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From: <ha...@us...> - 2008-08-05 19:00:41
|
Revision: 9671
http://jmol.svn.sourceforge.net/jmol/?rev=9671&view=rev
Author: hansonr
Date: 2008-08-05 19:00:33 +0000 (Tue, 05 Aug 2008)
Log Message:
-----------
version=11.5.53_dev pointgroups
# new feature: pointgroups with vibration vectors
# bug fix: more testing with pointgroups
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/shapespecial/Vectors.java
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-05 18:40:14 UTC (rev 9670)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-05 19:00:33 UTC (rev 9671)
@@ -429,8 +429,10 @@
}
private int calculatePointGroupForFirstModel(BitSet bsAtoms, boolean forceNew) {
+ int modelIndex = viewer.getCurrentModelIndex();
int iAtom = BitSetUtil.firstSetBit(bsAtoms);
- int modelIndex = (iAtom < 0 ? -1 : atoms[iAtom].getModelIndex());
+ if (modelIndex < 0 && iAtom >= 0)
+ modelIndex = atoms[iAtom].getModelIndex();
if (modelIndex < 0) {
modelIndex = BitSetUtil.firstSetBit(viewer.getVisibleFramesBitSet());
bsAtoms = null;
@@ -443,6 +445,10 @@
if (!bsAtoms.get(i))
bs.clear(i);
iAtom = BitSetUtil.firstSetBit(bs);
+ if (iAtom < 0) {
+ bs = getModelAtomBitSet(modelIndex, true);
+ iAtom = BitSetUtil.firstSetBit(bs);
+ }
Object obj = getShapeProperty(JmolConstants.SHAPE_VECTORS, "mad", iAtom);
boolean haveVibration = (obj != null && ((Integer)obj).intValue() != 0
|| viewer.isVibrationOn());
Modified: trunk/Jmol/src/org/jmol/shapespecial/Vectors.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Vectors.java 2008-08-05 18:40:14 UTC (rev 9670)
+++ trunk/Jmol/src/org/jmol/shapespecial/Vectors.java 2008-08-05 19:00:33 UTC (rev 9671)
@@ -44,7 +44,7 @@
public Object getProperty(String propertyName, int param) {
if (propertyName == "mad")
- return new Integer(mads == null || mads.length <= param ? 0 : mads[param]);
+ return new Integer(mads == null || param < 0 || mads.length <= param ? 0 : mads[param]);
return super.getProperty(propertyName, param);
}
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|
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From: <ha...@us...> - 2008-08-06 06:09:43
|
Revision: 9676
http://jmol.svn.sourceforge.net/jmol/?rev=9676&view=rev
Author: hansonr
Date: 2008-08-06 06:09:36 +0000 (Wed, 06 Aug 2008)
Log Message:
-----------
version=11.6.RC1
# bug fix: measures were messed up
# new feature: echo myecho IMAGE "filename"
# -- reads a JPG, GIF, or PNG image and displays it the
# same as text is displayed.
# new feature: echo myecho DEPTH xx
# -- sets the depth in percent (0% far back, 100% front) for the placement of the image
# -- note that images can be placed in 3D, just as for text.
# -- setting "background echo xxx" then specifies the color
# that is to be designated as the background color (the color that should be omitted).
# -- using "background echo none" specifies that the first pixel
# of the image specifies the color that should be omitted.
# bug fix: 11.5.52 may have lost "true" as a keyword
# new feature: pointgroups with vibration vectors
# bug fix: more testing with pointgroups
# new feature: spacefill/dots/geosurface/cartoon/trace/etc. ONLY
# -- show only this rendering type
# -- same as restrict not selected; spacefill ON
# bug fix: application rubberband selecting inappropriately selects atoms not visible
# new feature: wildcard at beginning for draw/pmesh/isosurface/etc. *xxx on/off/delete allowed
# bug fix: in draw pointGroup -- height of cylinder was too small
# bug fix: longstanding exception: isosurface fullylit --> isosurface backlit --> isosurface frontlit
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/shape/Measures.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/shape/Measures.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Measures.java 2008-08-06 05:58:05 UTC (rev 9675)
+++ trunk/Jmol/src/org/jmol/shape/Measures.java 2008-08-06 06:09:36 UTC (rev 9676)
@@ -173,14 +173,14 @@
} else if ("deleteVector".equals(propertyName)) {
define(setSingleItem((Vector) value), true, false, false);
setIndices();
- } else if ("defineVector_ALL".equals(propertyName)) {
+ } else if ("defineVector_All".equals(propertyName)) {
define((Vector) value, false, false, false);
- } else if ("deleteVector_ALL".equals(propertyName)) {
+ } else if ("deleteVector_All".equals(propertyName)) {
define((Vector) value, true, false, false);
setIndices();
- } else if ("hideVector_ALL".equals(propertyName)) {
+ } else if ("hideVector_All".equals(propertyName)) {
define((Vector) value, false, false, true);
- } else if ("showVector_ALL".equals(propertyName)) {
+ } else if ("showVector_All".equals(propertyName)) {
define((Vector) value, false, true, false);
} else if ("deleteModelAtoms".equals(propertyName)) {
atoms = (Atom[])((Object[])value)[1];
@@ -415,7 +415,7 @@
boolean isHide) {
if (thispt > ptLastAtom) {
// all atom bitsets have been iterated
- if (isAllConnected && !isConnected(m, ptLastAtom))
+ if (isAllConnected && !isConnected(m, thispt))
return;
int iThis = findMeasurement(m);
if (iThis >= 0) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-06 05:58:05 UTC (rev 9675)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-06 06:09:36 UTC (rev 9676)
@@ -1,8 +1,9 @@
# Developers: to add a description of changes you have made,
# add it on line starting with # below the "version=..." line
-version=11.6.RC1_dev
+version=11.6.RC1
+# bug fix: measures were messed up
# new feature: echo myecho IMAGE "filename"
# -- reads a JPG, GIF, or PNG image and displays it the
# same as text is displayed.
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|
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From: <ha...@us...> - 2008-08-06 14:40:47
|
Revision: 9679
http://jmol.svn.sourceforge.net/jmol/?rev=9679&view=rev
Author: hansonr
Date: 2008-08-06 14:40:42 +0000 (Wed, 06 Aug 2008)
Log Message:
-----------
version=11.6.RC1 (pointgroup enhancements)
# new feature: write/show pointgroup gives counts and tab-separated listing;
# new feature: write pointgroup draw delivers draw commands
# new feature: better draw pointgroup
# new feature: no saving of point group -- just recalculated each time
# bug fix: measures were messed up
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-06 06:59:49 UTC (rev 9678)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-06 14:40:42 UTC (rev 9679)
@@ -424,11 +424,16 @@
}
public String calculatePointGroup(BitSet bsAtoms) {
- int modelIndex = calculatePointGroupForFirstModel(bsAtoms, true);
- return models[modelIndex].pointGroup.getName();
+ return calculatePointGroupForFirstModel(bsAtoms, true).getName();
}
- private int calculatePointGroupForFirstModel(BitSet bsAtoms, boolean forceNew) {
+ public String getPointGroupAsString(BitSet bsAtoms, boolean asDraw) {
+ PointGroup pg = calculatePointGroupForFirstModel(bsAtoms, false);
+ return (modelCount > 1 ? "frame " + getModelNumberDotted(pg.getModelIndex()) + "; "
+ : "") + pg.getInfo(asDraw);
+ }
+
+ private PointGroup calculatePointGroupForFirstModel(BitSet bsAtoms, boolean forceNew) {
int modelIndex = viewer.getCurrentModelIndex();
int iAtom = BitSetUtil.firstSetBit(bsAtoms);
if (modelIndex < 0 && iAtom >= 0)
@@ -437,7 +442,6 @@
modelIndex = BitSetUtil.firstSetBit(viewer.getVisibleFramesBitSet());
bsAtoms = null;
}
- if (forceNew || models[modelIndex].pointGroup == null) {
BitSet bs = getModelAtomBitSet(modelIndex, true);
if (bsAtoms != null)
for (int i = 0; i < atomCount; i++)
@@ -452,18 +456,9 @@
Object obj = getShapeProperty(JmolConstants.SHAPE_VECTORS, "mad", iAtom);
boolean haveVibration = (obj != null && ((Integer)obj).intValue() != 0
|| viewer.isVibrationOn());
- PointGroup pg = new PointGroup(atoms, bs, haveVibration);
- models[modelIndex].pointGroup = pg;
- }
- return modelIndex;
+ return new PointGroup(atoms, bs, haveVibration, modelIndex);
}
- public String getPointGroupDraw(BitSet bsAtoms) {
- int modelIndex = calculatePointGroupForFirstModel(bsAtoms, false);
- return (modelCount > 1 ? "frame " + getModelNumberDotted(modelIndex) + "; " : "")
- + models[modelIndex].pointGroup.drawInfo();
- }
-
private BitSet modelsOf(BitSet bsAtoms, BitSet bsAllAtoms) {
BitSet bsModels = new BitSet(modelCount);
for (int i = 0; i < atomCount; i++) {
Modified: trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-06 06:59:49 UTC (rev 9678)
+++ trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-06 14:40:42 UTC (rev 9679)
@@ -33,6 +33,7 @@
import org.jmol.util.Escape;
import org.jmol.util.Logger;
import org.jmol.util.Quaternion;
+import org.jmol.util.TextFormat;
/*
* Bob Hanson 7/2008
@@ -69,6 +70,32 @@
1, // C8
};
+ private final static int[] nUnique = new int[] {
+ 1, // used for plane count
+ 0, // n/a
+ 0, // not used -- would be S2 (inversion)
+ 2, // S3
+ 2, // S4
+ 4, // S5
+ 2, // S6
+ 0, // n/a
+ 4, // S8
+ 0, // n/a
+ 4, // S10
+ 0, // n/a
+ 4, // S12
+ 0, // n/a
+ 0, // n/a firstProper = 14
+ 0, // n/a
+ 1, // C2
+ 2, // C3
+ 2, // C4
+ 4, // C5
+ 2, // C6
+ 0, // C7
+ 4, // C8
+ };
+
private final static int s3 = 3;
private final static int s4 = 4;
