Revision: 18480
http://sourceforge.net/p/jmol/code/18480
Author: hansonr
Date: 2013-07-19 18:57:54 +0000 (Fri, 19 Jul 2013)
Log Message:
-----------
reorganization of tensor methods
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java
trunk/Jmol/src/org/jmol/render/RepaintManager.java
trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
Modified: trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java 2013-07-19 18:01:27 UTC
(rev 18479)
+++ trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java 2013-07-19 18:57:54 UTC
(rev 18480)
@@ -4,7 +4,6 @@
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;
import org.jmol.util.SB;
@@ -81,9 +80,6 @@
public float getChemicalShift(Atom atom);
public boolean setChemicalShiftReference(String element, float value);
- public JmolList<Tensor> getAllAtomTensors(String type);
- 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/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-07-19
18:01:27 UTC (rev 18479)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-07-19
18:57:54 UTC (rev 18480)
@@ -28,7 +28,9 @@
import org.jmol.util.JmolList;
import java.util.Arrays;
import java.util.Comparator;
+import java.util.Hashtable;
import java.util.Map;
+import java.util.Map.Entry;
import org.jmol.atomdata.AtomData;
import org.jmol.atomdata.RadiusData;
@@ -154,15 +156,6 @@
public Tensor[][] atomTensorList; // specifically now for {*}.adpmin
{*}.adpmax
public Map<String, JmolList<Tensor>> atomTensors;
- public void addTensor(Tensor t, String type) {
- type = type.toLowerCase();
- JmolList<Tensor> tensors = atomTensors.get(type);
- if (tensors == null)
- atomTensors.put(type, tensors = new JmolList<Tensor>());
- tensors.addLast(t);
- }
-
-
protected int[] surfaceDistance100s;
protected boolean haveStraightness;
@@ -253,11 +246,6 @@
return atoms[i].getChainIDStr();
}
- public Tensor[] getAtomTensorList(int i) {
- return (i < 0 || atomTensorList == null || i >= atomTensorList.length ?
null
- : atomTensorList[i]);
- }
-
public Quaternion getQuaternion(int i, char qtype) {
return (i < 0 ? null : atoms[i].group.getQuaternion(qtype));
}
@@ -2548,6 +2536,19 @@
// what about data?
}
+ public void getAtomIdentityInfo(int i, Map<String, Object> info) {
+ info.put("_ipt", Integer.valueOf(i));
+ info.put("atomIndex", Integer.valueOf(i));
+ info.put("atomno", Integer.valueOf(getAtomNumber(i)));
+ info.put("info", getAtomInfo(i, null));
+ info.put("sym", getElementSymbol(i));
+ }
+
+ public Tensor[] getAtomTensorList(int i) {
+ return (i < 0 || atomTensorList == null || i >= atomTensorList.length ?
null
+ : atomTensorList[i]);
+ }
+
// clean out deleted model atom tensors (ellipsoids)
private void deleteAtomTensors(BS bsAtoms) {
if (atomTensors == null)
@@ -2567,14 +2568,91 @@
atomTensors.remove(toDelete.get(i));
}
- public void getAtomIdentityInfo(int i, Map<String, Object> info) {
- info.put("_ipt", Integer.valueOf(i));
- info.put("atomIndex", Integer.valueOf(i));
- info.put("atomno", Integer.valueOf(getAtomNumber(i)));
- info.put("info", getAtomInfo(i, null));
- info.put("sym", getElementSymbol(i));
+ public void setAtomTensors(int atomIndex, JmolList<Tensor> list) {
+ if (list == null || list.size() == 0)
+ return;
+ if (atomTensors == null)
+ atomTensors = new Hashtable<String, JmolList<Tensor>>();
+ if (atomTensorList == null)
+ atomTensorList = new Tensor[atoms.length][];
+ atomTensorList = (Tensor[][]) ArrayUtil.ensureLength(atomTensorList,
atoms.length);
+ atomTensorList[atomIndex] = getTensorList(list);
+ for (int i = list.size(); --i >= 0;) {
+ Tensor t = list.get(i);
+ t.atomIndex1 = atomIndex;
+ t.atomIndex2 = -1;
+ t.modelIndex = atoms[atomIndex].modelIndex;
+ addTensor(t, t.type);
+ if (t.altType != null)
+ addTensor(t, t.altType);
+ }
}
+ private static Tensor[] getTensorList(JmolList<Tensor> list) {
+ int pt = -1;
+ boolean haveTLS = false;
+ int n = list.size();
+ for (int i = n; --i >= 0;) {
+ Tensor t = list.get(i);
+ if (t.forThermalEllipsoid)
+ pt = i;
+ else if (t.iType == Tensor.TYPE_TLS_U)
+ haveTLS = true;
