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[Jmol-commits] SF.net SVN: jmol:[14901] trunk/Jmol/src/org
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From: <ha...@us...> - 2010-12-26 13:18:28
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Revision: 14901
http://jmol.svn.sourceforge.net/jmol/?rev=14901&view=rev
Author: hansonr
Date: 2010-12-26 13:18:20 +0000 (Sun, 26 Dec 2010)
Log Message:
-----------
VERSION
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/jvxl/data/MeshData.java
trunk/Jmol/src/org/jmol/jvxl/readers/IsoShapeReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/Parameters.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/Token.java
trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
trunk/Jmol/src/org/jmol/smiles/SmilesBond.java
trunk/Jmol/src/org/jmol/smiles/SmilesMeasure.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/AppConsole.java
Modified: trunk/Jmol/src/org/jmol/jvxl/data/MeshData.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/data/MeshData.java 2010-12-26 05:08:39 UTC (rev 14900)
+++ trunk/Jmol/src/org/jmol/jvxl/data/MeshData.java 2010-12-26 13:18:20 UTC (rev 14901)
@@ -118,6 +118,7 @@
import java.util.Comparator;
import javax.vecmath.Point3f;
+import javax.vecmath.Vector3f;
import org.jmol.util.MeshSurface;
@@ -283,6 +284,48 @@
return (val1 >= 0 && val2 >= 0 && val3 >= 0
|| val1 <= 0 && val2 <= 0 && val3 <= 0);
}
+
+ public Object calculateVolumes() {
+ // TODO
+ return null;
+ }
+
+
+ public Object calculateVolumeOrArea(int thisSet, boolean isArea, boolean getSets) {
+ if (getSets)
+ getSurfaceSet();
+ boolean justOne = (nSets == 0 || thisSet >= 0);
+ int n = (justOne ? 1 : nSets);
+ double[] v = new double[n];
+ Vector3f vAB = new Vector3f();
+ Vector3f vAC = new Vector3f();
+ Vector3f vTemp = new Vector3f();
+ for (int i = polygonCount; --i >= 0;) {
+ if (!setABC(i))
+ continue;
+ int iSet = (nSets == 0 ? 0 : vertexSets[iA]);
+ if (thisSet >= 0 && iSet != thisSet)
+ continue;
+ if (isArea) {
+ vAB.sub(vertices[iB], vertices[iA]);
+ vAC.sub(vertices[iC], vertices[iA]);
+ vTemp.cross(vAB, vAC);
+ v[justOne ? 0 : iSet] += vTemp.length();
+ } else {
+ // volume
+ vAB.set(vertices[iB]);
+ vAC.set(vertices[iC]);
+ vTemp.cross(vAB, vAC);
+ vAC.set(vertices[iA]);
+ v[justOne ? 0 : iSet] += vAC.dot(vTemp);
+ }
+ }
+ for (int i = 0; i < n; i++)
+ v[i] /= 6;
+ if (justOne)
+ return Float.valueOf((float) v[0]);
+ return v;
+ }
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/IsoShapeReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/IsoShapeReader.java 2010-12-26 05:08:39 UTC (rev 14900)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/IsoShapeReader.java 2010-12-26 13:18:20 UTC (rev 14901)
@@ -214,11 +214,13 @@
if (params.isSquared)
min = Math.sqrt(min / 2);
}
+ float r0 = 0;
for (radius = 100; radius > 0; radius--) {
- if (Math.abs(radialPart(radius)) >= min)
- break;
+ double d = radialPart(radius);
+ if (Math.abs(d) >= min && r0 == 0)
+ r0 = radius;
}
- radius += 1;
+ radius = r0 + 1;
if (isAnisotropic) {
float aMax = 0;
for (int i = 3; --i >= 0;)
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2010-12-26 05:08:39 UTC (rev 14900)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2010-12-26 13:18:20 UTC (rev 14901)
@@ -239,6 +239,27 @@
params.cappingObject = null;
}
}
+
+ @Override
+ protected void postProcessVertices() {
+ if (isMsMs) {
+ // creates two surfaces, one inside, one outside --
+ // the inside one will have negative volume.
