Revision: 18436
http://sourceforge.net/p/jmol/code/18436
Author: hansonr
Date: 2013-07-05 23:08:08 +0000 (Fri, 05 Jul 2013)
Log Message:
-----------
___JmolVersion="13.1.19_dev_2013.07.05"
code: org.jmol.quantum.NMRCalculation smoothly handles J-coupling and dipolar
coupling constant display.
new feature: unitcell center {atomset}
new feature: unitcell center {fx fy fz}
new feature: {*}.ms, {*}.cs %[ms] %[cs] magnetic shielding and chemical shift
new feature: label <color red>xxx</color>
new feature: set shift_H xxx (ppm)
new feature: getProperty("nmrInfo")
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java
trunk/Jmol/src/org/jmol/modelset/Measurement.java
trunk/Jmol/src/org/jmol/modelset/MeasurementData.java
trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/shape/Measures.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-07-05 17:26:35 UTC (rev 18435)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-07-05 23:08:08 UTC (rev 18436)
@@ -1049,7 +1049,7 @@
Text text = newTextLabel(strFormat, offset, clabel,
(int) floatSetting(PyMOL.label_font_id),
floatSetting(PyMOL.label_size));
- md.set(T.define, null, strFormat, "angstroms", null, false, false, null,
+ md.set(T.define, null, null, strFormat, "angstroms", null, false, false,
null,
false, (int) (rad * 2000), colix, text);
addJmolObject(JC.SHAPE_MEASURES, bs, md);
}
Modified: trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java 2013-07-05 17:26:35 UTC
(rev 18435)
+++ trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java 2013-07-05 23:08:08 UTC
(rev 18436)
@@ -1,6 +1,9 @@
package org.jmol.api;
+import java.util.Map;
+
import org.jmol.modelset.Atom;
+import org.jmol.modelset.MeasurementData;
import org.jmol.modelset.ModelSet;
import org.jmol.util.BS;
import org.jmol.util.JmolList;
@@ -51,16 +54,6 @@
public float getDipolarCouplingHz(Atom a1, Atom a2, V3 vField);
/**
- * Finds a set of interaction tensors based on a set of atoms -- all within
the
- * set if bs.cardinality() > 1; all for this atom when bs.cardinality() == 1.
- *
- * @param type
- * @param bs
- * @return list of matching tensors
- */
- public JmolList<Tensor> getInteractionTensorList(String type, BS bs);
-
- /**
* An attempt to find unique atoms using tensors.
*
* @param bs
@@ -91,5 +84,7 @@
public void setAtomTensors(ModelSet ms, int i, JmolList<Tensor> tensors);
public JmolList<Object> getTensorInfo(String tensorType, String infoType, BS
bs);
+
+ public Map<String, Float> getMinDistances(MeasurementData md);
}
Modified: trunk/Jmol/src/org/jmol/modelset/Measurement.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Measurement.java 2013-07-05 17:26:35 UTC
(rev 18435)
+++ trunk/Jmol/src/org/jmol/modelset/Measurement.java 2013-07-05 23:08:08 UTC
(rev 18436)
@@ -23,6 +23,8 @@
*/
package org.jmol.modelset;
+import java.util.Map;
+
import org.jmol.util.AxisAngle4f;
import org.jmol.util.Escape;
import org.jmol.util.P3;
@@ -262,9 +264,8 @@
return "";
if (units == null) {
int pt = strFormat.indexOf("//");
- if (pt >= 0) {
- units = strFormat.substring(pt + 2);
- } else {
+ units = (pt >= 0 ? strFormat.substring(pt + 2) : null);
+ if (units == null) {
units = viewer.getMeasureDistanceUnits();
strFormat += "//" + units;
}
@@ -306,8 +307,8 @@
Atom a2 = (Atom) getAtom(2);
dist = (isPercent ? dist
/ a1.getVanderwaalsRadiusFloat(viewer, EnumVdw.AUTO)
- + a2.getVanderwaalsRadiusFloat(viewer, EnumVdw.AUTO) : units
- .startsWith("dc_") || units.equals("khz") ?
