Revision: 18615
http://sourceforge.net/p/jmol/code/18615
Author: hansonr
Date: 2013-08-22 05:32:34 +0000 (Thu, 22 Aug 2013)
Log Message:
-----------
NMRCalculation simplification of code
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java
trunk/Jmol/src/org/jmol/modelset/Measurement.java
trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java
Modified: trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java 2013-08-22 05:13:37 UTC
(rev 18614)
+++ trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java 2013-08-22 05:32:34 UTC
(rev 18615)
@@ -28,13 +28,14 @@
* If t is null, then a1, a2, and type are used to find the appropriate
* tensor.
*
+ * @param isIso
* @param a1
* @param a2
* @param type
* @param t
* @return 0 if not found
*/
- public float getJCouplingHz(Atom a1, Atom a2, String type, Tensor t);
+ public float getIsoOrAnisoHz(boolean isIso, Atom a1, Atom a2, String type,
Tensor t);
/**
*
Modified: trunk/Jmol/src/org/jmol/modelset/Measurement.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Measurement.java 2013-08-22 05:13:37 UTC
(rev 18614)
+++ trunk/Jmol/src/org/jmol/modelset/Measurement.java 2013-08-22 05:32:34 UTC
(rev 18615)
@@ -313,7 +313,7 @@
/ (a1.getVanderwaalsRadiusFloat(viewer, EnumVdw.AUTO)
+ a2.getVanderwaalsRadiusFloat(viewer, EnumVdw.AUTO))
: isDC ? viewer.getNMRCalculation().getDipolarConstantHz(a1, a2)
- : viewer.getNMRCalculation().getJCouplingHz(a1, a2, units,
+ : viewer.getNMRCalculation().getIsoOrAnisoHz(true, a1, a2,
units,
null));
isValid = !Float.isNaN(dist);
if (isPercent)
Modified: trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java
===================================================================
--- trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java 2013-08-22 05:13:37 UTC
(rev 18614)
+++ trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java 2013-08-22 05:32:34 UTC
(rev 18615)
@@ -196,6 +196,10 @@
}
public float getJCouplingHz(Atom a1, Atom a2, String type, Tensor isc) {
+ return getIsoOrAnisoHz(true, a1, a2, type, isc);
+ }
+
+ public float getIsoOrAnisoHz(boolean isIso, Atom a1, Atom a2, String type,
Tensor isc) {
if (isc == null) {
type = getISCtype(a1, type);
if (type == null || a1.modelIndex != a2.modelIndex)
@@ -212,29 +216,9 @@
a2 = viewer.modelSet.atoms[isc.atomIndex2];
}
return (float) (getIsotopeData(a1, MAGNETOGYRIC_RATIO)
- * getIsotopeData(a2, MAGNETOGYRIC_RATIO) * isc.getIso() * J_FACTOR);
+ * getIsotopeData(a2, MAGNETOGYRIC_RATIO) * (isIso ? isc.isotropy() :
isc.anisotropy()) * J_FACTOR);
}
- public float getAnisoHz(Atom a1, Atom a2, String type, Tensor isc) {
- if (isc == null) {
- type = getISCtype(a1, type);
- if (type == null || a1.modelIndex != a2.modelIndex)
- return 0;
- BS bs = new BS();
- 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);
- } else {
- a1 = viewer.modelSet.atoms[isc.atomIndex1];
- a2 = viewer.modelSet.atoms[isc.atomIndex2];
- }
- return (float) (getIsotopeData(a1, MAGNETOGYRIC_RATIO)
- * getIsotopeData(a2, MAGNETOGYRIC_RATIO) * isc.getAnisotropy() *
J_FACTOR);
- }
-
@SuppressWarnings("unchecked")
private String getISCtype(Atom a1, String type) {
JmolList<Tensor> tensors = (JmolList<Tensor>)
viewer.getModelAuxiliaryInfoValue(a1.modelIndex, "interactionTensors");
@@ -386,7 +370,7 @@
public float getMagneticShielding(Atom atom) {
Tensor t = viewer.modelSet.getAtomTensor(atom.index, "ms");
- return (t == null ? Float.NaN : t.getIso());
+ return (t == null ? Float.NaN : t.isotropy());
}
private Map<String, Float> shiftRefsPPM = new Hashtable<String, Float>();
@@ -440,8 +424,8 @@
list1 = new JmolList<Object>();
list1.addLast(Integer.valueOf(t.atomIndex1));
list1.addLast(Integer.valueOf(t.atomIndex2));
- list1.addLast(isEta? Float.valueOf(getAnisoHz(null, null, null, t)) :
isJ ? Float.valueOf(getJCouplingHz(null, null, null, t))
- : t.getInfo(infoType));
+ list1.addLast(isEta || isJ ? Float.valueOf(getIsoOrAnisoHz(isJ, null,
+ null, null, t)) : t.getInfo(infoType));
data.addLast(list1);
}
if (tensorType != null)
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