Revision: 18515
http://sourceforge.net/p/jmol/code/18515
Author: hansonr
Date: 2013-07-31 12:28:48 +0000 (Wed, 31 Jul 2013)
Log Message:
-----------
___JmolVersion="13.3.4_dev_2013.07.31"
TODO: CIF reader is not handling modulation for symmetry-related atoms
correctly yet.
new feature: msCIF file reading of incommensurate modulation data as vibration
new feature: msCIF file filter "MODAXES=xxx" where xxx = X,XY,XYZ,YZ,etc.
new feature: msCIF file filter "MODAVE" gives average structure with vibration
vectors.
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/quantum/MoldenReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-07-31 01:52:42 UTC (rev 18514)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-07-31 12:28:48 UTC (rev 18515)
@@ -45,9 +45,11 @@
import org.jmol.util.BS;
import org.jmol.util.Logger;
import org.jmol.util.Matrix4f;
+import org.jmol.util.Modulation;
import org.jmol.util.P3;
import org.jmol.util.SimpleUnitCell;
import org.jmol.util.TextFormat;
+import org.jmol.util.V3;
/**
@@ -94,7 +96,8 @@
private int conformationIndex;
private boolean filterAssembly;
private boolean allowRotations = true;
- private String modulationAxes;
+ private boolean modVib;
+ private String modAxes;
@@ -116,13 +119,14 @@
}
protected void initializeReaderCif() throws Exception {
- if (checkFilterKey("CONF "))
- configurationPtr = parseIntAt(filter, filter.indexOf("CONF ") + 5);
appendedData = (String) htParams.get("appendedData");
- isMolecular = (filter != null && filter.indexOf("MOLECUL") >= 0);
- filterAssembly = (filter != null && filter.indexOf("$") >= 0);
- int pt = (filter == null ? -1 : filter.indexOf("MODULATIONAXES="));
- modulationAxes = (pt >= 0 ? filter.substring(pt + 15) : null);
+ String conf = getFilter("CONF ");
+ if (conf != null)
+ configurationPtr = parseIntStr(conf);
+ isMolecular = checkFilterKey("MOLECUL");
+ filterAssembly = checkFilterKey("$");
+ modAxes = getFilter("MODAXES=");
+ modVib = checkFilterKey("MODVIB");
if (isMolecular) {
if (!doApplySymmetry) {
doApplySymmetry = true;
@@ -151,13 +155,14 @@
if (!readAllData())
break;
if (appendedData != null) {
- tokenizer = new CifDataReader(new BufferedReader(new
StringReader(appendedData)));
+ tokenizer = new CifDataReader(new BufferedReader(new StringReader(
+ appendedData)));
while ((key = tokenizer.peekToken()) != null)
if (!readAllData())
break;
- }
+ }
continuing = false;
- }
+ }
public String readNextLine() throws Exception {
// from CifDataReader
@@ -220,9 +225,9 @@
appendLoadNote("CIF Reader: Too high modulation dimension (" +
modDim + ") -- ignored");
modDim = 0;
} else {
- appendLoadNote("CIF Reader: modulation dimension = " + modDim + "
symmetry operations are disabled.");
+ appendLoadNote("CIF Reader: modulation dimension = " + modDim);
htModulation = new Hashtable<String, P3>();
- allowRotations = false;
+ //allowRotations = false;
}
} else if (key.startsWith("_cell_")) {
processCellParameter();
@@ -1902,7 +1907,12 @@
};
/**
- * creates entries in htModulation
+ * creates entries in htModulation with a key of
+ * the form: type_id_axis;atomLabel where
+ * type = W|F|D|O (wave vector, Fourier index, displacement, occupancy);
+ * id = 1|2|3|S (Fourier index or special -- sawtooth or crenel);
+ * axis (optional) = o|x|y|z (o indicates irrelevant -- occupancy);
+ * and ;atomLabel is only for D and O.