+ // TODO -- note that this removes any cavity as well,
+ // and in principal will leave a cavity's inside cavity.
+ if (meshDataServer == null)
+ return; //can't do this without help!
+ meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
+ double[] volumes = (double[]) meshData.calculateVolumeOrArea(-1, false, true);
+ int nSets = meshData.nSets;
+ for (int i = 0; i < nSets; i++)
+ if (volumes[i] < 0)
+ meshData.invalidateSurfaceSet(i);
+ updateSurfaceData();
+ meshDataServer.fillMeshData(meshData, MeshData.MODE_PUT_SETS, null);
+ meshData = new MeshData();
+ }
+ }
private void generateSolventCavity() {
//we have a ring of dots around the model.
@@ -306,8 +327,11 @@
final Point3f ptXyzTemp = new Point3f();
private AtomIndexIterator iter;
-
+ private boolean isMsMs;
+
+
void generateSolventCubeMsMs() {
+ isMsMs = true;
volumeData.getYzCount();
resetVoxelData(Float.MAX_VALUE);
if (dataType == Parameters.SURFACE_NOMAP)
@@ -603,9 +627,9 @@
if (type < 10)
nFaces[type < 0 ? 0 : type + 1]++;
}
- for (int i = 0; i < 10; i++)
- System.out.print((i-1) + ": " + nFaces[i] + "\t");
- System.out.println("edge types");
+ //for (int i = 0; i < 10; i++)
+ // System.out.print((i-1) + ": " + nFaces[i] + "\t");
+ //System.out.println("edge types");
}
private Point3f ptY0 = new Point3f();
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/Parameters.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/Parameters.java 2010-12-26 05:08:39 UTC (rev 14900)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/Parameters.java 2010-12-26 13:18:20 UTC (rev 14901)
@@ -416,7 +416,7 @@
float[] anisoB;
public void setEllipsoid(float[] bList) {
anisoB = bList;
- for (int i = 0; i < 6; i++)System.out.print(bList[i] + " ");System.out.println( " in Parameters setEllipsoid" + center);
+ //for (int i = 0; i < 6; i++)System.out.print(bList[i] + " ");System.out.println( " in Parameters setEllipsoid" + center);
dataType = SURFACE_ELLIPSOID3;
distance = 0.3f * (Float.isNaN(scale) ? 1f : scale);
cutoff = Float.MIN_VALUE;
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-12-26 05:08:39 UTC (rev 14900)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-12-26 13:18:20 UTC (rev 14901)
@@ -16034,7 +16034,7 @@
sbCommand.append(" ").append(radius);
}
propertyValue = Float.valueOf(radius);
- if (optParameterAsString(i + 1).equalsIgnoreCase("full")) {
+ if (tokAt(i + 1) == Token.full) {
addShapeProperty(propertyList, "doFullMolecular", null);
sbCommand.append(" full");
i++;
Modified: trunk/Jmol/src/org/jmol/script/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/Token.java 2010-12-26 05:08:39 UTC (rev 14900)
+++ trunk/Jmol/src/org/jmol/script/Token.java 2010-12-26 13:18:20 UTC (rev 14901)
@@ -1081,10 +1081,11 @@
final static int from = misc | 128;// new
public final static int front = misc | 130;
final static int frontedges = misc | 132;// new
- public final static int frontlit = misc | 134;
+ public final static int frontlit = misc | 134;
public final static int frontonly = misc | 136;
- final static int fullplane = misc | 138;// new
- public final static int fullylit = misc | 140;
+ final static int full = misc | 137;// new
+ final static int fullplane = misc | 138;// new
+ public final static int fullylit = misc | 140;
final static int functionxy = misc | 142;// new
final static int functionxyz = misc | 144;// new
final static int gridpoints = misc | 146;// new
@@ -1921,6 +1922,7 @@
"fps", new Token(fps),