private final static int s5 = 5;
@@ -85,11 +112,16 @@
private final static int c8 = firstProper + 8;
private final static int maxAxis = axesMaxN.length;
- private int[] nAxes;
- private Operation[][] axes;
-
+ private int[] nAxes = new int[maxAxis];
+ private Operation[][] axes = new Operation[maxAxis][];
+ private int nAtoms;
private String name = "C_1?";
+ private int modelIndex;
+ public int getModelIndex() {
+ return modelIndex;
+ }
+
public String getName() {
return name;
}
@@ -100,9 +132,8 @@
final private Point3f center = new Point3f();
- public PointGroup(Atom[] atomset, BitSet bsAtoms, boolean haveVibration) {
- nAxes = new int[maxAxis];
- axes = new Operation[maxAxis][];
+ public PointGroup(Atom[] atomset, BitSet bsAtoms, boolean haveVibration, int modelIndex) {
+ this.modelIndex = modelIndex;
Point3f[] atoms;
if ((atoms = getCenter(atomset, bsAtoms)) == null) {
Logger.error("Too many atoms for point group calculation");
@@ -236,7 +267,7 @@
Atom[] atoms = new Atom[atomCount];
if (atomCount == 0)
return atoms;
- int nAtoms = 0;
+ nAtoms = 0;
for (int i = BitSetUtil.length(bsAtoms); --i >= 0;)
if (bsAtoms.get(i)) {
atoms[nAtoms] = atomset[i];
@@ -742,7 +773,7 @@
public String getLabel() {
switch (type) {
case OPERATION_PLANE:
- return "";
+ return "Cs";
case OPERATION_IMPROPER_AXIS:
return "S" + order;
default:
@@ -751,64 +782,112 @@
}
}
- public String drawInfo() {
+ public String getInfo(boolean asDraw) {
Vector3f v = new Vector3f();
Operation op;
- int n = 0;
- int[] nType = new int[4];
- for (int i = 1; i < maxAxis; i++) {
- n += nAxes[i];
+ int[][] nType = new int[4][2];
+ for (int i = 1; i < maxAxis; i++)
for (int j = nAxes[i]; --j >= 0;)
- nType[axes[i][j].type]++;
- }
- StringBuffer sb = new StringBuffer("set perspectivedepth off;\n");
- sb.append("draw p0" + (haveInversionCenter ? "inv " : " ") + Escape.escape(center)
- + (haveInversionCenter ? "\"i\";\n" : ";\n"));
- for (int i = 2; i < maxAxis; i++) {
- for (int j = 0; j < nAxes[i]; j++) {
- op = axes[i][j];
+ nType[axes[i][j].type][0]++;
+ StringBuffer sb = new StringBuffer("# " + nAtoms + " atoms\n");
+ if (asDraw) {
+ String m = "_" + modelIndex + "_";
+ sb.append("draw delete pg0" + m + "*;draw delete pgva" + m + "*;draw delete pgvp" + m + "*;");
+ sb.append("set perspectivedepth off;\n");
+ sb.append("draw pg0").append(m).append(haveInversionCenter ? "inv " : " ");
+ sb.append(Escape.escape(center) + (haveInversionCenter ? "\"i\";\n" : ";\n"));
+ for (int i = 2; i < maxAxis; i++) {
+ for (int j = 0; j < nAxes[i]; j++) {
+ op = axes[i][j];
+ v.set(op.normalOrAxis);
+ v.add(center);
+ float scale = (4.0f + op.order / 4.0f)
+ * (op.type == OPERATION_IMPROPER_AXIS ? -1 : 1);
+ sb.append("draw pgva").append(m).append(op.getLabel()).append("_").append(j + 1)
+ .append(" width 0.05 scale " + scale + " ").append(
+ Escape.escape(v));
+ v.scaleAdd(-2, op.normalOrAxis, v);
+ sb.append(Escape.escape(v)).append("\"" + op.getLabel() + "\"")
+ .append(op.type == OPERATION_IMPROPER_AXIS ? " color red" : "")
+ .append(";\n");
+ }
+ }
+ for (int j = 0; j < nAxes[0]; j++) {
+ op = axes[0][j];
v.set(op.normalOrAxis);
+ v.scale(0.025f);
v.add(center);
- float scale = (4.0f + op.order / 4.0f) * (op.type == OPERATION_IMPROPER_AXIS ? -1 : 1);
- sb.append("draw va").append(op.getLabel()).append("_").append(j).append(
- " width 0.05 scale " + scale + " ").append(Escape.escape(v));
+ sb.append("draw pgvp").append(m).append(j + 1).append("disk width 6.0 cylinder ")
+ .append(Escape.escape(v));
+ v.scaleAdd(-0.05f, op.normalOrAxis, v);
+ sb.append(Escape.escape(v)).append(" color translucent;\n");
+
+ v.set(op.normalOrAxis);
+ v.add(center);
+ sb.append("draw pgvp").append(m).append(j + 1).append(
+ "ring width 0.05 scale 3.0 arc ").append(Escape.escape(v));
v.scaleAdd(-2, op.normalOrAxis, v);
- sb.append(Escape.escape(v)).append("\"" + op.getLabel() + "\"").append(
- op.type == OPERATION_IMPROPER_AXIS ? " color red" : "").append(
- ";\n");
+ sb.append(Escape.escape(v));
+ v.x += 0.011;
+ v.y += 0.012;
+ v.z += 0.013;
+ sb.append(Escape.escape(v)).append("{0 360 0.5} color red;\n");
}
- }
- for (int j = 0; j < nAxes[0]; j++) {
- op = axes[0][j];
- v.set(op.normalOrAxis);
- v.scale(0.025f);
- v.add(center);
- sb.append("draw vp").append(j).append("disk width 6.0 cylinder ").append(
- Escape.escape(v));
- v.scaleAdd(-0.05f, op.normalOrAxis, v);
- sb.append(Escape.escape(v)).append(" color translucent;\n");
+ sb.append("# name=" + name);
+ sb.append(", nCi=" + (haveInversionCenter ? 1 : 0));
+ sb.append(", nCs=" + nAxes[0]);
+ sb.append(", nCn=" + nType[OPERATION_PROPER_AXIS][0]);
+ sb.append(", nSn=" + nType[OPERATION_IMPROPER_AXIS][0]);
+ sb.append(": ");
+ for (int i = maxAxis; --i >= 2;)
+ if (nAxes[i] > 0)
+ sb.append(" n" + (i < firstProper ? "S" : "C") + (i % firstProper)
+ + "=" + nAxes[i]);
+ sb.append(";\n");
+ } else {
+ int n = 0;
+ int nTotal = 1;
+ for (int i = maxAxis; --i >= 0;) {
+ if (nAxes[i] > 0) {
+ n = nUnique[i];
+ String label = axes[i][0].getLabel();
+ sb.append("\n\n" + name + "\tn" + label + "\t" + nAxes[i] + "\t" + n);
+ n *= nAxes[i];
+ nTotal += n;
+ nType[axes[i][0].type][1] += n;
+ for (int j = 0; j < nAxes[i]; j++) {
+ sb.append("\n" + name + "\t" + label + "_" + (j + 1) + "\t"
+ + axes[i][j].normalOrAxis);
+ }
+ }
+ }
+ if (haveInversionCenter) {
+ nTotal++;
+ sb.append("\n\n" + name + "\tCi\t" + Escape.escape(center));
+ }
+ sb.append("\n");
+ sb.append("\n" + name + "\ttype\tnType\tnUnique");
+ sb.append("\n" + name + "\tE\t 1\t 1");
+
+ n = (haveInversionCenter ? 1 : 0);
+ sb.append("\n" + name + "\tCi\t " + n + "\t " + n);
+
+ sb.append("\n" + name + "\tCs\t");
+ TextFormat.rFill(sb, " ",nAxes[0] + "\t");
+ TextFormat.rFill(sb, " ",nAxes[0] + "\n");
- v.set(op.normalOrAxis);
- v.add(center);
- sb.append("draw vp").append(j).append("ring width 0.05 scale 3.0 arc ")
- .append(Escape.escape(v));
- v.scaleAdd(-2, op.normalOrAxis, v);
- sb.append(Escape.escape(v));
- v.x += 0.011;
- v.y += 0.012;
- v.z += 0.013;
- sb.append(Escape.escape(v)).append("{0 360 0.5} color red;\n");
+ sb.append(name + "\tCn\t");
+ TextFormat.rFill(sb, " ",nType[OPERATION_PROPER_AXIS][0] + "\t");
+ TextFormat.rFill(sb, " ",nType[OPERATION_PROPER_AXIS][1] + "\n");
+
+ sb.append(name + "\tSn\t");
+ TextFormat.rFill(sb, " ",nType[OPERATION_IMPROPER_AXIS][0] + "\t");
+ TextFormat.rFill(sb, " ",nType[OPERATION_IMPROPER_AXIS][1] + "\n");
+
+ sb.append(name + "\t\tTOTAL\t");
+ TextFormat.rFill(sb, " ",nTotal + "\n");
}
- sb.append("# name=" + name);
- sb.append(", nCi=" + (haveInversionCenter ? 1 : 0));
- sb.append(", nCs=" + nAxes[0]);
- sb.append(", nCn=" + nType[OPERATION_PROPER_AXIS]);
- sb.append(", nSn=" + nType[OPERATION_IMPROPER_AXIS]);
- sb.append(": ");
- for (int i = maxAxis; --i >= 2; )
- if (nAxes[i] > 0)
- sb.append(" n" + (i < firstProper ? "S" : "C") + (i % firstProper) + "=" + nAxes[i]);
- sb.append(";\n");
return sb.toString();
}
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-06 06:59:49 UTC (rev 9678)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-06 14:40:42 UTC (rev 9679)
@@ -6233,7 +6233,7 @@
if (isSyntaxCheck)
return;
if (tokAt(0) == Token.draw)
- runScript(viewer.getPointGroupDraw());
+ runScript(viewer.getPointGroupAsString(true));
else
showString(viewer.calculatePointGroup());
return;
@@ -8744,6 +8744,9 @@
case Token.pointgroup:
type = "PGRP";
pt++;
+ type2 = Token.sValue(tokenAt(pt, args)).toLowerCase();
+ if (type2.equals("draw"))
+ pt++;
break;
case Token.quaternion:
pt++;
@@ -8946,7 +8949,7 @@
return "";
}
} else if (data == "PGRP") {
- data = viewer.getPointGroupDraw();
+ data = viewer.getPointGroupAsString((type2.equals("draw")));
} else if (data == "PDB") {
data = viewer.getPdbData(null);
} else if (data == "XYZ" || data == "MOL") {
@@ -9341,6 +9344,10 @@
if (!isSyntaxCheck)
msg = viewer.getPDBHeader();
break;
+ case Token.pointgroup:
+ if (!isSyntaxCheck)
+ msg = viewer.getPointGroupAsString(false);
+ break;
case Token.symmetry:
if (!isSyntaxCheck)
msg = viewer.getSymmetryInfoAsString();
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-06 06:59:49 UTC (rev 9678)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-06 14:40:42 UTC (rev 9679)
@@ -3,6 +3,10 @@
version=11.6.RC1
+# new feature: write/show pointgroup gives counts and tab-separated listing;
+# new feature: write pointgroup draw delivers draw commands
+# new feature: better draw pointgroup
+# new feature: no saving of point group -- just recalculated each time
# bug fix: measures were messed up
# new feature: echo myecho IMAGE "filename"
# -- reads a JPG, GIF, or PNG image and displays it the
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-06 06:59:49 UTC (rev 9678)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-06 14:40:42 UTC (rev 9679)
@@ -6825,8 +6825,8 @@
return modelSet.calculatePointGroup(selectionManager.bsSelection);
}
- public String getPointGroupDraw() {
- return modelSet.getPointGroupDraw(selectionManager.bsSelection);
+ public String getPointGroupAsString(boolean asDraw) {
+ return modelSet.getPointGroupAsString(selectionManager.bsSelection, asDraw);