viewer.getNMRCalculation()
+ + a2.getVanderwaalsRadiusFloat(viewer, EnumVdw.AUTO) :
+ nmrType(units) == NMR_DC ? viewer.getNMRCalculation()
.getDipolarConstantHz(a1, a2) : viewer.getNMRCalculation()
.getJCouplingHz(a1, a2, units, null));
isValid = !Float.isNaN(dist);
@@ -322,12 +323,20 @@
if (units.equals("au"))
return (andRound ? Math.round(dist / JC.ANGSTROMS_PER_BOHR * 1000) /
1000f
: dist / JC.ANGSTROMS_PER_BOHR);
- if (units.equals("khz"))
+ if (units.endsWith("khz"))
return (andRound ? Math.round(dist / 10) / 100f : dist / 1000);
}
return (andRound ? Math.round(dist * 100) / 100f : dist);
}
+ public final static int NMR_NOT = 0;
+ public final static int NMR_DC = 1;
+ public final static int NMR_JC = 2;
+
+ public static int nmrType(String units) {
+ return (units.indexOf("hz") < 0 ? NMR_NOT : units.startsWith("dc_") ||
units.equals("khz") ? NMR_DC : NMR_JC);
+ }
+
private String formatAngle(float angle) {
String label = getLabelString();
if (label.indexOf("%V") >= 0)
@@ -521,4 +530,13 @@
return true;
}
+ public boolean isMin(Map<String, Float> htMin) {
+ Atom a1 = (Atom) getAtom(1);
+ Atom a2 = (Atom) getAtom(2);
+ float d = a2.distanceSquared(a1);
+ String key = (a1.index < a2.index ? a1.getAtomName() + a2.getAtomName() :
a2.getAtomName() + a1.getAtomName());
+ Float min = htMin.get(key);
+ return (min != null && d == min.floatValue());
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/modelset/MeasurementData.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/MeasurementData.java 2013-07-05
17:26:35 UTC (rev 18435)
+++ trunk/Jmol/src/org/jmol/modelset/MeasurementData.java 2013-07-05
23:08:08 UTC (rev 18436)
@@ -23,6 +23,8 @@
*/
package org.jmol.modelset;
+import java.util.Map;
+
import org.jmol.util.JmolList;
@@ -81,7 +83,8 @@
/*
* the general constructor. tokAction is not used here
*/
- public MeasurementData set(int tokAction, RadiusData radiusData, String
strFormat, String units,
+ public MeasurementData set(int tokAction, Map<String, Float> htMin,
+ RadiusData radiusData, String strFormat, String
units,
TickInfo tickInfo,
boolean mustBeConnected, boolean mustNotBeConnected,
Boolean intramolecular, boolean isAll,
@@ -94,6 +97,7 @@
viewer.getModelBitSet((BS) points.get(1), false));
}
//this.rangeMinMax = rangeMinMax;
+ this.htMin = htMin;
this.radiusData = radiusData;
this.strFormat = strFormat;
this.units = units;
@@ -118,7 +122,7 @@
public void processNextMeasure(Measurement m) {
float value = m.getMeasurement();
// here's where we check vdw
- if (radiusData != null && !m.isInRange(radiusData, value))
+ if (htMin != null && !m.isMin(htMin) || radiusData != null &&
!m.isInRange(radiusData, value))
return;
if (measurementStrings == null) {
float f = minArray[iFirstAtom];
@@ -157,6 +161,7 @@
private Viewer viewer;
private int iFirstAtom;
private boolean justOneModel = true;
+ public Map<String, Float> htMin;
/**
* called by the client to generate a set of measurements
Modified: trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java
===================================================================
--- trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java 2013-07-05 17:26:35 UTC
(rev 18435)
+++ trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java 2013-07-05 23:08:08 UTC
(rev 18436)
@@ -34,6 +34,7 @@
import org.jmol.api.JmolNMRInterface;
import org.jmol.io.JmolBinary;
import org.jmol.modelset.Atom;
+import org.jmol.modelset.MeasurementData;
import org.jmol.modelset.ModelSet;
import org.jmol.util.BS;
import org.jmol.util.Escape;
@@ -91,10 +92,11 @@
*