*
* @throws Exception
*/
@@ -1923,7 +1933,7 @@
case FWV_ID:
case FWV_DISP_ID:
case FWV_OCC_ID:
- switch(tok) {
+ switch (tok) {
case WV_ID:
id = "W_" + field;
break;
@@ -1937,16 +1947,15 @@
id = "O_" + field;
break;
}
- c = w = 99999;
break;
case DISP_SPEC_LABEL:
- if (id == null)
- id = "D_S";
+ id = "D_S";
atomLabel = field;
+ axis = "0";
break;
case OCC_SPECIAL_LABEL:
- id = "O_C";
- c = w = 99999;
+ id = "O_S";
+ axis = "0";
//$FALL-THROUGH$
case FWV_DISP_LABEL:
case FWV_OCC_LABEL:
@@ -1955,18 +1964,19 @@
break;
case FWV_DISP_AXIS:
axis = field;
- if (modulationAxes != null &&
modulationAxes.indexOf(axis.toUpperCase()) < 0)
+ if (modAxes != null
+ && modAxes.indexOf(axis.toUpperCase()) < 0)
ignore = true;
break;
case WV_X:
case FWV_X:
case FWV_DISP_COS:
case FWV_OCC_COS:
- case OCC_CRENEL_C:
+ case OCC_CRENEL_C:
case DISP_SAW_AX:
pt.x = parseFloatStr(field);
break;
- case FWV_Q1_COEF:
+ case FWV_Q1_COEF:
id += "_q_";
pt.x = parseFloatStr(field);
switch (modDim) {
@@ -2006,16 +2016,30 @@
w = parseFloatStr(field);
break;
}
- if (ignore || Float.isNaN(pt.x + pt.y + pt.z + c + w) || id == null)
+ if (ignore || Float.isNaN(pt.x + pt.y + pt.z) || id == null)
continue;
- if (axis != null)
- id += axis;
- if (c != 99999)
- addModulation("D_s;" + atomLabel, P3.new3(c, w, 0));
- if (atomLabel != null)
- id += ";" + atomLabel;
- addModulation(id, pt);
- break;
+ switch (id.charAt(0)) {
+ case 'W':
+ case 'F':
+ break;
+ case 'D':
+ case 'O':
+ if (atomLabel == null || axis == null)
+ continue;
+ if (id.equals("D_S")) {
+ // saw tooth displacement center/width/Axyz
+ if (pt.x != 0)
+ addModulation("D_Sx;" + atomLabel, P3.new3(c, w, pt.x));
+ if (pt.y != 0)
+ addModulation("D_Sy;" + atomLabel, P3.new3(c, w, pt.y));
+ if (pt.z != 0)
+ addModulation("D_Sz;" + atomLabel, P3.new3(c, w, pt.z));
+ continue;
+ }
+ id += axis + ";" + atomLabel;
+ break;
+ }
+ addModulation(id, pt);
}
}
}
@@ -2037,8 +2061,8 @@
switch (key.charAt(0)) {
case 'D':
case 'O':
- // displacement - fix modulus/phase option
- if (pt.z > 0) {
+ // fix modulus/phase option only for non-special modulations;
+ if (pt.z == 1 && key.charAt(2) != 'S') {
// modulus/phase M cos(2pi(q.r) + 2pi(p))
// --> A cos(2pi(p)) cos(2pi(q.r)) + A sin(-2pi(p)) sin(2pi(q.r))
double a = pt.x;
@@ -2072,22 +2096,57 @@
for (Entry<String, P3> e : htModulation.entrySet()) {
String key = e.getKey();
switch (key.charAt(0)) {
+ case 'O':
+ // TODO
+ break;
case 'D':
- P3 coefs = e.getValue();
- String label = key.substring(key.indexOf(";") + 1);
- P3 q = htModulation.get("F_" + key.substring(2, 3));
char axis = key.charAt(3);
- atomSetCollection.addAtomModulation(label, q, axis, coefs);
- haveAtomMods = true;
+ if (key.charAt(2) == 'S') {
+ // TODO -- sawtooth, so now what?