}
Object getFileAsImage(String pathName, Hashtable htParams) {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-06 15:25:50
|
Revision: 9682
http://jmol.svn.sourceforge.net/jmol/?rev=9682&view=rev
Author: hansonr
Date: 2008-08-06 15:25:44 +0000 (Wed, 06 Aug 2008)
Log Message:
-----------
version=11.6.RC1 (c)
# bug fix: LOAD "..." nn loading of model numbers for PDB files should read real model number, not sequentially.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2008-08-06 15:08:51 UTC (rev 9681)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2008-08-06 15:25:44 UTC (rev 9682)
@@ -120,7 +120,9 @@
if (isModel) {
getHeader = false;
iHaveModelStatement = true;
- if (++modelNumber != desiredModelNumber && desiredModelNumber > 0) {
+ // PDB is different -- targets actual model number
+ int modelNumber = getModelNumber();
+ if (desiredModelNumber != Integer.MIN_VALUE && modelNumber != desiredModelNumber) {
if (iHaveModel)
break;
continue;
@@ -129,7 +131,7 @@
atomSetCollection.connectAll(maxSerial);
applySymmetry();
//supposedly MODEL is only for NMR
- model();
+ model(modelNumber);
continue;
}
/*
@@ -631,8 +633,19 @@
endSequenceNumber, endInsertionCode);
atomSetCollection.addStructure(structure);
}
-
- void model() {
+
+ private int getModelNumber() {
+ try {
+ int startModelColumn = 6; // should be 10 0-based
+ int endModelColumn = 14;
+ if (endModelColumn > lineLength)
+ endModelColumn = lineLength;
+ return modelNumber = parseInt(line, startModelColumn, endModelColumn);
+ } catch (NumberFormatException e) {
+ return 0;
+ }
+ }
+ void model(int modelNumber) {
/****************************************************************
* mth 2004 02 28
* note that the pdb spec says:
@@ -644,19 +657,10 @@
* but I received a file with the serial
* number right after the word MODEL :-(
****************************************************************/
- try {
- int startModelColumn = 6; // should be 10 0-based
- int endModelColumn = 14;
- if (endModelColumn > lineLength)
- endModelColumn = lineLength;
- int modelNumber = parseInt(line, startModelColumn, endModelColumn);
haveMappedSerials = false;
atomSetCollection.newAtomSet();
atomSetCollection.setAtomSetAuxiliaryInfo("isPDB", Boolean.TRUE);
atomSetCollection.setAtomSetNumber(modelNumber);
- } catch (NumberFormatException e) {
- //ingore model number errors
- }
}
void cryst1() throws Exception {
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2008-08-06 15:08:51 UTC (rev 9681)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2008-08-06 15:25:44 UTC (rev 9682)
@@ -224,7 +224,7 @@
public void initialize() {
// called by the resolver
modelNumber = 0;
- desiredModelNumber = -1;
+ desiredModelNumber = Integer.MIN_VALUE;
iHaveDesiredModel = false;
getHeader = false;
latticeCells[0] = latticeCells[1] = latticeCells[2] = 0;
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-06 15:08:51 UTC (rev 9681)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-06 15:25:44 UTC (rev 9682)
@@ -4213,6 +4213,7 @@
boolean appendNew = viewer.getAppendNew();
StringBuffer loadScript = new StringBuffer("load");
int[] params = new int[4];
+ params[0] = Integer.MIN_VALUE;
int nFiles = 1;
Point3f unitCells = viewer.getDefaultLattice();
Hashtable htParams = new Hashtable();
@@ -4246,7 +4247,7 @@
loadScript.append(" " + modelName);
isAppend = (modelName.equalsIgnoreCase("append"));
if (modelName.equalsIgnoreCase("trajectory"))
- params[0] = -1;
+ params[0] = Integer.MIN_VALUE;
}
if (getToken(i).tok != Token.string)
error(ERROR_filenameExpected);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-06 15:08:51 UTC (rev 9681)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-06 15:25:44 UTC (rev 9682)
@@ -3,6 +3,8 @@
version=11.6.RC1
+# bug fix: LOAD "..." nn loading of model numbers for PDB files should read real model number, not sequentially.
+
# new feature: write/show pointgroup gives counts and tab-separated listing;
# new feature: write pointgroup draw delivers draw commands
# new feature: better draw pointgroup
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-06 18:07:15
|
Revision: 9685
http://jmol.svn.sourceforge.net/jmol/?rev=9685&view=rev
Author: hansonr
Date: 2008-08-06 18:07:10 +0000 (Wed, 06 Aug 2008)
Log Message:
-----------
version=11.6.RC1 # bug fix: D3h point group
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-06 16:42:44 UTC (rev 9684)
+++ trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-06 18:07:10 UTC (rev 9685)
@@ -641,9 +641,6 @@
}
private int findPlanes(Point3f[] atoms, int[] elements) {
- Operation[] axesC2 = axes[c2];
- int nC2 = nAxes[c2];
-
Point3f pt = new Point3f();
Vector3f v1 = new Vector3f();
Vector3f v2 = new Vector3f();
@@ -685,10 +682,11 @@
}
}
- // also look for planes normal to any C2 axis
+ // also look for planes normal to any C axis
- for (int i = 0; i < nC2; i++)
- nPlanes = getPlane(nPlanes, axesC2[i].normalOrAxis, atoms, elements,
+ for (int i = c2; i < maxAxis; i++)
+ for (int j = 0; j < nAxes[i]; i++)
+ nPlanes = getPlane(nPlanes, axes[i][j].normalOrAxis, atoms, elements,
center);
return nPlanes;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-06 16:42:44 UTC (rev 9684)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-06 18:07:10 UTC (rev 9685)
@@ -3,6 +3,7 @@
version=11.6.RC1
+# bug fix: D3h point group
# bug fix: LOAD "..." nn loading of model numbers for PDB files should read real model number, not sequentially.
# new feature: write/show pointgroup gives counts and tab-separated listing;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-07 14:12:42
|
Revision: 9689
http://jmol.svn.sourceforge.net/jmol/?rev=9689&view=rev
Author: hansonr
Date: 2008-08-07 14:12:38 +0000 (Thu, 07 Aug 2008)
Log Message:
-----------
version=11.6.RC2 bug fixes; help menu in console; Java permissions
# bug fix: Cs pointgroup not found
# bug fix: set echo DEPTH/IMAGE
# bug fix: workaround for Java 1.6.0_10 diallowing popup menu
# new feature: in Java 1.6.0_10, right-click activates the console, and the
# console has a menubar menu item "Jmol" that is the pop-up menu.
# new feature: applet console has "help" menu item, which includes several hundred items.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/shape/Object2d.java
trunk/Jmol/src/org/jmol/shape/Text.java
trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/shape/Object2d.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Object2d.java 2008-08-07 03:09:39 UTC (rev 9688)
+++ trunk/Jmol/src/org/jmol/shape/Object2d.java 2008-08-07 14:12:38 UTC (rev 9689)
@@ -154,7 +154,7 @@
}
public void setMovableZ(int z) {
- if (valign == VALIGN_XYZ)
+ if (valign != VALIGN_XYZ)
valign = VALIGN_XY;
movableZ = z;
movableZPercent = Integer.MAX_VALUE;
@@ -173,7 +173,7 @@
}
public void setMovableZPercent(int z) {
- if (valign == VALIGN_XYZ)
+ if (valign != VALIGN_XYZ)
valign = VALIGN_XY;
movableZ = Integer.MAX_VALUE;
movableZPercent = z;
@@ -318,7 +318,7 @@
boxXY[1] = windowHeight;
break;
default:
- float y = (movableXPercent != Integer.MAX_VALUE ? movableYPercent
+ float y = (movableYPercent != Integer.MAX_VALUE ? movableYPercent
* windowHeight / 100 : is3dEcho? movableY : movableY * scale);
float offsetY = this.offsetY * scale;
boxXY[1] = (is3dEcho ? y : (windowHeight - y)) + offsetY;
Modified: trunk/Jmol/src/org/jmol/shape/Text.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Text.java 2008-08-07 03:09:39 UTC (rev 9688)
+++ trunk/Jmol/src/org/jmol/shape/Text.java 2008-08-07 14:12:38 UTC (rev 9689)
@@ -208,7 +208,7 @@
// adjust positions if necessary
if (adjustForWindow)
- setBoxOffsetsInWindow(fontScale, isLabelOrHover ? 16 * fontScale
+ setBoxOffsetsInWindow(image == null ? fontScale : 0, isLabelOrHover ? 16 * fontScale
+ lineHeight : 0, boxY - textHeight);
// draw the box if necessary
@@ -220,25 +220,25 @@
// now set x and y positions for text from (new?) box position
- int adj = (fontScale >= 2 ? 8 : 4);
- int x0 = (int) boxX;
- switch (align) {
- case ALIGN_CENTER:
- x0 += boxWidth / 2;
- break;
- case ALIGN_RIGHT:
- x0 += boxWidth - adj;
- break;
- default:
- x0 += adj;
- }
-
if (image != null) {
g3d.drawImage(image, (int) boxX, (int) boxY, z, zSlab, (int) boxWidth,
(int) boxHeight, bgcolix);
} else {
// now write properly aligned text
+ int adj = (fontScale >= 2 ? 8 : 4);
+ int x0 = (int) boxX;
+ switch (align) {
+ case ALIGN_CENTER:
+ x0 += boxWidth / 2;
+ break;
+ case ALIGN_RIGHT:
+ x0 += boxWidth - adj;
+ break;
+ default:
+ x0 += adj;
+ }
+
float x = x0;
float y = boxY + ascent + adj;
//System.out.println("scale=" + fontScale + " boxwidth/height=" + boxWidth
Modified: trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-07 03:09:39 UTC (rev 9688)
+++ trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-07 14:12:38 UTC (rev 9689)
@@ -646,13 +646,14 @@
Vector3f v2 = new Vector3f();
Vector3f v3 = new Vector3f();
int nPlanes = 0;
+ boolean haveAxes = (getHighestOrder() > 1);
for (int i = atoms.length; --i >= 0;) {
if (i == centerAtomIndex)
continue;
Point3f a1 = atoms[i];
int e1 = elements[i];
for (int j = atoms.length; --j > i;) {