* @param type
* @param bs
+ * @param bs2
* @return list of Tensors
*/
@SuppressWarnings("unchecked")
- public JmolList<Tensor> getInteractionTensorList(String type, BS bs) {
+ private JmolList<Tensor> getInteractionTensorList(String type, BS bs, BS
bs2) {
type = type.toLowerCase();
BS bsModels = viewer.getModelBitSet(bs, false);
int iAtom = (bs.cardinality() == 1 ? bs.nextSetBit(0) : -1);
@@ -106,13 +108,19 @@
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))
+ if (t.type.equals(type) && t.isSelected(bs, iAtom)
+ && (bs2 == null || bs2.get(getOtherAtom(t, iAtom))))
+
list.addLast(t);
}
}
return list;
}
+ private int getOtherAtom(Tensor t, int iAtom) {
+ return (t.atomIndex1 == iAtom ? t.atomIndex2 : t.atomIndex1);
+ }
+
public BS getUniqueTensorSet(BS bsAtoms) {
BS bs = new BS();
Atom[] atoms = viewer.modelSet.atoms;
@@ -161,22 +169,16 @@
return bs;
}
- @SuppressWarnings("unchecked")
public float getJCouplingHz(Atom a1, Atom a2, String type, Tensor isc) {
if (isc == null) {
- JmolList<Tensor> tensors = (JmolList<Tensor>)
viewer.getModelAuxiliaryInfoValue(a1.modelIndex, "interactionTensors");
- if (tensors == null)
+ type = getISCtype(a1, type);
+ if (type == null)
return 0;
BS bs = new BS();
+ BS bs2 = new BS();
bs.set(a1.index);
- bs.set(a2.index);
- type = (type == null ? "" : type.toLowerCase());
- int pt = -1;
- if ((pt = type.indexOf("_")) >= 0)
- type = type.substring(0, pt);
- if (type.length() == 0)
- type = "isc";
- JmolList<Tensor> list = getInteractionTensorList(type, bs);
+ bs2.set(a2.index);
+ JmolList<Tensor> list = getInteractionTensorList(type, bs, bs2);
if (list.size() == 0)
return Float.NaN;
isc = list.get(0);
@@ -188,6 +190,21 @@
* getIsotopeData(a2, MAGNETOGYRIC_RATIO) * isc.getIso() * J_FACTOR);
}
+ @SuppressWarnings("unchecked")
+ private String getISCtype(Atom a1, String type) {
+ JmolList<Tensor> tensors = (JmolList<Tensor>)
viewer.getModelAuxiliaryInfoValue(a1.modelIndex, "interactionTensors");
+ if (tensors == null)
+ return null;
+ type = (type == null ? "" : type.toLowerCase());
+ int pt = -1;
+ if ((pt = type.indexOf("_hz")) >= 0 || (pt = type.indexOf("_khz")) >= 0
+ || (pt = type.indexOf("hz")) >= 0 || (pt = type.indexOf("khz")) >= 0)
+ type = type.substring(0, pt);
+ if (type.length() == 0)
+ type = "isc";
+ return type;
+ }
+
public float getDipolarConstantHz(Atom a1, Atom a2) {
if (Logger.debugging)
Logger.debug(a1 + " g=" + getIsotopeData(a1, MAGNETOGYRIC_RATIO) + "; "
+ a2 + " g=" + getIsotopeData(a2, MAGNETOGYRIC_RATIO));
@@ -382,7 +399,7 @@
boolean isJ = tensorType.equals("isc") && infoType.equals(";jcoupling.");
boolean isChi = tensorType.equals("efg") && infoType.equals(";chi.");
if (tensorType.equals("isc")) {
- JmolList<Tensor> list = getInteractionTensorList("isc", bs);
+ JmolList<Tensor> list = getInteractionTensorList("isc", bs, null);
int n = (list == null ? 0 : list.size());
for (int i = 0; i < n; i++) {
Tensor t = list.get(i);
@@ -444,4 +461,39 @@
return null;
}
+ public Map<String, Float> getMinDistances(MeasurementData md) {
+ BS bsPoints1 = (BS) md.points.get(0);
+ int n1 = bsPoints1.cardinality();
+ if (n1 == 0 || !(md.points.get(1) instanceof BS))
+ return null;
+ BS bsPoints2 = (BS) md.points.get(1);
+ int n2 = bsPoints2.cardinality();
+ if (n1 < 2 && n2 < 2)
+ return null;
+ Map<String, Float> htMin = new Hashtable<String, Float>();
+ Atom[] atoms = viewer.modelSet.atoms;
+ for (int i = bsPoints1.nextSetBit(0); i >= 0; i = bsPoints1
+ .nextSetBit(i + 1)) {
+ Atom a1 = atoms[i];
+ String name = a1.getAtomName();