"from", new Token(from),
"frontEdges", new Token(frontedges),
+ "full", new Token(full),
"fullPlane", new Token(fullplane),
"functionXY", new Token(functionxy),
"functionXYZ", new Token(functionxyz),
Modified: trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2010-12-26 05:08:39 UTC (rev 14900)
+++ trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2010-12-26 13:18:20 UTC (rev 14901)
@@ -561,9 +561,9 @@
if (property == "moNumber")
return Integer.valueOf(moNumber);
if (property == "area")
- return (thisMesh == null ? new Float(Float.NaN) : thisMesh.calculateArea());
+ return (thisMesh == null ? new Float(Float.NaN) : calculateVolumeOrArea(true));
if (property == "volume")
- return (thisMesh == null ? new Float(Float.NaN) : thisMesh.calculateVolume());
+ return (thisMesh == null ? new Float(Float.NaN) : calculateVolumeOrArea(false));
if (thisMesh == null)
return null;//"no current isosurface";
if (property == "cutoff")
@@ -587,6 +587,26 @@
return null;
}
+ private Object calculateVolumeOrArea(boolean isArea) {
+ if (isArea) {
+ if (thisMesh.calculatedArea != null)
+ return thisMesh.calculatedArea;
+ } else {
+ if (thisMesh.calculatedVolume != null)
+ return thisMesh.calculatedVolume;
+ }
+ MeshData meshData = new MeshData();
+ fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
+ meshData.nSets = thisMesh.nSets;
+ meshData.vertexSets = thisMesh.vertexSets;
+ Object ret = meshData.calculateVolumeOrArea(thisMesh.thisSet, isArea, false);
+ if (isArea)
+ thisMesh.calculatedArea = ret;
+ else
+ thisMesh.calculatedVolume = ret;
+ return ret;
+ }
+
public static String getPolygonColorData(int ccount, short[] colixes) {
if (colixes == null)
return null;
Modified: trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2010-12-26 05:08:39 UTC (rev 14900)
+++ trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2010-12-26 13:18:20 UTC (rev 14901)
@@ -142,55 +142,6 @@
Graphics3D.getColixTranslucent(vertexColixes[i], isTranslucent, iLevel);
}
- Object calculateArea() {
- if (calculatedArea != null)
- return calculatedArea;
- boolean justOne = (nSets == 0 || thisSet >= 0);
- int n = (justOne ? 1 : nSets);
- double[] v = new double[n];
- for (int i = polygonCount; --i >= 0;) {
- if (!setABC(i))
- continue;
- int iSet = (nSets == 0 ? 0 : vertexSets[iA]);
- if (thisSet >= 0 && iSet != thisSet)
- continue;
- vAB.sub(vertices[iB], vertices[iA]);
- vAC.sub(vertices[iC], vertices[iA]);
- vTemp.cross(vAB, vAC);
- v[justOne ? 0 : iSet] += vTemp.length();
- }
- for (int i = 0; i < n; i++)
- v[i] /= 2;
- if (justOne)
- return calculatedArea = Float.valueOf((float) v[0]);
- return calculatedArea = v;
- }
-
- Object calculateVolume() {
- if (calculatedVolume != null)
- return calculatedVolume;
- boolean justOne = (nSets == 0 || thisSet >= 0);
- int n = (justOne ? 1 : nSets);
- double[] v = new double[n];
- for (int i = polygonCount; --i >= 0;) {
- if (!setABC(i))
- continue;
- int iSet = (nSets == 0 ? 0 : vertexSets[iA]);
- if (thisSet >= 0 && iSet != thisSet)
- continue;
- vAB.set(vertices[iB]);
- vAC.set(vertices[iC]);
- vTemp.cross(vAB, vAC);
- vAC.set(vertices[iA]);
- v[justOne ? 0 : iSet] += vAC.dot(vTemp);
- }
- for (int i = 0; i < n; i++)
- v[i] /= 6;
- if (justOne)
- return calculatedVolume = Float.valueOf((float) v[0]);
- return calculatedVolume = v;
- }
-
int thisSet = -1;
@Override