- if (elements[j] != e1)
+ if (haveAxes && elements[j] != e1)
continue;
// plane are treated as S2 axes here
@@ -683,11 +684,11 @@
}
// also look for planes normal to any C axis
-
- for (int i = c2; i < maxAxis; i++)
- for (int j = 0; j < nAxes[i]; i++)
- nPlanes = getPlane(nPlanes, axes[i][j].normalOrAxis, atoms, elements,
- center);
+ if (haveAxes)
+ for (int i = c2; i < maxAxis; i++)
+ for (int j = 0; j < nAxes[i]; i++)
+ nPlanes = getPlane(nPlanes, axes[i][j].normalOrAxis, atoms, elements,
+ center);
return nPlanes;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-07 03:09:39 UTC (rev 9688)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-07 14:12:38 UTC (rev 9689)
@@ -8277,16 +8277,14 @@
case Token.script:
propertyName = "script";
propertyValue = parameterAsString(4);
- setShapeProperty(JmolConstants.SHAPE_ECHO, propertyName, propertyValue);
- return;
+ break;
case Token.model:
int modelIndex = modelNumberParameter(4);
if (!isSyntaxCheck && modelIndex >= viewer.getModelCount())
error(ERROR_invalidArgument);
propertyName = "model";
propertyValue = new Integer(modelIndex);
- setShapeProperty(JmolConstants.SHAPE_ECHO, propertyName, propertyValue);
- return;
+ break;
case Token.image:
//set echo name image "xxx"
echo(4, true);
@@ -8294,6 +8292,10 @@
case Token.depth:
propertyName = "%zpos";
propertyValue = new Integer((int) floatParameter(4));
+ break;
+ }
+ if (propertyValue != null) {
+ setShapeProperty(JmolConstants.SHAPE_ECHO, propertyName, propertyValue);
return;
}
}
@@ -8308,9 +8310,8 @@
setShapeProperty(JmolConstants.SHAPE_ECHO, "xyz", centerParameter(i));
return;
}
- propertyValue = xypParameter(i);
String type = "xypos";
- if (propertyValue == null) {
+ if ((propertyValue = xypParameter(i)) == null) {
int pos = intParameter(i++);
propertyValue = new Integer(pos);
if (tokAt(i) == Token.percent) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-07 03:09:39 UTC (rev 9688)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-07 14:12:38 UTC (rev 9689)
@@ -1,8 +1,10 @@
# Developers: to add a description of changes you have made,
# add it on line starting onlwith # below the "version=..." line
-version=11.6.RC2_dev
+version=11.6.RC2
+# bug fix: Cs pointgroup not found
+# bug fix: set echo DEPTH/IMAGE
# bug fix: workaround for Java 1.6.0_10 diallowing popup menu
# new feature: in Java 1.6.0_10, right-click activates the console, and the
# console has a menubar menu item "Jmol" that is the pop-up menu.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-07 14:39:42
|
Revision: 9690
http://jmol.svn.sourceforge.net/jmol/?rev=9690&view=rev
Author: hansonr
Date: 2008-08-07 14:39:33 +0000 (Thu, 07 Aug 2008)
Log Message:
-----------
version=11.6.RC2 point group tolerances
# new feature: set pointGroupDistanceTolerance (default 0.2 angstroms)
# new feature: set pointGroupLinearTolerance (default 8 degrees)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/symmetry/PointGroup.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/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-07 14:12:38 UTC (rev 9689)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-07 14:39:33 UTC (rev 9690)
@@ -433,7 +433,8 @@
: "") + pg.getInfo(asDraw);
}
- private PointGroup calculatePointGroupForFirstModel(BitSet bsAtoms, boolean forceNew) {
+ private PointGroup calculatePointGroupForFirstModel(BitSet bsAtoms,
+ boolean forceNew) {
int modelIndex = viewer.getCurrentModelIndex();
int iAtom = BitSetUtil.firstSetBit(bsAtoms);
if (modelIndex < 0 && iAtom >= 0)
@@ -442,21 +443,22 @@
modelIndex = BitSetUtil.firstSetBit(viewer.getVisibleFramesBitSet());
bsAtoms = null;
}
- BitSet bs = getModelAtomBitSet(modelIndex, true);
- if (bsAtoms != null)
- for (int i = 0; i < atomCount; i++)
- if (atoms[i].modelIndex == modelIndex)
- if (!bsAtoms.get(i))
- bs.clear(i);
+ BitSet bs = getModelAtomBitSet(modelIndex, true);
+ if (bsAtoms != null)
+ for (int i = 0; i < atomCount; i++)
+ if (atoms[i].modelIndex == modelIndex)
+ if (!bsAtoms.get(i))
+ bs.clear(i);
+ iAtom = BitSetUtil.firstSetBit(bs);
+ if (iAtom < 0) {
+ bs = getModelAtomBitSet(modelIndex, true);
iAtom = BitSetUtil.firstSetBit(bs);
- if (iAtom < 0) {
- bs = getModelAtomBitSet(modelIndex, true);
- iAtom = BitSetUtil.firstSetBit(bs);
- }
- Object obj = getShapeProperty(JmolConstants.SHAPE_VECTORS, "mad", iAtom);
- boolean haveVibration = (obj != null && ((Integer)obj).intValue() != 0
- || viewer.isVibrationOn());
- return new PointGroup(atoms, bs, haveVibration, modelIndex);
+ }
+ Object obj = getShapeProperty(JmolConstants.SHAPE_VECTORS, "mad", iAtom);
+ boolean haveVibration = (obj != null && ((Integer) obj).intValue() != 0 || viewer
+ .isVibrationOn());
+ return new PointGroup(atoms, bs, haveVibration, modelIndex, viewer
+ .getPointGroupTolerance(0), viewer.getPointGroupTolerance(1));
}
private BitSet modelsOf(BitSet bsAtoms, BitSet bsAllAtoms) {
Modified: trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-07 14:12:38 UTC (rev 9689)
+++ trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-07 14:39:33 UTC (rev 9690)
@@ -117,6 +117,8 @@
private int nAtoms;
private String name = "C_1?";
private int modelIndex;
+ private float distanceTolerance = 0.2f;
+ private float linearTolerance = 0.99f; // 8 degrees
public int getModelIndex() {
return modelIndex;
@@ -132,12 +134,16 @@
final private Point3f center = new Point3f();
- public PointGroup(Atom[] atomset, BitSet bsAtoms, boolean haveVibration, int modelIndex) {
+ public PointGroup(Atom[] atomset, BitSet bsAtoms, boolean haveVibration,
+ int modelIndex, float distanceTolerance, float linearTolerance) {
this.modelIndex = modelIndex;
+ this.distanceTolerance = distanceTolerance;
+ this.linearTolerance = (float) (Math.cos(linearTolerance / 180 * Math.PI));
Point3f[] atoms;
if ((atoms = getCenter(atomset, bsAtoms)) == null) {
Logger.error("Too many atoms for point group calculation");
- name = "point group not determined -- atomCount > " + ATOM_COUNT_MAX + " -- select fewer atoms and try again.";
+ name = "point group not determined -- atomCount > " + ATOM_COUNT_MAX
+ + " -- select fewer atoms and try again.";
return;
}
int[] elements = new int[atoms.length];
@@ -152,7 +158,7 @@
Point3f[] atomVibs = new Point3f[atoms.length];
for (int i = atoms.length; --i >= 0;) {
atomVibs[i] = new Point3f(atoms[i]);
- Vector3f v = ((Atom)atoms[i]).getVibrationVector();
+ Vector3f v = ((Atom) atoms[i]).getVibrationVector();
if (v != null)
atomVibs[i].add(v);
}
@@ -290,7 +296,6 @@
}
}
- private final static float DISTANCE_TOLERANCE = 0.2f;
private boolean checkOperation(Point3f[] atoms, int[] elements, Quaternion q,
Point3f center, int iOrder) {
Point3f pt = new Point3f();
@@ -321,7 +326,7 @@
vTemp.sub(center, pt);
pt.scaleAdd(2, vTemp, pt);
}
- if ((q != null || isInversion) && pt.distance(a1) < DISTANCE_TOLERANCE) {
+ if ((q != null || isInversion) && pt.distance(a1) < distanceTolerance) {
nFound++;
continue;
}
@@ -331,7 +336,7 @@
Point3f a2 = atoms[j];
// System.out.println(i + " " + j + " " + a1 + " " + a2 + " " + pt
// + nFound + " " + pt.distance(a2));
- if (pt.distance(a2) < DISTANCE_TOLERANCE) {
+ if (pt.distance(a2) < distanceTolerance) {
nFound++;
continue out;
}
@@ -360,10 +365,9 @@
return true;
}
- private final static float LINEAR_DOT_MINIMUM = 0.99f; // 8 degrees
-
- private static boolean isParallel(Vector3f v1, Vector3f v2) {
- return (Math.abs(v1.dot(v2)) >= LINEAR_DOT_MINIMUM);
+ private boolean isParallel(Vector3f v1, Vector3f v2) {
+ // note -- these MUST be unit vectors
+ return (Math.abs(v1.dot(v2)) >= linearTolerance);
}
int maxElement = 0;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-07 14:12:38 UTC (rev 9689)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-07 14:39:33 UTC (rev 9690)
@@ -3,6 +3,9 @@
version=11.6.RC2
+# new feature: set pointGroupDistanceTolerance (default 0.2 angstroms)
+# new feature: set pointGroupLinearTolerance (default 8 degrees)
+
# bug fix: Cs pointgroup not found
# bug fix: set echo DEPTH/IMAGE
# bug fix: workaround for Java 1.6.0_10 diallowing popup menu
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-08-07 14:12:38 UTC (rev 9689)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-08-07 14:39:33 UTC (rev 9690)
@@ -621,6 +621,8 @@
boolean messageStyleChime = false;
int pickingSpinRate = 10;
String pickLabel = "";
+ float pointGroupDistanceTolerance = 0.2f;
+ float pointGroupLinearTolerance = 8.0f;
String propertyColorScheme = "roygb";
String quaternionFrame = "c";
float solventProbeRadius = 1.2f;
@@ -1178,6 +1180,8 @@
setParameterValue("pickingSpinRate", pickingSpinRate);
setParameterValue("pickingStyle", "toggle");
setParameterValue("pickLabel", pickLabel);
+ setParameterValue("pointGroupLinearTolerance", pointGroupLinearTolerance);
+ setParameterValue("pointGroupDistanceTolerance", pointGroupDistanceTolerance);
setParameterValue("propertyColorScheme", propertyColorScheme);
setParameterValue("propertyDataField", 0);
setParameterValue("propertyAtomNumberField", 0);
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-07 14:12:38 UTC (rev 9689)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-07 14:39:33 UTC (rev 9690)