+ } else {
+ P3 coefs = e.getValue();
+ String label = key.substring(key.indexOf(";") + 1);
+ key = "F_" + key.substring(2, 3);
+ P3 q = htModulation.get(key);
+ addAtomModulation(label, q, axis, coefs);
+ haveAtomMods = true;
+ }
break;
}
}
- if (haveAtomMods)
- for (int i = atomSetCollection.getAtomCount(); --i >= 0;)
- atomSetCollection.modulateAtom(i);
+ if (!haveAtomMods)
+ return;
+ atoms = atomSetCollection.getAtoms();
+ symmetry = atomSetCollection.getSymmetry();
+ for (int i = atomSetCollection.getAtomCount(); --i >= 0;)
+ modulateAtom(i, modVib);
}
+
+ private Map<String, JmolList<Modulation>> htAtomMods;
+
+ public void addAtomModulation(String label, P3 q, char axis, P3 coefs) {
+ if (htAtomMods == null)
+ htAtomMods = new Hashtable<String, JmolList<Modulation>>();
+ JmolList<Modulation> list = htAtomMods.get(label);
+ if (list == null)
+ htAtomMods.put(label, list = new JmolList<Modulation>());
+ list.addLast(new Modulation(q, axis, coefs));
+ }
+
+ public void modulateAtom(int i, boolean modvib) {
+ Atom a = atoms[i];
+ a.vib = new V3();
+ JmolList<Modulation> list = htAtomMods.get(a.atomName);
+ if (list == null || symmetry == null)
+ return;
+ Modulation.modulateAtom(a, list, a.vib);
+ if (!modvib) {
+ a.add(a.vib);
+ a.vib.scale(-1);
+ }
+ symmetry.toCartesian(a.vib, true);
+ }
-
////////////////////////////////////////////////////////////////
// symmetry operations
////////////////////////////////////////////////////////////////
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-07-31 01:52:42 UTC (rev 18514)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-07-31 12:28:48 UTC (rev 18515)
@@ -194,10 +194,10 @@
// from load files "tls.out" "xxxx.pdb"
vTlsModels = ( JmolList<Map<String, Object>>)
htParams.remove("vTlsModels");
}
- if (checkFilterKey("TYPE ")) {
+ String s = getFilter("TYPE ");
+ if (s != null) {
// first column, nColumns;
- String s = filter.substring(filter.indexOf("TYPE ") + 5).replace(',', '
').replace(';', ' ');
- String[] tokens = Parser.getTokens(s);
+ String[] tokens = Parser.getTokens(s.replace(',', ' '));
atomTypePt0 = Integer.parseInt(tokens[0]) - 1;
int pt = tokens[1].indexOf("=");
if (pt >= 0) {
@@ -207,8 +207,9 @@
}
atomTypeLen = Integer.parseInt(tokens[1].substring(0, pt));
}
- if (checkFilterKey("CONF ")) {
- configurationPtr = parseIntAt(filter, filter.indexOf("CONF ") + 5);
+ String conf = getFilter("CONF ");
+ if (conf != null) {
+ configurationPtr = parseIntStr(conf);
sbIgnored = new SB();
sbSelected = new SB();
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java
2013-07-31 01:52:42 UTC (rev 18514)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java
2013-07-31 12:28:48 UTC (rev 18515)
@@ -47,10 +47,8 @@
filter = "alpha";
else if (checkFilterKey("BETA"))
filter = "beta";
- else if (checkFilterKey("SYM="))
- filter = filter.substring(filter.indexOf("SYM=") + 4);
- else
- filter = null;
+ else
+ filter = getFilter("SYM=");
}
@Override
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
2013-07-31 01:52:42 UTC (rev 18514)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
2013-07-31 12:28:48 UTC (rev 18515)
@@ -114,14 +114,12 @@
@Override
public void initializeReader() throws Exception {
if (filter != null) {
- if (checkFilterKey("CHARGE=")) {
- chargeType = filter.substring(filter.indexOf("CHARGE=") + 7);
- if (chargeType.length() > 4)
- chargeType = chargeType.substring(0, 4);
- }
+ chargeType = getFilter("CHARGE=");
+ if (chargeType != null && chargeType.length() > 4)
+ chargeType = chargeType.substring(0, 4);
filter = filter.replace('(', '{').replace(')', '}');
filter = TextFormat.simpleReplace(filter, " ", " ");
- isAllQ = (filter.indexOf("Q=ALL") >= 0);
+ isAllQ = checkFilterKey("Q=ALL");
if (!isAllQ && filter.indexOf("{") >= 0)
setDesiredQpt(filter.substring(filter.indexOf("{")));
filter = TextFormat.simpleReplace(filter, "-PT", "");
@@ -713,7 +711,7 @@
lastQPt = tokens[1];
//TODO not quite right: can have more than two options.