+ }
+ Tensor[] a = new Tensor[(pt >= 0 || !haveTLS ? 0 : 1) + n];
+ if (pt >= 0) {
+ a[0] = list.get(pt);
+ if (list.size() == 1)
+ return a;
+ }
+ // back-fills list for TLS:
+ // 0 = temp, 1 = TLS-R, 2 = TLS-U
+ if (haveTLS) {
+ pt = 0;
+ for (int i = n; --i >= 0;) {
+ Tensor t = list.get(i);
+ if (t.forThermalEllipsoid)
+ continue;
+ a[++pt] = t;
+ }
+ } else {
+ for (int i = 0; i < n; i++)
+ a[i] = list.get(i);
+ }
+ return a;
+ }
+ public Tensor getAtomTensor(int i, String type) {
+ Tensor[] tensors = getAtomTensorList(i);
+ if (tensors == null || type == null)
+ return null;
+ type = type.toLowerCase();
+ for (int j = 0; j < tensors.length; j++)
+ if (tensors[j] != null && type.equals(tensors[j].type))
+ return tensors[j];
+ return null;
+ }
+
+ public void addTensor(Tensor t, String type) {
+ type = type.toLowerCase();
+ JmolList<Tensor> tensors = atomTensors.get(type);
+ if (tensors == null)
+ atomTensors.put(type, tensors = new JmolList<Tensor>());
+ tensors.addLast(t);
+ }
+
+ public JmolList<Tensor> getAllAtomTensors(String type) {
+ if (atomTensors == null)
+ return null;
+ if (type != null)
+ return atomTensors.get(type.toLowerCase());
+ JmolList<Tensor> list = new JmolList<Tensor>();
+ for (Entry<String, JmolList<Tensor>> e : atomTensors.entrySet())
+ list.addAll(e.getValue());
+ return list;
+ }
+
+
+
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-07-19
18:01:27 UTC (rev 18479)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-07-19
18:57:54 UTC (rev 18480)
@@ -3165,7 +3165,7 @@
setOccupancy(atomCount, occupancy);
setPartialCharge(atomCount, partialCharge);
if (tensors != null)
- viewer.getNMRCalculation().setAtomTensors((ModelSet) this, atomCount,
tensors);
+ setAtomTensors(atomCount, tensors);
atom.group = group;
atom.colixAtom = viewer.getColixAtomPalette(atom, EnumPalette.CPK.id);
if (atomName != null) {
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-07-19 18:01:27 UTC
(rev 18479)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-07-19 18:57:54 UTC
(rev 18480)
@@ -105,7 +105,7 @@
viewer.resetShapes(false);
}
modelSet.preserveState = viewer.getPreserveState();
- modelSet.showRebondTimes = viewer.global.showTiming;
+ modelSet.showRebondTimes = viewer.getBoolean(T.showtiming);
if (bsNew == null) {
initializeInfo(modelSetName, null);
createModelSet(null, null, null);
Modified: trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java
===================================================================
--- trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java 2013-07-19 18:01:27 UTC
(rev 18479)
+++ trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java 2013-07-19 18:57:54 UTC
(rev 18480)
@@ -35,7 +35,6 @@
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;
import org.jmol.util.JmolList;
@@ -342,7 +341,7 @@
}
public float getMagneticShielding(Atom atom) {
- Tensor t = getAtomTensor(atom.index, "ms");
+ Tensor t = viewer.modelSet.getAtomTensor(atom.index, "ms");
return (t == null ? Float.NaN : t.getIso());
}
@@ -366,39 +365,6 @@
return true;
}
- public void setAtomTensors(ModelSet ms, int atomIndex, JmolList<Tensor>
list) {
- if (list == null || list.size() == 0)
- return;
- if (ms.atomTensors == null)
- ms.atomTensors = new Hashtable<String, JmolList<Tensor>>();
- if (ms.atomTensorList == null)
- ms.atomTensorList = new Tensor[ms.atoms.length][];
- ms.atomTensorList[atomIndex] = getTensorList(list);
- Atom[] atoms = ms.atoms;
- for (int i = list.size(); --i >= 0;) {
- Tensor t = list.get(i);
- t.atomIndex1 = atomIndex;
- t.atomIndex2 = -1;
- t.modelIndex = atoms[atomIndex].modelIndex;
- ms.addTensor(t, t.type);
- if (t.altType != null)
- ms.addTensor(t, t.altType);
- }
- }
-
- public JmolList<Tensor> getAllAtomTensors(String type) {
- if (viewer.modelSet.atomTensors == null)
- return null;
- if (type != null)
- return viewer.modelSet.atomTensors.get(type.toLowerCase());
- JmolList<Tensor> list = new JmolList<Tensor>();
- for (Entry<String, JmolList<Tensor>> e :
viewer.modelSet.atomTensors.entrySet()) {