@@ -4348,6 +4348,16 @@
//Eval
boolean notFound = false;
while (true) {
+ //11.6.RC2//
+ if (key.equalsIgnoreCase("pointGroupDistanceTolerance")) {
+ setPointGroupTolerance(value, 0);
+ break;
+ }
+ if (key.equalsIgnoreCase("pointGroupLinearTolerance")) {
+ setPointGroupTolerance(value, 1);
+ break;
+ }
+
//11.5.30//
if (key.equalsIgnoreCase("ellipsoidAxisDiameter")) {
if (isInt)
@@ -4488,7 +4498,7 @@
else
global.setUserVariable(key, new Token(Token.decimal, new Float(value)));
return true;
- }
+ }
public void setIntProperty(String key, int value) {
if (key.charAt(0) == '_') {
@@ -6829,6 +6839,27 @@
return modelSet.getPointGroupAsString(selectionManager.bsSelection, asDraw);
}
+ private void setPointGroupTolerance(float value, int type) {
+ switch (type) {
+ case 0:
+ global.pointGroupDistanceTolerance = value;
+ break;
+ case 1:
+ global.pointGroupLinearTolerance = value;
+ break;
+ }
+ }
+
+ public float getPointGroupTolerance(int type) {
+ switch (type) {
+ case 0:
+ return global.pointGroupDistanceTolerance;
+ case 1:
+ return global.pointGroupLinearTolerance;
+ }
+ return 0;
+ }
+
Object getFileAsImage(String pathName, Hashtable htParams) {
if (!haveDisplay)
return "no display";
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-07 15:29:38
|
Revision: 9691
http://jmol.svn.sourceforge.net/jmol/?rev=9691&view=rev
Author: hansonr
Date: 2008-08-07 15:29:30 +0000 (Thu, 07 Aug 2008)
Log Message:
-----------
version=11.6.RC2 (b) # bug fix: image background transparency
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/g3d/Platform3D.java
trunk/Jmol/src/org/jmol/g3d/Text3D.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/g3d/Platform3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Platform3D.java 2008-08-07 14:39:33 UTC (rev 9690)
+++ trunk/Jmol/src/org/jmol/g3d/Platform3D.java 2008-08-07 15:29:30 UTC (rev 9691)
@@ -175,12 +175,12 @@
abstract Image allocateOffscreenImage(int width, int height);
abstract Graphics getGraphics(Image imageOffscreen);
- void checkOffscreenSize(int width, int height) {
+ boolean checkOffscreenSize(int width, int height) {
if (width <= widthOffscreen && height <= heightOffscreen)
- return;
+ return true;
if (imageOffscreen != null) {
- gOffscreen.dispose();
- imageOffscreen.flush();
+ gOffscreen.dispose();
+ imageOffscreen.flush();
}
if (width > widthOffscreen)
widthOffscreen = (width + 63) & ~63;
@@ -188,6 +188,7 @@
heightOffscreen = (height + 15) & ~15;
imageOffscreen = allocateOffscreenImage(widthOffscreen, heightOffscreen);
gOffscreen = getGraphics(imageOffscreen);
+ return false;
}
class ClearingThread extends Thread implements Runnable {
Modified: trunk/Jmol/src/org/jmol/g3d/Text3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Text3D.java 2008-08-07 14:39:33 UTC (rev 9690)
+++ trunk/Jmol/src/org/jmol/g3d/Text3D.java 2008-08-07 15:29:30 UTC (rev 9691)
@@ -121,6 +121,7 @@
return;
g3d.platform.checkOffscreenSize(width, height);
Graphics g = g3d.platform.gOffscreen;
+ g.clearRect(0,0,width,height);
if (g3d.isAntialiased()) {
g.drawImage(image, 0, 0, width, height, 0, 0, width >> 1, height >> 1, null);
} else {
@@ -150,12 +151,14 @@
if (jmolRenderer == null)
jmolRenderer = g3d;
int bgcolor = (argbBackground == 0 ? buffer[0] : argbBackground);
- for (int i = 0, offset = 0; i < height; i++)
+ for (int i = 0, offset = 0; i < height; i++) {
+ //System.out.println(Integer.toHexString(buffer[offset]));
for (int j = 0; j < width; j++) {
int argb = buffer[offset++];
- if (argb != bgcolor)
+ if (argb != bgcolor && (argb & 0xFF000000) == 0xFF000000)
jmolRenderer.plotPixelClippedNoSlab(argb, x + j, y + i, z);
}
+ }
}
private static void plotImageUnClipped(int x, int y, int z, Graphics3D g3d,
@@ -169,10 +172,11 @@
int offset = 0;
int bgcolor = (argbBackground == 0 ? buffer[0] : argbBackground);
while (i < textHeight) {
+ //System.out.println(Integer.toHexString(buffer[offset]));
while (j < textWidth) {
if (z < zbuf[pbufOffset]) {
int argb = buffer[offset];
- if (argb != bgcolor)
+ if (argb != bgcolor && (argb & 0xFF000000) == 0xFF000000)
g3d.addPixel(pbufOffset, z, argb);
}
++offset;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-07 14:39:33 UTC (rev 9690)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-07 15:29:30 UTC (rev 9691)
@@ -3,6 +3,8 @@
version=11.6.RC2
+# bug fix: image background transparency
+
# new feature: set pointGroupDistanceTolerance (default 0.2 angstroms)
# new feature: set pointGroupLinearTolerance (default 8 degrees)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-08 15:15:09
|
Revision: 9693
http://jmol.svn.sourceforge.net/jmol/?rev=9693&view=rev
Author: hansonr
Date: 2008-08-08 15:15:03 +0000 (Fri, 08 Aug 2008)
Log Message:
-----------
version=11.6.RC3_dev pointgroup enhancements, dot Density
# new feature: set dotDensity [-3 to 3]
# bug fix: minor error in pointgroup
# new feature: draw pointGroup [type] [index] SCALE [x]
# where [type] is one of Cs, Ci, Cn, or Sn, where n is an integer or the character "n"
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/applet/Jmol.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/shape/DotsRenderer.java
trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
trunk/Jmol/src/org/jmol/util/Quaternion.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateManager.java
trunk/Jmol/src/org/jmol/viewer/Token.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/applet/Jmol.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jmol.java 2008-08-07 19:09:42 UTC (rev 9692)
+++ trunk/Jmol/src/org/jmol/applet/Jmol.java 2008-08-08 15:15:03 UTC (rev 9693)
@@ -377,7 +377,7 @@
"setWindowAlwaysOnTop"));
}
} catch (Exception e) {
- popupMenuAllowed = false;
+ //popupMenuAllowed = false;
System.out.println("popup menu not available");
}
getPopupMenu(false);
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-07 19:09:42 UTC (rev 9692)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-08 15:15:03 UTC (rev 9693)
@@ -427,10 +427,12 @@
return calculatePointGroupForFirstModel(bsAtoms, true).getName();
}
- public String getPointGroupAsString(BitSet bsAtoms, boolean asDraw) {
+ public String getPointGroupAsString(BitSet bsAtoms, boolean asDraw,
+ String type, int index, float scale) {
PointGroup pg = calculatePointGroupForFirstModel(bsAtoms, false);
- return (modelCount > 1 ? "frame " + getModelNumberDotted(pg.getModelIndex()) + "; "
- : "") + pg.getInfo(asDraw);
+ return (modelCount > 1 ? "frame "
+ + getModelNumberDotted(pg.getModelIndex()) + "; " : "")
+ + pg.getInfo(asDraw, type, index, scale);
}
private PointGroup calculatePointGroupForFirstModel(BitSet bsAtoms,
Modified: trunk/Jmol/src/org/jmol/shape/DotsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/DotsRenderer.java 2008-08-07 19:09:42 UTC (rev 9692)
+++ trunk/Jmol/src/org/jmol/shape/DotsRenderer.java 2008-08-08 15:15:03 UTC (rev 9693)
@@ -63,6 +63,10 @@
int sppa = (int) viewer.getScalePixelsPerAngstrom();
screenLevel = (iShowSolid || sppa > 20 ? 3 : sppa > 10 ? 2 : sppa > 5 ? 1
: 0);
+ if (!iShowSolid) {
+ screenLevel += viewer.getDotDensity() - 3;
+ screenLevel = Math.max(Math.min(screenLevel, 3), 0);
+ }
screenDotCount = Geodesic.getVertexCount(screenLevel);
for (int i = screenDotCount; --i >= 0;)
viewer.transformVector(Geodesic.getVertexVector(i),
Modified: trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-07 19:09:42 UTC (rev 9692)
+++ trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-08 15:15:03 UTC (rev 9693)
@@ -119,6 +119,8 @@
private int modelIndex;
private float distanceTolerance = 0.2f;
private float linearTolerance = 0.99f; // 8 degrees
+ private Operation principalAxis = new Operation(null);
+ private Operation principalPlane = new Operation(null);
public int getModelIndex() {
return modelIndex;
@@ -172,6 +174,13 @@
} else {
name = "C(infinity)v";
}
+ vTemp.sub(atoms[1], atoms[0]);
+ addAxis(c2, vTemp);
+ principalAxis = axes[c2][0];
+ if (haveInversionCenter) {
+ axes[0] = new Operation[1];
+ principalPlane = axes[0][nAxes[0]++] = new Operation(vTemp);
+ }
return;
}
axes[0] = new Operation[15];
@@ -227,6 +236,7 @@
// and more than one C2 if even order (since the one will be part of the
// principal axis
+ principalAxis = setPrincipalAxis(n, nPlanes);
if (nPlanes == 0) {
if (n < firstProper) {
name = "S" + n;
@@ -247,14 +257,18 @@
}
} else if (nPlanes == 0) {
// Cn, S3, S6
+ principalAxis = axes[n][0];
if (n < firstProper) {
name = "S" + n;
} else {
name = "C" + (n - firstProper);
}
} else if (nPlanes == n - firstProper) {
+ principalAxis = axes[n][0];
name = "C" + nPlanes + "v";
} else {
+ principalAxis = axes[n < firstProper ? n + firstProper : n][0];
+ principalPlane = axes[0][0];
if (n < firstProper)
n /= 2;
else
@@ -265,6 +279,47 @@
//System.out.println(drawInfo());
}
+ private Operation setPrincipalAxis(int n, int nPlanes) {
+ Operation principalPlane = setPrincipalPlane(n, nPlanes);
+ if (nPlanes == 0 && n < firstProper || nAxes[n] == 1) {
+ if (nPlanes > 0 && n < firstProper)
+ n = firstProper + n / 2;
+ return axes[n][0];
+ }
+ // D2, D2d, D2h -- which c2 axis is it?