- if (!isOK && filter != null && checkFilterKey("Q=")) {
+ if (!isOK && checkFilterKey("Q=")) {
// check for an explicit q=n or q={1/4 1/2 1/4}
if (desiredQpt != null) {
v.sub2(desiredQpt, qvec);
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-07-31 01:52:42 UTC (rev 18514)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-07-31 12:28:48 UTC (rev 18515)
@@ -41,7 +41,6 @@
import org.jmol.util.Escape;
import org.jmol.util.Matrix3f;
import org.jmol.util.Matrix4f;
-import org.jmol.util.Modulation;
import org.jmol.util.P3;
import org.jmol.util.P3i;
import org.jmol.util.Tensor;
@@ -1373,8 +1372,6 @@
atom1.atomSite = atomSite;
atom1.bsSymmetry = BSUtil.newAndSetBit(iCellOpPt + iSym);
atom1.bsSymmetry.set(iSym);
- if (htAtomMods != null)
- modulateAtom(atom1.index);
if (addCartesian)
cartesians[pt++] = cartesian;
if (atoms[i].tensors != null) {
@@ -2006,26 +2003,4 @@
setAtomSetCollectionAuxiliaryInfo("trajectorySteps", trajectorySteps);
}
- private Map<String, JmolList<Modulation>> htAtomMods;
-
- public void addAtomModulation(String label, P3 q, char axis, P3 coefs) {
- if (htAtomMods == null)
- htAtomMods = new Hashtable<String, JmolList<Modulation>>();
- JmolList<Modulation> list = htAtomMods.get(label);
- if (list == null)
- htAtomMods.put(label, list = new JmolList<Modulation>());
- list.addLast(new Modulation(q, axis, coefs));
- }
-
- public void modulateAtom(int i) {
- Atom a = atoms[i];
- a.vib = new V3();
- JmolList<Modulation> list = htAtomMods.get(a.atomName);
- if (list == null || symmetry == null)
- return;
- Modulation.modulateAtom(a, list, a.vib);
- symmetry.toCartesian(a.vib, true);
-
- }
-
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-07-31 01:52:42 UTC (rev 18514)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-07-31 12:28:48 UTC (rev 18515)
@@ -885,7 +885,12 @@
private String filter1, filter2;
- public boolean checkFilterKey(String key) {
+ protected String getFilter(String key) {
+ int pt = (filter == null ? -1 : filter.indexOf(key));
+ return (pt < 0 ? null : filter.substring(pt + key.length(),
filter.indexOf(";", pt)));
+ }
+
+ protected boolean checkFilterKey(String key) {
return (filter != null && filter.indexOf(key) >= 0);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-31 01:52:42 UTC
(rev 18514)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-31 12:28:48 UTC
(rev 18515)
@@ -11,10 +11,13 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.3.4_dev_2013.07.30"
+___JmolVersion="13.3.4_dev_2013.07.31"
+TODO: CIF reader is not handling modulation for symmetry-related atoms
correctly yet.
+
new feature: msCIF file reading of incommensurate modulation data as vibration
-new feature: msCIF file filter "MODULATIONAXES=xxx" where xxx =
X,XY,XYZ,YZ,etc.
+new feature: msCIF file filter "MODAXES=xxx" where xxx = X,XY,XYZ,YZ,etc.
+new feature: msCIF file filter "MODAVE" gives average structure with vibration
vectors.
bug fix: minimization can fail after MMFF switches to UFF.
bug fix: CIF reader fix for no element given "phenyl1" in ZjzxlegN.cif
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