Revision: 18402
http://sourceforge.net/p/jmol/code/18402
Author: hansonr
Date: 2013-07-02 07:17:11 +0000 (Tue, 02 Jul 2013)
Log Message:
-----------
{*}.tensor("ms","all")
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
trunk/Jmol/src/org/jmol/util/Tensor.java
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-07-02
06:54:14 UTC (rev 18401)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-07-02
07:17:11 UTC (rev 18402)
@@ -3431,6 +3431,7 @@
public JmolList<Tensor> getInteractionTensorList(String type, BS bs) {
type = type.toLowerCase();
BS bsModels = getModelBitSet(bs, false);
+ int iAtom = (bs.cardinality() == 1 ? bs.nextSetBit(0) : -1);
JmolList<Tensor> list = new JmolList<Tensor>();
for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i +
1)) {
JmolList<Tensor> tensors = (JmolList<Tensor>)
getModelAuxiliaryInfoValue(i, "interactionTensors");
@@ -3439,7 +3440,7 @@
int n = tensors.size();
for (int j = 0; j < n; j++) {
Tensor t = tensors.get(j);
- if (t.type.equals(type) && t.isSelected(bs))
+ if (t.type.equals(type) && t.isSelected(bs, iAtom))
list.addLast(t);
}
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-02
06:54:14 UTC (rev 18401)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-02
07:17:11 UTC (rev 18402)
@@ -838,9 +838,11 @@
// {*}.tensor("efg","eigenvalues")
// T.tensor is set to allow exactly 2 parameters
// change that in T.java to adjust
+ if (args.length == 0 || args.length > 2)
+ return false;
BS bs = SV.getBitSet(getX(), false);
String tensorType = SV.sValue(args[0]).toLowerCase();
- String infoType = ";" + SV.sValue(args[1]).toLowerCase() + ".";
+ String infoType = ";" + (args.length == 1 ? "all" :
SV.sValue(args[1]).toLowerCase()) + ".";
JmolList<Object> data = new JmolList<Object>();
if (tensorType.equals("isc")) {
JmolList<Tensor> list = viewer.modelSet.getInteractionTensorList("isc",
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2013-07-02 06:54:14 UTC (rev
18401)
+++ trunk/Jmol/src/org/jmol/script/T.java 2013-07-02 07:17:11 UTC (rev
18402)
@@ -695,6 +695,8 @@
public final static int within = 20 | 0 << 9 | mathfunc;
final static int write = 21 | 0 << 9 | mathfunc | scriptCommand;
final static int cache = 22 | 0 << 9 | mathfunc | scriptCommand;
// new in Jmol 13.1.2
+ final static int tensor = 23 | 0 << 9 | mathfunc | mathproperty;
+
// xxx(a)
final static int acos = 3 | 1 << 9 | mathfunc;
@@ -746,7 +748,6 @@
public final static int add = 1 | 2 << 9 | mathfunc | mathproperty;
public final static int distance = 2 | 2 << 9 | mathfunc | mathproperty;
final static int replace = 3 | 2 << 9 | mathfunc | mathproperty;
- final static int tensor = 4 | 2 << 9 | mathfunc | mathproperty;
// xxx(a,b,c)
Modified: trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2013-07-02
06:54:14 UTC (rev 18401)
+++ trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2013-07-02
07:17:11 UTC (rev 18402)
@@ -78,7 +78,7 @@
Atom[] atoms = modelSet.atoms;
for (int i = tensors.size(); --i >= 0;) {
Tensor t = tensors.get(i);
- if (isAll || t.isSelected(bsSelected)) {
+ if (isAll || t.isSelected(bsSelected, -1)) {
Ellipsoid e = atomEllipsoids.get(t);
boolean isNew = (size != 0 && e == null);
if (isNew)
@@ -214,7 +214,7 @@
if (isOn)
setSize(Integer.MAX_VALUE, bs);
for (Ellipsoid e : atomEllipsoids.values())
- if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs))
+ if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs, -1))
e.isOn = isOn;
return;
}
@@ -225,7 +225,7 @@
if (selectedAtoms != null)