+ if (principalPlane == null)
+ return null;
+ for (int i = 0; i < nAxes[c2]; i++)
+ if (isParallel(principalPlane.normalOrAxis, axes[c2][i].normalOrAxis)) {
+ if (i != 0) {
+ Operation o = axes[c2][0];
+ axes[c2][0] = axes[c2][i];
+ axes[c2][i] = o;
+ }
+ return axes[c2][0];
+ }
+ return null;
+ }
+
+ private Operation setPrincipalPlane(int n, int nPlanes) {
+ // principal plane is perpendicular to more than two other planes
+ if (nPlanes == 1)
+ return principalPlane = axes[0][0];
+ if (nPlanes == 0 || nPlanes == n - firstProper)
+ return null;
+ for (int i = 0; i < nPlanes; i++)
+ for (int j = 0, nPerp = 0; j < nPlanes; j++)
+ if (isPerpendicular(axes[0][i].normalOrAxis, axes[0][j].normalOrAxis) && ++nPerp > 2) {
+ if (i != 0) {
+ Operation o = axes[0][0];
+ axes[0][0] = axes[0][i];
+ axes[0][i] = o;
+ }
+ return principalPlane = axes[0][0];
+ }
+ return null;
+ }
+
private final static int ATOM_COUNT_MAX = 100;
private Atom[] getCenter(Atom[] atomset, BitSet bsAtoms) {
int atomCount = BitSetUtil.cardinalityOf(bsAtoms);
@@ -370,6 +425,11 @@
return (Math.abs(v1.dot(v2)) >= linearTolerance);
}
+ private boolean isPerpendicular(Vector3f v1, Vector3f v2) {
+ // note -- these MUST be unit vectors
+ return (Math.abs(v1.dot(v2)) <= 1 - linearTolerance);
+ }
+
int maxElement = 0;
int[] eCounts;
@@ -690,7 +750,7 @@
// also look for planes normal to any C axis
if (haveAxes)
for (int i = c2; i < maxAxis; i++)
- for (int j = 0; j < nAxes[i]; i++)
+ for (int j = 0; j < nAxes[i]; j++)
nPlanes = getPlane(nPlanes, axes[i][j].normalOrAxis, atoms, elements,
center);
return nPlanes;
@@ -740,32 +800,38 @@
final static String[] typeNames = { "plane", "proper axis", "improper axis",
"center of inversion" };
+ int nOps = 0;
public class Operation {
-
int type;
int order;
+ int index;
Vector3f normalOrAxis;
Operation() {
+ index = ++nOps;
type = OPERATION_INVERSION_CENTER;
- //if (Logger.debugging)
+ order = 1;
+ if (Logger.debugging)
Logger.info("new operation -- " + typeNames[type]);
- order = 1;
}
Operation(Vector3f v, int i) {
+ index = ++nOps;
type = (i < firstProper ? OPERATION_IMPROPER_AXIS : OPERATION_PROPER_AXIS);
order = i % firstProper;
normalOrAxis = new Quaternion(v, 180).getNormal();
- //if (Logger.debugging)
+ if (Logger.debugging)
Logger.info("new operation -- " + (order == i ? "S" : "C") + order + " "
+ normalOrAxis);
}
Operation(Vector3f v) {
+ if (v == null)
+ return;
+ index = ++nOps;
type = OPERATION_PLANE;
normalOrAxis = new Quaternion(v, 180).getNormal();
- //if (Logger.debugging)
+ if (Logger.debugging)
Logger.info("new operation -- plane " + normalOrAxis);
}
@@ -785,57 +851,84 @@
}
}
- public String getInfo(boolean asDraw) {
+ public String getInfo(boolean asDraw, String type, int index,
+ float scaleFactor) {
Vector3f v = new Vector3f();
Operation op;
+ if (scaleFactor == 0)
+ scaleFactor = 1;
int[][] nType = new int[4][2];
for (int i = 1; i < maxAxis; i++)
for (int j = nAxes[i]; --j >= 0;)
nType[axes[i][j].type][0]++;
StringBuffer sb = new StringBuffer("# " + nAtoms + " atoms\n");
if (asDraw) {
+ boolean haveType = (type.length() > 0);
+ boolean anyProperAxis = (type.equalsIgnoreCase("Cn"));
+ boolean anyImproperAxis = (type.equalsIgnoreCase("Sn"));
+ sb.append("set perspectivedepth off;\n");
String m = "_" + modelIndex + "_";
- sb.append("draw delete pg0" + m + "*;draw delete pgva" + m + "*;draw delete pgvp" + m + "*;");
- sb.append("set perspectivedepth off;\n");
- sb.append("draw pg0").append(m).append(haveInversionCenter ? "inv " : " ");
- sb.append(Escape.escape(center) + (haveInversionCenter ? "\"i\";\n" : ";\n"));
+ if (!haveType)
+ sb.append("draw delete pg0" + m + "*;draw delete pgva" + m
+ + "*;draw delete pgvp" + m + "*;");
+ if (!haveType || type.equalsIgnoreCase("Ci"))
+ sb.append("draw pg0").append(m).append(
+ haveInversionCenter ? "inv " : " ").append(
+ Escape.escape(center) + (haveInversionCenter ? "\"i\";\n" : ";\n"));
for (int i = 2; i < maxAxis; i++) {
+ if (nAxes[i] == 0)
+ continue;
+ String label = axes[i][0].getLabel();
+ if (!haveType || type.equalsIgnoreCase(label)
+ || anyProperAxis && i >= firstProper
+ || anyImproperAxis && i < firstProper)
for (int j = 0; j < nAxes[i]; j++) {
+ if (index > 0 && j + 1 != index)
+ continue;
op = axes[i][j];
v.set(op.normalOrAxis);
v.add(center);
- float scale = (4.0f + op.order / 4.0f)
- * (op.type == OPERATION_IMPROPER_AXIS ? -1 : 1);
- sb.append("draw pgva").append(m).append(op.getLabel()).append("_").append(j + 1)
- .append(" width 0.05 scale " + scale + " ").append(
- Escape.escape(v));
+ float scale = scaleFactor * (4.0f + op.order / 4.0f)
+ * (op.type == OPERATION_IMPROPER_AXIS ? -1 : 1);
+ sb.append("draw pgva").append(m).append(label).append("_").append(
+ j + 1).append(" width 0.05 scale " + scale + " ").append(
+ Escape.escape(v));
+ v.scaleAdd(-2, op.normalOrAxis, v);
+ sb.append(Escape.escape(v)).append("\"" + label +
+ (op.index == principalAxis.index ? "*" : "") + "\" color ").append(
+ op.index == principalAxis.index ? "red"
+ : op.type == OPERATION_IMPROPER_AXIS ? "blue" : "yellow")
+ .append(";\n");
+ }
+ }
+ if (!haveType || type.equalsIgnoreCase("Cs"))
+ for (int j = 0; j < nAxes[0]; j++) {
+ if (index > 0 && j + 1 != index)
+ continue;
+ op = axes[0][j];
+ v.set(op.normalOrAxis);
+ v.scale(0.025f);
+ v.add(center);
+ sb.append("draw pgvp").append(m).append(j + 1).append(
+ "disk width " + (scaleFactor * 6.0) + " cylinder ").append(
+ Escape.escape(v));
+ v.scaleAdd(-0.05f, op.normalOrAxis, v);
+ sb.append(Escape.escape(v)).append(" color translucent yellow;\n");
+ v.set(op.normalOrAxis);
+ v.add(center);
+ sb.append("draw pgvp").append(m).append(j + 1).append(
+ "ring width 0.05 scale " + (scaleFactor * 3.0) + " arc ").append(
+ Escape.escape(v));
v.scaleAdd(-2, op.normalOrAxis, v);
- sb.append(Escape.escape(v)).append("\"" + op.getLabel() + "\"")
- .append(op.type == OPERATION_IMPROPER_AXIS ? " color red" : "")
+ sb.append(Escape.escape(v));
+ v.x += 0.011;
+ v.y += 0.012;
+ v.z += 0.013;
+ sb.append(Escape.escape(v))
+ .append("{0 360 0.5} color ")
+ .append(op.index == principalPlane.index ? "red" : "blue")
.append(";\n");
}
- }
- for (int j = 0; j < nAxes[0]; j++) {
- op = axes[0][j];
- v.set(op.normalOrAxis);
- v.scale(0.025f);
- v.add(center);
- sb.append("draw pgvp").append(m).append(j + 1).append("disk width 6.0 cylinder ")
- .append(Escape.escape(v));
- v.scaleAdd(-0.05f, op.normalOrAxis, v);
- sb.append(Escape.escape(v)).append(" color translucent;\n");
-
- v.set(op.normalOrAxis);
- v.add(center);
- sb.append("draw pgvp").append(m).append(j + 1).append(
- "ring width 0.05 scale 3.0 arc ").append(Escape.escape(v));
- v.scaleAdd(-2, op.normalOrAxis, v);
- sb.append(Escape.escape(v));
- v.x += 0.011;
- v.y += 0.012;
- v.z += 0.013;
- sb.append(Escape.escape(v)).append("{0 360 0.5} color red;\n");
- }
sb.append("# name=" + name);
sb.append(", nCi=" + (haveInversionCenter ? 1 : 0));
sb.append(", nCs=" + nAxes[0]);
@@ -871,24 +964,24 @@
sb.append("\n");
sb.append("\n" + name + "\ttype\tnType\tnUnique");
sb.append("\n" + name + "\tE\t 1\t 1");
-
+
n = (haveInversionCenter ? 1 : 0);
sb.append("\n" + name + "\tCi\t " + n + "\t " + n);
-
+
sb.append("\n" + name + "\tCs\t");
- TextFormat.rFill(sb, " ",nAxes[0] + "\t");
- TextFormat.rFill(sb, " ",nAxes[0] + "\n");
+ TextFormat.rFill(sb, " ", nAxes[0] + "\t");
+ TextFormat.rFill(sb, " ", nAxes[0] + "\n");
sb.append(name + "\tCn\t");
- TextFormat.rFill(sb, " ",nType[OPERATION_PROPER_AXIS][0] + "\t");
- TextFormat.rFill(sb, " ",nType[OPERATION_PROPER_AXIS][1] + "\n");
+ TextFormat.rFill(sb, " ", nType[OPERATION_PROPER_AXIS][0] + "\t");
+ TextFormat.rFill(sb, " ", nType[OPERATION_PROPER_AXIS][1] + "\n");
sb.append(name + "\tSn\t");
- TextFormat.rFill(sb, " ",nType[OPERATION_IMPROPER_AXIS][0] + "\t");
- TextFormat.rFill(sb, " ",nType[OPERATION_IMPROPER_AXIS][1] + "\n");
-
+ TextFormat.rFill(sb, " ", nType[OPERATION_IMPROPER_AXIS][0] + "\t");
+ TextFormat.rFill(sb, " ", nType[OPERATION_IMPROPER_AXIS][1] + "\n");
+
sb.append(name + "\t\tTOTAL\t");
- TextFormat.rFill(sb, " ",nTotal + "\n");
+ TextFormat.rFill(sb, " ", nTotal + "\n");
}
return sb.toString();
}
Modified: trunk/Jmol/src/org/jmol/util/Quaternion.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Quaternion.java 2008-08-07 19:09:42 UTC (rev 9692)
+++ trunk/Jmol/src/org/jmol/util/Quaternion.java 2008-08-08 15:15:03 UTC (rev 9693)
@@ -365,7 +365,8 @@
}
private void fixQ(Quaternion qNew) {
- float f = (q0 < 0 ? -1 : 1);
+ float f = (q0 < 0 || q0 == 0
+ && (q1 < 0 || q1 == 0 && (q2 < 0 || q2 == 0 && q3 < 0)) ? -1 : 1);
qNew.q0 = q0 * f;
qNew.q1 = q1 * f;
qNew.q2 = q2 * f;
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-07 19:09:42 UTC (rev 9692)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-08 15:15:03 UTC (rev 9693)
@@ -6005,7 +6005,7 @@
}
break;
case 3:
- if (parameterAsString(1).equalsIgnoreCase("scale")) {
+ if (tokAt(1) == Token.scale) {
setFloatProperty("vectorScale", floatParameter(2, -10, 10));
return;
}
@@ -6176,12 +6176,11 @@
checkLength(2);
period = floatParameter(1);
break;
+ case Token.scale:
+ setFloatProperty("vibrationScale", floatParameter(2, -10, 10));
+ return;
case Token.identifier:
String cmd = optParameterAsString(1);
- if (cmd.equalsIgnoreCase("scale")) {
- setFloatProperty("vibrationScale", floatParameter(2, -10, 10));
- return;
- }
if (cmd.equalsIgnoreCase("period")) {
setFloatProperty("vibrationPeriod", floatParameter(2));
return;
@@ -6231,12 +6230,7 @@
}
return;
case Token.pointgroup:
- if (isSyntaxCheck)
- return;
- if (tokAt(0) == Token.draw)
- runScript(viewer.getPointGroupAsString(true));
- else
- showString(viewer.calculatePointGroup());