+ for (int j = bsPoints2.nextSetBit(0); j >= 0; j = bsPoints2
+ .nextSetBit(j + 1)) {
+ Atom a2 = atoms[j];
+ float d = a2.distanceSquared(a1);
+ if (d == 0)
+ continue;
+ String key = (i < j ? name + a2.getAtomName() : a2.getAtomName() +
name);
+ Float min = htMin.get(key);
+ if (min == null) {
+ min = Float.valueOf(d);
+ htMin.put(key, min);
+ continue;
+ }
+ if (d < min.floatValue())
+ htMin.put(key, Float.valueOf(d));
+ }
+ }
+ return htMin;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-07-05 17:26:35 UTC
(rev 18435)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-07-05 23:08:08 UTC
(rev 18436)
@@ -9850,7 +9850,7 @@
if (text != null)
text.pymolOffset = offset;
setShapeProperty(JC.SHAPE_MEASURES, "measure",
- (new MeasurementData(id, viewer, points)).set(tokAction, rd,
strFormat, null, tickInfo,
+ (new MeasurementData(id, viewer, points)).set(tokAction, null, rd,
strFormat, null, tickInfo,
isAllConnected, isNotConnected, intramolecular, isAll, mad,
colix, text));
return;
}
@@ -13802,8 +13802,8 @@
}
private boolean setUnits(String units, int tok) throws ScriptException {
- if (tok == T.measurementunits && Parser.isOneOf(units.toLowerCase(),
- ";angstroms;au;bohr;nanometers;nm;picometers;pm;vanderwaals;vdw;")) {
+ if (tok == T.measurementunits && (units.endsWith("hz") ||
Parser.isOneOf(units.toLowerCase(),
+ ";angstroms;au;bohr;nanometers;nm;picometers;pm;vanderwaals;vdw;"))) {
if (!chk)
viewer.setUnits(units, true);
} else if (tok == T.energyunits && Parser.isOneOf(units.toLowerCase(),
";kcal;kj;")) {
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-05
17:26:35 UTC (rev 18435)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-05
23:08:08 UTC (rev 18436)
@@ -1445,7 +1445,7 @@
return addXStr("");
rd = (vdw == Float.MAX_VALUE ? new RadiusData(rangeMinMax, 0, null, null)
: new RadiusData(null, vdw, EnumType.FACTOR, EnumVdw.AUTO));
- return addXObj((new MeasurementData(null, viewer, points)).set(0, rd,
strFormat, units, null, isAllConnected,
+ return addXObj((new MeasurementData(null, viewer, points)).set(0, null,
rd, strFormat, units, null, isAllConnected,
isNotConnected, null, true, 0, (short) 0,
null).getMeasurements(asArray));
case T.angle:
if ((nPoints = args.length) != 3 && nPoints != 4)
Modified: trunk/Jmol/src/org/jmol/shape/Measures.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Measures.java 2013-07-05 17:26:35 UTC (rev
18435)
+++ trunk/Jmol/src/org/jmol/shape/Measures.java 2013-07-05 23:08:08 UTC (rev
18436)
@@ -67,6 +67,7 @@
TickInfo tickInfo;
TickInfo defaultTickInfo;
public JmolFont font3d;
+ private Map<String, Float> htMin;
@Override
protected void initModelSet() {
@@ -182,7 +183,13 @@
defaultTickInfo = md.tickInfo;
return;
}
+ if (md.isAll && md.points.size() == 2 && md.points.get(0) instanceof BS
+ && Measurement.nmrType(viewer.getDistanceUnits(md.strFormat))
+ == Measurement.NMR_JC)
+ md.htMin = viewer.getNMRCalculation().getMinDistances(md);
+ tickInfo = md.tickInfo;
radiusData = md.radiusData;
+ htMin = md.htMin;
mustBeConnected = md.mustBeConnected;
mustNotBeConnected = md.mustNotBeConnected;
intramolecular = md.intramolecular;
@@ -297,7 +304,7 @@
if (value instanceof String) {
doAction(null, (String) value, T.opToggle);
} else {
- toggle(new Measurement().setPoints(modelSet, (int[]) value, null, null));
+ toggle(new Measurement().setPoints(modelSet, (int[]) value, null,
null));
}
return;
}
@@ -310,7 +317,6 @@
}
return;
}
-
}
private Measurement setSingleItem(JmolList<Object> vector) {
@@ -397,6 +403,7 @@
private void toggle(Measurement m) {
radiusData = null;
+ htMin = null;