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesBond.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesBond.java 2010-12-26 05:08:39 UTC (rev 14900)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesBond.java 2010-12-26 13:18:20 UTC (rev 14901)
@@ -262,7 +262,6 @@
}
void switchAtoms() {
- System.out.println("FIXING BOND " + this);
SmilesAtom a = atom1;
atom1 = atom2;
atom2 = a;
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesMeasure.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesMeasure.java 2010-12-26 05:08:39 UTC (rev 14900)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesMeasure.java 2010-12-26 13:18:20 UTC (rev 14901)
@@ -77,9 +77,9 @@
boolean check() {
for (int i = 0; i < type; i++) {
int iAtom = search.patternAtoms[indices[i]].getMatchingAtom();
- System.out.print(iAtom + "-");
+ //System.out.print(iAtom + "-");
points[i] = (Point3f) search.jmolAtoms[iAtom];
- System.out.println(points[i]);
+ //System.out.println(points[i]);
}
float d = 0;
switch (type) {
@@ -96,7 +96,7 @@
d = search.v.vTemp1.angle(search.v.vTemp2) / radiansPerDegree * (search.v.vNorm1.dot(search.v.vNorm2) < 0 ? 1 : -1);
break;
}
- System.out.println(type + " " + min + " " + max + " " + d + " " + isNot);
+ //System.out.println(type + " " + min + " " + max + " " + d + " " + isNot);
return ((d < min || d > max) == isNot);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-12-26 05:08:39 UTC (rev 14900)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-12-26 13:18:20 UTC (rev 14901)
@@ -1,8 +1,10 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=12.1.27_dev
+version=12.1.27
+# code: System.out.println comments out
+# new feature: isosurface molecular FULL
# new feature: isosurface solvent [optionalRadius default:1.2] FULL
# -- very fast solvent excluded surface
# -- FULL option does reduced-surface analysis,
@@ -10,7 +12,8 @@
# -- very close fit to MSMS; slightly smaller area and volume
# -- replaces work from 12.1.24
# -- use isosurface SET 1 generally
-# -- TODO: prevent irrelevant inner surface.
+# -- irrelevant inner surface removed due to negative volume.
+# TODO: test for this with cavities
# bug fix: isosurface sets not sorted by number of vertices
# new feature: isosurface MSMS xxxx.vert -- creates isosurface from MSMS output files
# -- implies xxxx.face is also present in the same directory as xxxx.vert.
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/AppConsole.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/AppConsole.java 2010-12-26 05:08:39 UTC (rev 14900)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/AppConsole.java 2010-12-26 13:18:20 UTC (rev 14901)
@@ -399,6 +399,8 @@
//dumpUndo("undoRedo DONE");
}
+ private boolean dontsave;
+
private void undoSave(boolean incrementPtr) {
if (undoButton == null)
return;
@@ -409,7 +411,8 @@
for (int i = undoPointer + 1; i <= MAXUNDO; i++)
undoStack[i] = null;
Logger.startTimer();
- undoStack[undoPointer] = (String) viewer.getProperty("readable",
+ try {
+ undoStack[undoPointer] = (String) viewer.getProperty("readable",
"stateInfo", null);
//shift stack if full
if (incrementPtr && undoPointer == MAXUNDO) {
@@ -418,7 +421,10 @@
undoStack[MAXUNDO] = null;
} else if (incrementPtr)
undoPointer++;
- if (Logger.checkTimer(null) > 1000) {
+ } catch (Error e) {
+ dontsave = true;
+ }
+ if (dontsave || Logger.checkTimer(null) > 1000) {
//viewer.setBooleanProperty("undo", false);
//undoClear();
Logger.info("command processing slow; undo disabled");
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