+ pointGroup();
return;
case Token.surface:
isSurface = true;
@@ -6298,6 +6292,32 @@
"aromatic? hbonds? polymers? straightness? structure? surfaceDistance FROM? surfaceDistance WITHIN?");
}
+ private void pointGroup() throws ScriptException {
+ switch (tokAt(0)) {
+ case Token.calculate:
+ if (!isSyntaxCheck)
+ showString(viewer.calculatePointGroup());
+ return;
+ case Token.show:
+ if (!isSyntaxCheck)
+ showString(viewer.getPointGroupAsString(false, null, 0, 0));
+ return;
+ }
+ // draw pointgroup [C2|C3|Cs|Ci|etc.] [n] [scale x]
+ int pt = 2;
+ String type = (tokAt(pt) == Token.scale ? "" : optParameterAsString(pt));
+ float scale = 1;
+ int index = 0;
+ if (type.length() > 0) {
+ if (isFloatParameter(++pt))
+ index = intParameter(pt++);
+ }
+ if (tokAt(pt) == Token.scale)
+ scale = floatParameter(++pt);
+ if (!isSyntaxCheck)
+ runScript(viewer.getPointGroupAsString(true, type, index, scale));
+ }
+
private void dots(int iShape) throws ScriptException {
if (!isSyntaxCheck)
viewer.loadShape(iShape);
@@ -8951,7 +8971,7 @@
return "";
}
} else if (data == "PGRP") {
- data = viewer.getPointGroupAsString((type2.equals("draw")));
+ data = viewer.getPointGroupAsString(type2.equals("draw"), null, 0, 1.0f);
} else if (data == "PDB") {
data = viewer.getPdbData(null);
} else if (data == "XYZ" || data == "MOL") {
@@ -9347,9 +9367,8 @@
msg = viewer.getPDBHeader();
break;
case Token.pointgroup:
- if (!isSyntaxCheck)
- msg = viewer.getPointGroupAsString(false);
- break;
+ pointGroup();
+ return;
case Token.symmetry:
if (!isSyntaxCheck)
msg = viewer.getSymmetryInfoAsString();
@@ -9601,7 +9620,7 @@
return;
break;
case Token.pointgroup:
- calculate();
+ pointGroup();
return;
case Token.quaternion:
dataFrame(JmolConstants.JMOL_DATA_QUATERNION);
@@ -9699,6 +9718,18 @@
intScale = intParameter(i);
}
break;
+ case Token.scale:
+ if (++i >= statementLength)
+ error(ERROR_numberExpected);
+ switch (getToken(i).tok) {
+ case Token.integer:
+ intScale = intParameter(i);
+ continue;
+ case Token.decimal:
+ intScale = (int) (floatParameter(i) * 100);
+ continue;
+ }
+ error(ERROR_numberExpected);
case Token.times:
case Token.identifier:
String str = parameterAsString(i);
@@ -9768,20 +9799,6 @@
propertyValue = pt;
break;
}
- if (str.equalsIgnoreCase("SCALE")) {
- if (++i >= statementLength)
- error(ERROR_numberExpected);
- switch (getToken(i).tok) {
- case Token.integer:
- intScale = intParameter(i);
- continue;
- case Token.decimal:
- intScale = (int) (floatParameter(i) * 100);
- continue;
- default:
- error(ERROR_numberExpected);
- }
- }
if (str.equalsIgnoreCase("DIAMETER")) { //pixels
propertyValue = new Float(floatParameter(++i));
propertyName = (tokAt(i) == Token.decimal ? "width" : "diameter");
@@ -9812,7 +9829,7 @@
break;
case Token.color:
i++;
- //fall through
+ //fall through
case Token.translucent:
case Token.opaque:
isTranslucent = false;
@@ -9856,8 +9873,8 @@
setShapeProperty(JmolConstants.SHAPE_DRAW, "set", null);
}
if (colorArgb != Integer.MIN_VALUE)
- setShapeProperty(JmolConstants.SHAPE_DRAW, "color", new Integer(
- colorArgb));
+ setShapeProperty(JmolConstants.SHAPE_DRAW, "color",
+ new Integer(colorArgb));
if (isTranslucent)
setShapeTranslucency(JmolConstants.SHAPE_DRAW, "", "translucent",
translucentLevel);
@@ -9865,7 +9882,7 @@
setShapeProperty(JmolConstants.SHAPE_DRAW, "scale", new Integer(intScale));
}
if (iptDisplayProperty > 0) {
- if (!setMeshDisplayProperty(JmolConstants.SHAPE_DRAW, iptDisplayProperty,
+ if (!setMeshDisplayProperty(JmolConstants.SHAPE_DRAW, iptDisplayProperty,
getToken(iptDisplayProperty).tok))
error(ERROR_invalidArgument);
}
@@ -10178,13 +10195,12 @@
propertyValue = parameterAsString(++i);
}
break;
+ case Token.scale:
+ propertyName = "scale";
+ propertyValue = new Float(floatParameter(++i));
+ break;
case Token.identifier:
String str = parameterAsString(i);
- if (str.equalsIgnoreCase("SCALE")) {
- propertyName = "scale";
- propertyValue = new Float(floatParameter(++i));
- break;
- }
if (str.equalsIgnoreCase("MOLECULAR")) {
propertyName = "molecular";
break;
@@ -10257,6 +10273,10 @@
propertyName = "plane";
propertyValue = planeParameter(2);
break;
+ case Token.scale:
+ propertyName = "scale";
+ propertyValue = new Float(floatParameter(2));
+ break;
case Token.identifier:
str = parameterAsString(1);
if ((offset = moOffset(1)) != Integer.MAX_VALUE) {
@@ -10279,11 +10299,6 @@
propertyValue = new Float(floatParameter(2));
break;
}
- if (str.equalsIgnoreCase("SCALE")) {
- propertyName = "scale";
- propertyValue = new Float(floatParameter(2));
- break;
- }
if (str.equalsIgnoreCase("SQUARED")) {
propertyName = "squareData";
propertyValue = Boolean.TRUE;
@@ -10624,6 +10639,10 @@
propertyValue = planeParameter(++i);
i = iToken;
break;
+ case Token.scale:
+ propertyName = "scale";
+ propertyValue = new Float(floatParameter(++i));
+ break;
case Token.identifier:
str = parameterAsString(i);
if (str.equalsIgnoreCase("id")) {
@@ -10697,11 +10716,6 @@
propertyValue = Boolean.FALSE;
break;
}
- if (str.equalsIgnoreCase("SCALE")) {
- propertyName = "scale";
- propertyValue = new Float(floatParameter(++i));
- break;
- }
if (str.equalsIgnoreCase("MINSET")) {
propertyName = "minset";
propertyValue = new Integer(intParameter(++i));
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-07 19:09:42 UTC (rev 9692)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-08 15:15:03 UTC (rev 9693)
@@ -3,6 +3,11 @@
version=11.6.RC3_dev
+# new feature: set dotDensity [-3 to 3]
+# bug fix: minor error in pointgroup
+# new feature: draw pointGroup [type] [index] SCALE [x]
+# where [type] is one of Cs, Ci, Cn, or Sn, where n is an integer or the character "n"
+
# -----------------------------------------------------------------------------
#version=11.6.RC2
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-08-07 19:09:42 UTC (rev 9692)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-08-08 15:15:03 UTC (rev 9693)
@@ -564,6 +564,7 @@
boolean displayCellParameters = true;
boolean dotsSelectedOnly = false;
boolean dotSurface = true;
+ int dotDensity = 3;
boolean dynamicMeasurements = false;
boolean greyscaleRendering = false;
boolean isosurfacePropertySmoothing = true;
@@ -1128,6 +1129,7 @@
setParameterValue("dipoleScale", dipoleScale);
setParameterValue("disablePopupMenu", disablePopupMenu);
setParameterValue("displayCellParameters", displayCellParameters);
+ setParameterValue("dotDensity", dotDensity);
setParameterValue("dotsSelectedOnly", dotsSelectedOnly);
setParameterValue("dotSurface", dotSurface);
setParameterValue("drawHover", false);
Modified: trunk/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Token.java 2008-08-07 19:09:42 UTC (rev 9692)
+++ trunk/Jmol/src/org/jmol/viewer/Token.java 2008-08-08 15:15:03 UTC (rev 9693)
@@ -957,6 +957,7 @@
final static int absolute = misc | 1;
final static int average = misc | 2;
+ final static int axis = misc | 3;
final static int babel = misc | 4;
final static int back = misc | 5;
final public static int backlit = misc | 6;
@@ -1010,20 +1011,21 @@
final static int rotation = misc | 50;
final static int rubberband = misc | 51;
final static int sasurface = misc | 52;
- final static int shape = misc | 53;
- final static int shapely = misc | 54;
- final static int solid = misc | 55;
- final static int spacegroup = misc | 56;
- final static int state = misc | 57;
- final static int top = misc | 58;
- final static int torsion = misc | 59;
- final static int transform = misc | 60;
- final static int translation = misc | 61;
- final public static int translucent = misc | 62;
- final public static int triangles = misc | 63;
- final static int url = misc | 64;
- final static int user = misc | 65; //color option
- final static int qw = misc | 66;
+ final static int scale = misc | 53;
+ final static int shape = misc | 54;
+ final static int shapely = misc | 55;
+ final static int solid = misc | 56;
+ final static int spacegroup = misc | 57;
+ final static int state = misc | 58;
+ final static int top = misc | 59;
+ final static int torsion = misc | 60;
+ final static int transform = misc | 61;
+ final static int translation = misc | 62;
+ final public static int translucent = misc | 63;
+ final public static int triangles = misc | 64;
+ final static int url = misc | 65;
+ final static int user = misc | 66; //color option
+ final static int qw = misc | 67;
// predefined Tokens:
@@ -1214,7 +1216,8 @@
"fontsize", new Token(fontsize),
"picking", new Token(picking),
"pickingStyle", new Token(pickingStyle),
- "radius", new Token(radius),
+ "radius", new Token(radius),
+ "scale", new Token(scale),
"scale3D", new Token(scale3d),
// lighting
@@ -1232,7 +1235,8 @@
// show parameters
"atom", new Token(atoms),
- "atoms", null,
+ "atoms", null,
+ "axis", new Token(axis),
"axisangle", new Token(axisangle),
"orientation", new Token(orientation),
"pdbheader", new Token(pdbheader),
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-07 19:09:42 UTC (rev 9692)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-08 15:15:03 UTC (rev 9693)
@@ -4513,6 +4513,13 @@
private void setIntProperty(String key, int value, boolean defineNew) {
boolean notFound = false;
while (true) {
+
+ //11.6.RC2//
+ if (key.equalsIgnoreCase("dotDensity")) {
+ setDotDensity(value);
+ break;
+ }
+
//11.5.30//
// ellipsoidDotCount" just handled as getParameter()
@@ -5194,6 +5201,15 @@
global.dotsSelectedOnly = TF;
}
+ private void setDotDensity(int value) {
+ global.dotDensity = value;
+ refresh(0, "Viewer:setDotDensity()");
+ }
+
+ public int getDotDensity() {
+ return global.dotDensity;
+ }
+
public boolean isRangeSelected() {
return global.rangeSelected;
}