bs = selectedAtoms;
for (Ellipsoid e : atomEllipsoids.values())
- if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs)) {
+ if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs, -1))
{
e.colix = getColixI(colix, pid, e.tensor.atomIndex1);
e.pid = pid;
}
@@ -235,7 +235,7 @@
if ("translucency" == propertyName) {
boolean isTranslucent = (value.equals("translucent"));
for (Ellipsoid e : atomEllipsoids.values())
- if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs))
+ if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs, -1))
e.colix = C.getColixTranslucent3(e.colix, isTranslucent,
translucentLevel);
return;
Modified: trunk/Jmol/src/org/jmol/util/Tensor.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Tensor.java 2013-07-02 06:54:14 UTC (rev
18401)
+++ trunk/Jmol/src/org/jmol/util/Tensor.java 2013-07-02 07:17:11 UTC (rev
18402)
@@ -26,6 +26,8 @@
import java.util.Arrays;
import java.util.Comparator;
+import java.util.Hashtable;
+import java.util.Map;
/**
* @author Bob Hanson hans...@stolaf.edu 6/30/2013
@@ -113,6 +115,11 @@
public int atomIndex1 = -1;
public int atomIndex2 = -1;
+ private static final String infoList = ";............." + ";eigenvalues.." +
";eigenvectors."
+ + ";asymmetric..." + ";symmetric...." + ";trace........"
+ + ";haeberlen...." + ";eulerzyz....." + ";eulerzxz....."
+ + ";quaternion..." + ";indices......" + ";string......."
+ + ";type........." + ";all.........";
/**
* returns an object of the specified type, including "eigenvalues",
* "eigenvectors", "asymmetric", "symmetric", "trace", "indices", and "type"
@@ -123,11 +130,15 @@
public Object getInfo(String infoType) {
if (infoType.charAt(0) != ';')
infoType = ";" + infoType + ".";
- switch ((";............." + ";eigenvalues.." + ";eigenvectors."
- + ";asymmetric..." + ";symmetric...." + ";trace........"
- + ";haeberlen...." + ";eulerzyz....." + ";eulerzxz....."
- + ";quaternion..." + ";indices......" + ";string......." +
";type.........")
- .indexOf(infoType) / 14) {
+ switch (infoList.indexOf(infoType) / 14) {
+ default:
+ Map<String, Object> info = new Hashtable<String, Object>();
+ String[] s = Parser.getTokens(TextFormat.replaceAllCharacter(infoList,
";.", ' ').trim());
+ Arrays.sort(s);
+ for (int i = 0; i < s.length; i++)
+ if (!s[i].equals("all"))
+ info.put(s[i], getInfo(s[i]));
+ return info;
case 1:
return eigenValues;
case 2:
@@ -173,8 +184,6 @@
return this.toString();
case 12:
return type;
- default:
- return null;
}
}
@@ -361,8 +370,10 @@
atomIndex2 = index2;
}
- public boolean isSelected(BS bsSelected) {
- return bsSelected.get(atomIndex1) && (atomIndex2 < 0 ||
bsSelected.get(atomIndex2));
+ public boolean isSelected(BS bsSelected, int iAtom) {
+ return (iAtom >= 0 ? (atomIndex1 == iAtom || atomIndex2 == iAtom)
+ : bsSelected.get(atomIndex1)
+ && (atomIndex2 < 0 || bsSelected.get(atomIndex2)));
}
/**
@@ -468,7 +479,7 @@
@Override
public String toString() {
- return (type + "\n" + (eigenVectors == null ? ""
+ return (type + " " + modelIndex + " " + atomIndex1 + " " + atomIndex2 +
"\n" + (eigenVectors == null ? ""
+ eigenValues[0] : eigenVectors[0] + "\t" + eigenValues[0] + "\t"
+ "\n" + eigenVectors[1] + "\t" + eigenValues[1] + "\t" + "\n"
+ eigenVectors[2] + "\t" + eigenValues[2] + "\t" + "\n"));
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
This SF.net email is sponsored by Windows:
Build for Windows Store.
http://p.sf.net/sfu/windows-dev2dev
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