//toggling one that is hidden should be interpreted as DEFINE
int i = find(m);
Measurement mt;
@@ -409,6 +416,7 @@
private void toggleOn(int[] indices) {
radiusData = null;
+ htMin = null;
//toggling one that is hidden should be interpreted as DEFINE
bsSelected = new BS();
defineAll(Integer.MIN_VALUE, new Measurement().setPoints(modelSet,
indices, null, defaultTickInfo), false, true, true);
@@ -418,6 +426,7 @@
private void deleteM(Measurement m) {
radiusData = null;
+ htMin = null;
//toggling one that is hidden should be interpreted as DEFINE
int i = find(m);
if (i >= 0)
@@ -463,7 +472,7 @@
Integer.valueOf(atoms[atomIndex].getAtomNumber())) : (Object) m
.getAtom(i));
}
- define((new MeasurementData(null, viewer, points)).set(tokAction,
radiusData, strFormat, null, tickInfo,
+ define((new MeasurementData(null, viewer, points)).set(tokAction, htMin,
radiusData, strFormat, null, tickInfo,
mustBeConnected, mustNotBeConnected, intramolecular, true, 0, (short)
0, null),
(isDelete ? T.delete : T.define));
}
@@ -505,7 +514,8 @@
private void defineMeasurement(int i, Measurement m, boolean doSelect) {
float value = m.getMeasurement();
- if (radiusData != null && !m.isInRange(radiusData, value))
+ if (htMin != null && !m.isMin(htMin)
+ || radiusData != null && !m.isInRange(radiusData, value))
return;
if (i == Integer.MIN_VALUE)
i = find(m);
@@ -517,6 +527,8 @@
}
Measurement measureNew = new Measurement().setM(modelSet, m, value,
(m.colix == 0 ? colix : m.colix),
strFormat, measurementCount);
+ if (!measureNew.isValid)
+ return;
measurements.addLast(measureNew);
viewer.setStatusMeasuring("measureCompleted", measurementCount++,
measureNew.toVector(false).toString(), measureNew.getValue());
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-05 17:26:35 UTC
(rev 18435)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-05 23:08:08 UTC
(rev 18436)
@@ -11,11 +11,13 @@
___JmolVersion="13.1.19_dev_2013.07.05"
+code: org.jmol.quantum.NMRCalculation smoothly handles J-coupling and dipolar
coupling constant display.
+
new feature: unitcell center {atomset}
new feature: unitcell center {fx fy fz}
new feature: {*}.ms, {*}.cs %[ms] %[cs] magnetic shielding and chemical shift
new feature: label <color red>xxx</color>
-new feature: set shift_H_hz xxx, set shift_H_PPM_400 xxx
+new feature: set shift_H xxx (ppm)
new feature: getProperty("nmrInfo")
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-07-05 17:26:35 UTC
(rev 18435)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-07-05 23:08:08 UTC
(rev 18436)
@@ -1273,6 +1273,8 @@
measureDistanceUnits = "au";
else if (units.equalsIgnoreCase("vanderwaals") ||
units.equalsIgnoreCase("vdw"))
measureDistanceUnits = "vdw";
+ else if (units.toLowerCase().endsWith("hz") ||
units.toLowerCase().endsWith("khz"))
+ measureDistanceUnits = units.toLowerCase();
else if (units.equalsIgnoreCase("kj"))
energyUnits = "kJ";
else if (units.equalsIgnoreCase("kcal"))
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-07-05 17:26:35 UTC (rev
18435)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-07-05 23:08:08 UTC (rev
18436)
@@ -10109,4 +10109,12 @@
return (nmrCalculation == null ? (nmrCalculation = (JmolNMRInterface)
Interface
.getOptionInterface("quantum.NMRCalculation")).setViewer(this) :
nmrCalculation);
}
+
+ public String getDistanceUnits(String s) {
+ if (s == null)
+ s = getDefaultMeasurementLabel(2);
+ int pt = s.indexOf("//");
+ return (pt < 0 ? getMeasureDistanceUnits() : s.substring(pt + 2));
+ }
+
}
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