER"))
+ // doCentralize = false;
+ // appendLoadNote("CIF reader not using delta to recenter modulation.");
+ // }
+ }
+
+ private JmolList<float[]> lattvecs;
+
+ protected void addLatticeVector(String data) {
+ if (lattvecs == null)
+ lattvecs = new JmolList<float[]>();
+ float[] a = getTokensFloat(data, null, modDim + 3);
+ boolean isOK = false;
+ for (int i = a.length; --i >= 0 && !isOK;) {
+ if (Float.isNaN(a[i]))
+ return;
+ isOK |= (a[i] != 0);
}
+ if (isOK)
+ lattvecs.addLast(a);
}
+ protected void finalizeIncommensurate() {
+ if (incommensurate)
+
atomSetCollection.setBaseSymmetryAtomCount(atomSetCollection.getAtomCount());
+ if (lattvecs != null)
+ atomSetCollection.getSymmetry().addLatticeVectors(lattvecs);
+ }
+
+ protected void setModDim(String token) {
+ modDim = parseIntStr(token);
+ if (modAverage)
+ return;
+ if (modDim > 1) {
+ // not ready for dim=2
+ appendLoadNote("Too high modulation dimension (" + modDim + ") --
reading average structure");
+ modDim = 0;
+ modAverage = true;
+ } else {
+ appendLoadNote("Modulation dimension = " + modDim);
+ htModulation = new Hashtable<String, P3>();
+ }
+ incommensurate = (modDim > 0);
+ }
+ protected P3 getModulationVector(String id) {
+ return htModulation.get(id);
+ }
+
protected void addModulation(Map<String, P3> map, String id, P3 pt) {
+ if (map == null)
+ map = htModulation;
map.put(id, pt);
Logger.info("Adding " + id + " " + pt);
if (id.charAt(0) == 'W' || id.charAt(0) == 'F')
@@ -88,6 +133,8 @@
*
*/
protected void setModulation() {
+ if (!incommensurate || htModulation == null)
+ return;
Map<String, P3> map = new Hashtable<String, P3>();
for (Entry<String, P3> e : htModulation.entrySet()) {
String key = e.getKey();
@@ -201,8 +248,8 @@
*
* @param i
* @param modvib
- * @param pt0
- * @param sb
+ * @param pt0
+ * @param sb
*/
public void modulateAtom(int i, boolean modvib, P3 pt0, SB sb) {
Atom a = atoms[i];
@@ -210,54 +257,37 @@
JmolList<Modulation> list = htAtomMods.get(a.atomName);
if (list == null || symmetry == null)
return;
-// if (pt0 != null) {
- int iop = a.bsSymmetry.nextSetBit(0);
- if (iop < 0)
- iop = 0;
- Matrix4f m = symmetry.getSpaceGroupOperation(iop);
- m.getRotationScale(mtemp3);
- //mtemp3i.invertM(mtemp3);
- //opTrans = symmetry.getOriginalTranslation(iop);
- //m.get(opTrans);
- float epsilon = (modCentered ? symmetry.getModParam(iop, 0) : 1);
- float delta = (modCentered ? symmetry.getModParam(iop, 1) : 0);
- if (modOffset) {
- ptemp.setT(a);
- symmetry.unitize(ptemp);
- offset.sub2(a, ptemp);
- //getOffset(pt0, atoms[i]);
- }
- //System.out.println("=========CIF i=" + i + " " + a.atomName + " " + a);
- //System.out.println("op=" + (iop+1) + " " +
symmetry.getSpaceGroupXyz(iop, false) + " ep=" + epsilon + " de=" + delta +
"\nopTrans=" + opTrans + " a=" + a);
- qNorm = V3.newV(list.get(0).getWaveVector());
- qNorm.normalize();
- Modulation.modulateAtom(ptemp, offset, list, epsilon, delta, a.vib);
- System.out.println("a.vib(abc)=" + a.vib);
- //System.out.println("CIF R=" + mtemp3);
- //System.out.println("CIF R-1=" + mtemp3i);
- mtemp3.transform(a.vib);
- sb.append((int)(qNorm.dot(offset)*1.01f) + "\n");
-// } else {
-// Modulation.modulateAtom(a, null, list, 1, 0f, a.vib);
-// sb.append("0\n");
-// }
+ // if (pt0 != null) {
+ int iop = a.bsSymmetry.nextSetBit(0);
+ if (iop < 0)
+ iop = 0;
+ Matrix4f m = symmetry.getSpaceGroupOperation(iop);
+ m.getRotationScale(mtemp3);
+ //mtemp3i.invertM(mtemp3);
+ //opTrans = symmetry.getOriginalTranslation(iop);
+ //m.get(opTrans);
+ float epsilon = symmetry.getModParam(iop, 0);
+ float delta = symmetry.getModParam(iop, 1);
+ ptemp.setT(a);
+ symmetry.unitize(ptemp);
+ offset.sub2(a, ptemp);
+ //System.out.println("=========CIF i=" + i + " " + a.atomName + " " + a);
+ //System.out.println("op=" + (iop + 1) + " "
+ // + symmetry.getSpaceGroupXyz(iop, false) + " ep=" + epsilon + " de="
+ //+ delta + " a=" + a);
+ qNorm = V3.newV(list.get(0).getWaveVector());
+ qNorm.normalize();
+ Modulation.modulateAtom(ptemp, offset, list, epsilon, delta, a.vib);
+ System.out.println("a.vib(abc)=" + a.vib);
+ mtemp3.transform(a.vib);
+ sb.append((int) (qNorm.dot(offset) * 1.01f) + "\n");
if (!modvib) {
a.add(a.vib);
a.vib.scale(-1);
}
symmetry.toCartesian(a.vib, true);
- System.out.println("a.vib(xyz)=" + a.vib);
+ //System.out.println("a.vib(xyz)=" + a.vib);
//if (i == 98 || i == 99)
- //System.out.println("CIFTEST");
+ //System.out.println("CIFTEST");
}
-
- // private void getOffset(P3 pt0, P3 pt1) {
- // ptemp.setT(pt1);
- //
- // //ptemp.sub(opTrans);
- // //mtemp3i.transform(ptemp);
- // //offset.sub2(ptemp, pt0);
- // System.out.println("pt0=" + pt0 + " ptemp=" + ptemp);
- // }
-
}
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
Get 100% visibility into Java/.NET code with AppDynamics Lite!
It's a free troubleshooting tool designed for production.
Get down to code-level detail for bottlenecks, with <2% overhead.
Download for free and get started troubleshooting in minutes.
http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
