Revision: 18549
http://sourceforge.net/p/jmol/code/18549
Author: hansonr
Date: 2013-08-11 23:03:12 +0000 (Sun, 11 Aug 2013)
Log Message:
-----------
NMR interaction tensor correction -- needed atomSites.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java
Modified: trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java
===================================================================
--- trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java 2013-08-11 22:01:22 UTC
(rev 18548)
+++ trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java 2013-08-11 23:03:12 UTC
(rev 18549)
@@ -35,6 +35,7 @@
import org.jmol.io.JmolBinary;
import org.jmol.modelset.Atom;
import org.jmol.modelset.MeasurementData;
+import org.jmol.modelset.Model;
import org.jmol.util.BS;
import org.jmol.util.Escape;
import org.jmol.util.JmolList;
@@ -87,40 +88,64 @@
}
/**
- * Returns a list of tensors that are of the specified type and
- * have both atomIndex1 and atomIndex2 in bs.
+ * Returns a list of tensors that are of the specified type and have both
+ * atomIndex1 and atomIndex2 in bsA. If there is just one atom specified,
then
+ * the list is "all tensors involving this atom".
*
+ * We have to use atom sites, because interaction tensors are not duplicated.
+ *
* @param type
- * @param bs
- * @param bs2
+ * @param bsA
* @return list of Tensors
*/
@SuppressWarnings("unchecked")
- private JmolList<Tensor> getInteractionTensorList(String type, BS bs, BS
bs2) {
+ private JmolList<Tensor> getInteractionTensorList(String type, BS bsA) {
type = type.toLowerCase();
- BS bsModels = viewer.getModelBitSet(bs, false);
- int iAtom = (bs.cardinality() == 1 ? bs.nextSetBit(0) : -1);
+
+ BS bsModels = viewer.getModelBitSet(bsA, false);
+ BS bs1 = getAtomSiteBS(bsA);
+ int iAtom = (bs1.cardinality() == 1 ? bs1.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>)
viewer.getModelAuxiliaryInfoValue(i, "interactionTensors");
+ JmolList<Tensor> tensors = (JmolList<Tensor>) viewer
+ .getModelAuxiliaryInfoValue(i, "interactionTensors");
if (tensors == null)
continue;
int n = tensors.size();
for (int j = 0; j < n; j++) {
Tensor t = tensors.get(j);
- if (t.type.equals(type)
- && t.isSelected(bs, iAtom)
- && (bs2 == null || bs2.get(getOtherAtom(t, iAtom))))
-
+ if (t.type.equals(type) && t.isSelected(bs1, iAtom))
list.addLast(t);
- }
+ }
}
return list;
}
- private int getOtherAtom(Tensor t, int iAtom) {
- return (t.atomIndex1 == iAtom ? t.atomIndex2 : t.atomIndex1);
+ /**
+ * Interaction tensors are not repeated for every possible combination. They
are just for the
+ * base atom set. These are identified as a.atomIndex ==
models[b.modelIndex].firstAtomIndex + b.atomSite - 1
+ * @param bsA
+ * @return new bs in terms of atom sites
+ */
+ private BS getAtomSiteBS(BS bsA) {
+ if (bsA == null)
+ return null;
+ BS bs = new BS();
+ Atom[] atoms = viewer.modelSet.atoms;
+ Model[] models = viewer.modelSet.models;
+
+ for (int i = bsA.nextSetBit(0); i >= 0; i = bsA.nextSetBit(i + 1)) {
+ if (!bsA.get(i))
+ continue;
+ Atom a = atoms[i];
+ bs.set(models[a.modelIndex].firstAtomIndex - 1 + a.atomSite);
+ }
+ return bs;
}
+
+// private int getOtherAtom(Tensor t, int iAtom) {
+// return (t.atomIndex1 == iAtom ? t.atomIndex2 : t.atomIndex1);
+// }
public BS getUniqueTensorSet(BS bsAtoms) {
BS bs = new BS();
@@ -176,11 +201,9 @@
if (type == null || a1.modelIndex != a2.modelIndex)
return 0;
BS bs = new BS();
- BS bs2 = new BS();
- int i0 = viewer.modelSet.models[a1.modelIndex].firstAtomIndex - 1;
- bs.set(a1.atomSite + i0);
- bs2.set(a2.atomSite + i0);
- JmolList<Tensor> list = getInteractionTensorList(type, bs, bs2);
+ bs.set(a1.index);
+ bs.set(a2.index);
+ JmolList<Tensor> list = getInteractionTensorList(type, bs);
if (list.size() == 0)
return Float.NaN;
isc = list.get(0);
@@ -385,7 +408,7 @@
}
} else if (tensorType.startsWith("isc")) {
boolean isJ = infoType.equals(";j.");
- JmolList<Tensor> list = getInteractionTensorList(tensorType, bs, null);
+ JmolList<Tensor> list = getInteractionTensorList(tensorType, bs);
int n = (list == null ? 0 : list.size());
for (int i = 0; i < n; i++) {
Tensor t = list.get(i);
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