- JmolList<Tensor> list2 = e.getValue();
- list.addAll(list2);
- }
- return list;
- }
-
public JmolList<Object> getTensorInfo(String tensorType, String infoType,
BS bs) {
@@ -432,7 +398,7 @@
} else {
boolean isChi = tensorType.startsWith("efg") && infoType.equals(";chi.");
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
- Tensor t = getAtomTensor(i, tensorType);
+ Tensor t = viewer.modelSet.getAtomTensor(i, tensorType);
data.addLast(t == null ? null : isChi ? Float
.valueOf(getQuadrupolarConstant(t)) : t.getInfo(infoType));
}
@@ -440,51 +406,6 @@
return data;
}
- private static Tensor[] getTensorList(JmolList<Tensor> list) {
- int pt = -1;
- boolean haveTLS = false;
- int n = list.size();
- for (int i = n; --i >= 0;) {
- Tensor t = list.get(i);
- if (t.forThermalEllipsoid)
- pt = i;
- else if (t.iType == Tensor.TYPE_TLS_U)
- haveTLS = true;
- }
- Tensor[] a = new Tensor[(pt >= 0 || !haveTLS ? 0 : 1) + n];
- if (pt >= 0) {
- a[0] = list.get(pt);
- if (list.size() == 1)
- return a;
- }
- // back-fills list for TLS:
- // 0 = temp, 1 = TLS-R, 2 = TLS-U
- if (haveTLS) {
- pt = 0;
- for (int i = n; --i >= 0;) {
- Tensor t = list.get(i);
- if (t.forThermalEllipsoid)
- continue;
- a[++pt] = t;
- }
- } else {
- for (int i = 0; i < n; i++)
- a[i] = list.get(i);
- }
- return a;
- }
-
- private Tensor getAtomTensor(int i, String type) {
- Tensor[] tensors = viewer.modelSet.getAtomTensorList(i);
- if (tensors == null || type == null)
- return null;
- type = type.toLowerCase();
- for (int j = 0; j < tensors.length; j++)
- if (tensors[j] != null && type.equals(tensors[j].type))
- return tensors[j];
- return null;
- }
-
public Map<String, Float> getMinDistances(MeasurementData md) {
BS bsPoints1 = (BS) md.points.get(0);
int n1 = bsPoints1.cardinality();
Modified: trunk/Jmol/src/org/jmol/render/RepaintManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/RepaintManager.java 2013-07-19 18:01:27 UTC
(rev 18479)
+++ trunk/Jmol/src/org/jmol/render/RepaintManager.java 2013-07-19 18:57:54 UTC
(rev 18480)
@@ -26,6 +26,7 @@
import org.jmol.api.JmolRendererInterface;
import org.jmol.api.JmolRepaintManager;
import org.jmol.modelset.ModelSet;
+import org.jmol.script.T;
import org.jmol.shape.Shape;
import org.jmol.util.BS;
import org.jmol.util.GData;
@@ -183,7 +184,7 @@
/////////// actual rendering ///////////
public void render(GData gdata, ModelSet modelSet, boolean isFirstPass,
int[] minMax) {
- boolean logTime = viewer.global.showTiming;
+ boolean logTime = viewer.getBoolean(T.showtiming);
try {
JmolRendererInterface g3d = (JmolRendererInterface) gdata;
g3d.renderBackground(null);
@@ -224,7 +225,7 @@
public String renderExport(String type, GData gdata, ModelSet modelSet,
String fileName) {
boolean isOK;
- boolean logTime = viewer.global.showTiming;
+ boolean logTime = viewer.getBoolean(T.showtiming);
viewer.finalizeTransformParameters();
shapeManager.finalizeAtoms(null, null);
shapeManager.transformAtoms();
Modified: trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2013-07-19
18:01:27 UTC (rev 18479)
+++ trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2013-07-19
18:57:54 UTC (rev 18480)
@@ -72,7 +72,7 @@
boolean isAll = (bsSelected == null);
if (!isAll && selectedAtoms != null)
bsSelected = selectedAtoms;
- JmolList<Tensor> tensors =
viewer.getNMRCalculation().getAllAtomTensors(typeSelected);
+ JmolList<Tensor> tensors = viewer.modelSet.getAllAtomTensors(typeSelected);
if (tensors == null)
return;
Atom[] atoms = modelSet.atoms;
Modified: trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2013-07-19
18:01:27 UTC (rev 18479)
+++ trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2013-07-19
18:57:54 UTC (rev 18480)
@@ -161,7 +161,7 @@
protected void newSg() {
sg = new SurfaceGenerator(viewer, this, null, jvxlData = new JvxlData());
- sg.getParams().showTiming = viewer.global.showTiming;
+ sg.getParams().showTiming = viewer.getBoolean(T.showtiming);
sg.setVersion("Jmol " + Viewer.getJmolVersion());
}
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