@@ -6835,8 +6851,10 @@
return modelSet.calculatePointGroup(selectionManager.bsSelection);
}
- public String getPointGroupAsString(boolean asDraw) {
- return modelSet.getPointGroupAsString(selectionManager.bsSelection, asDraw);
+ public String getPointGroupAsString(boolean asDraw, String type, int index,
+ float scale) {
+ return modelSet.getPointGroupAsString(selectionManager.bsSelection, asDraw,
+ type, index, scale);
}
private void setPointGroupTolerance(float value, int type) {
@@ -6877,5 +6895,5 @@
}
return image;
}
-
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-08 19:53:43
|
Revision: 9696
http://jmol.svn.sourceforge.net/jmol/?rev=9696&view=rev
Author: hansonr
Date: 2008-08-08 19:53:36 +0000 (Fri, 08 Aug 2008)
Log Message:
-----------
11.6.RC3 -- final revision
# bug fix: minor error in pointgroup; dimension tied to radius
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-08 19:39:49 UTC (rev 9695)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-08 19:53:36 UTC (rev 9696)
@@ -459,8 +459,8 @@
Object obj = getShapeProperty(JmolConstants.SHAPE_VECTORS, "mad", iAtom);
boolean haveVibration = (obj != null && ((Integer) obj).intValue() != 0 || viewer
.isVibrationOn());
- return new PointGroup(atoms, bs, haveVibration, modelIndex, viewer
- .getPointGroupTolerance(0), viewer.getPointGroupTolerance(1));
+ return new PointGroup(atoms, bs, haveVibration, modelIndex,
+ viewer.getPointGroupTolerance(0), viewer.getPointGroupTolerance(1));
}
private BitSet modelsOf(BitSet bsAtoms, BitSet bsAllAtoms) {
Modified: trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-08 19:39:49 UTC (rev 9695)
+++ trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-08 19:53:36 UTC (rev 9696)
@@ -115,10 +115,11 @@
private int[] nAxes = new int[maxAxis];
private Operation[][] axes = new Operation[maxAxis][];
private int nAtoms;
- private String name = "C_1?";
+ private float radius;
private int modelIndex;
private float distanceTolerance = 0.2f;
private float linearTolerance = 0.99f; // 8 degrees
+ private String name = "C_1?";
private Operation principalAxis = new Operation(null);
private Operation principalPlane = new Operation(null);
@@ -133,16 +134,18 @@
private final Vector3f vTemp = new Vector3f();
private int centerAtomIndex = -1;
private boolean haveInversionCenter;
-
+
final private Point3f center = new Point3f();
- public PointGroup(Atom[] atomset, BitSet bsAtoms, boolean haveVibration,
- int modelIndex, float distanceTolerance, float linearTolerance) {
+ public PointGroup(Atom[] atomset, BitSet bsAtoms,
+ boolean haveVibration, int modelIndex,
+ float distanceTolerance, float linearTolerance) {
this.modelIndex = modelIndex;
this.distanceTolerance = distanceTolerance;
this.linearTolerance = (float) (Math.cos(linearTolerance / 180 * Math.PI));
+
Point3f[] atoms;
- if ((atoms = getCenter(atomset, bsAtoms)) == null) {
+ if ((atoms = getAtoms(atomset, bsAtoms)) == null) {
Logger.error("Too many atoms for point group calculation");
name = "point group not determined -- atomCount > " + ATOM_COUNT_MAX
+ " -- select fewer atoms and try again.";
@@ -276,7 +279,6 @@
name = "C" + n + "h";
}
}
- //System.out.println(drawInfo());
}
private Operation setPrincipalAxis(int n, int nPlanes) {
@@ -321,7 +323,7 @@
}
private final static int ATOM_COUNT_MAX = 100;
- private Atom[] getCenter(Atom[] atomset, BitSet bsAtoms) {
+ private Atom[] getAtoms(Atom[] atomset, BitSet bsAtoms) {
int atomCount = BitSetUtil.cardinalityOf(bsAtoms);
if (atomCount > ATOM_COUNT_MAX)
return null;
@@ -335,11 +337,12 @@
center.add(atoms[nAtoms++]);
}
center.scale(1f / nAtoms);
- for (int i = nAtoms; --i >= 0;)
- if (atoms[i].distance(center) < 0.1) {
+ for (int i = nAtoms; --i >= 0;) {
+ float r = center.distance(atoms[i]);
+ if (r < distanceTolerance)
centerAtomIndex = i;
- break;
- }
+ radius = Math.max(radius, r);
+ }
return atoms;
}
@@ -389,8 +392,6 @@
if (j == i || elements[j] != e1)
continue;
Point3f a2 = atoms[j];
- // System.out.println(i + " " + j + " " + a1 + " " + a2 + " " + pt
- // + nFound + " " + pt.distance(a2));
if (pt.distance(a2) < distanceTolerance) {
nFound++;
continue out;
@@ -693,7 +694,6 @@
private boolean haveAxis(int iOrder, Vector3f v) {
if (nAxes[iOrder] == axesMaxN[iOrder]) {
- //System.out.println(iOrder + " " + (iOrder-firstProper) + " is maxed at " + axesMaxN[iOrder]);
return true;
}
if (nAxes[iOrder] > 0)
@@ -875,31 +875,36 @@
sb.append("draw pg0").append(m).append(
haveInversionCenter ? "inv " : " ").append(
Escape.escape(center) + (haveInversionCenter ? "\"i\";\n" : ";\n"));
+ float offset = 0.1f;
for (int i = 2; i < maxAxis; i++) {
+ if (i == firstProper)
+ offset = 0.1f;
if (nAxes[i] == 0)
continue;
String label = axes[i][0].getLabel();
- if (!haveType || type.equalsIgnoreCase(label)
- || anyProperAxis && i >= firstProper
- || anyImproperAxis && i < firstProper)
- for (int j = 0; j < nAxes[i]; j++) {
- if (index > 0 && j + 1 != index)
- continue;
- op = axes[i][j];
- v.set(op.normalOrAxis);
- v.add(center);
- float scale = scaleFactor * (4.0f + op.order / 4.0f)
- * (op.type == OPERATION_IMPROPER_AXIS ? -1 : 1);
+ offset += 0.25f;
+ float scale = scaleFactor * radius + offset;
+ if (!haveType || type.equalsIgnoreCase(label) || anyProperAxis
+ && i >= firstProper || anyImproperAxis && i < firstProper)
+ for (int j = 0; j < nAxes[i]; j++) {
+ if (index > 0 && j + 1 != index)
+ continue;
+ op = axes[i][j];
+ v.set(op.normalOrAxis);
+ v.add(center);
+ if (op.type == OPERATION_IMPROPER_AXIS)
+ scale = -scale;
sb.append("draw pgva").append(m).append(label).append("_").append(
j + 1).append(" width 0.05 scale " + scale + " ").append(
Escape.escape(v));
v.scaleAdd(-2, op.normalOrAxis, v);
- sb.append(Escape.escape(v)).append("\"" + label +
- (op.index == principalAxis.index ? "*" : "") + "\" color ").append(
+ sb.append(Escape.escape(v)).append(
+ "\"" + label + (op.index == principalAxis.index ? "*" : "")
+ + "\" color ").append(
op.index == principalAxis.index ? "red"
: op.type == OPERATION_IMPROPER_AXIS ? "blue" : "yellow")
.append(";\n");
- }
+ }
}
if (!haveType || type.equalsIgnoreCase("Cs"))
for (int j = 0; j < nAxes[0]; j++) {
@@ -910,24 +915,22 @@
v.scale(0.025f);
v.add(center);
sb.append("draw pgvp").append(m).append(j + 1).append(
- "disk width " + (scaleFactor * 6.0) + " cylinder ").append(
- Escape.escape(v));
+ "disk width " + (scaleFactor * radius * 2) + " cylinder ")
+ .append(Escape.escape(v));
v.scaleAdd(-0.05f, op.normalOrAxis, v);
sb.append(Escape.escape(v)).append(" color translucent yellow;\n");
v.set(op.normalOrAxis);
v.add(center);
sb.append("draw pgvp").append(m).append(j + 1).append(
- "ring width 0.05 scale " + (scaleFactor * 3.0) + " arc ").append(
- Escape.escape(v));
+ "ring width 0.05 scale " + (scaleFactor * radius) + " arc ")
+ .append(Escape.escape(v));
v.scaleAdd(-2, op.normalOrAxis, v);
sb.append(Escape.escape(v));
v.x += 0.011;
v.y += 0.012;
v.z += 0.013;
- sb.append(Escape.escape(v))
- .append("{0 360 0.5} color ")
- .append(op.index == principalPlane.index ? "red" : "blue")
- .append(";\n");
+ sb.append(Escape.escape(v)).append("{0 360 0.5} color ").append(
+ op.index == principalPlane.index ? "red" : "blue").append(";\n");
}
sb.append("# name=" + name);
sb.append(", nCi=" + (haveInversionCenter ? 1 : 0));
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-08 19:39:49 UTC (rev 9695)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-08 19:53:36 UTC (rev 9696)
@@ -1,14 +1,10 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=11.6.RC4_dev
-
-# -----------------------------------------------------------------------------
-
#version=11.6.RC3
+# bug fix: minor error in pointgroup; dimension tied to radius
# new feature: set dotDensity [-3 to 3]
-# bug fix: minor error in pointgroup
# new feature: draw pointGroup [type] [index] SCALE [x]
# where [type] is one of Cs, Ci, Cn, or Sn, where n is an integer or the character "n"
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-11 13:03:11
|
Revision: 9704
http://jmol.svn.sourceforge.net/jmol/?rev=9704&view=rev
Author: hansonr
Date: 2008-08-11 13:02:36 +0000 (Mon, 11 Aug 2008)
Log Message:
-----------
version=11.6.RC5_dev # new feature: background IMAGE "filename"
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/JmolExportInterface.java
trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java
trunk/Jmol/src/org/jmol/export/Export3D.java
trunk/Jmol/src/org/jmol/export/_MayaExporter.java
trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
trunk/Jmol/src/org/jmol/export/_VrmlExporter.java
trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
trunk/Jmol/src/org/jmol/g3d/Text3D.java
trunk/Jmol/src/org/jmol/shape/Text.java
trunk/Jmol/src/org/jmol/viewer/Compiler.java
trunk/Jmol/src/org/jmol/viewer/Eval.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/api/JmolExportInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolExportInterface.java 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/api/JmolExportInterface.java 2008-08-11 13:02:36 UTC (rev 9704)
@@ -77,7 +77,7 @@
abstract void plotText(int x, int y, int z, int argb, String text, Font3D font3d);
- abstract void plotImage(int x, int y, int z, Image image, int width, int height, short bgcolix);
+ abstract void plotImage(int x, int y, int z, Image image, short bgcolix);
// NOT IMPLEMENTED, but could be if needed:
Modified: trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java 2008-08-11 13:02:36 UTC (rev 9704)
@@ -320,7 +320,7 @@
public abstract void renderEllipsoid(int x, int y, int z, int diameter, Matrix3f mToEllipsoidal, double[] coef, Matrix4f mDeriv, int selectedOctant, Point3i[] octantPoints);
- public abstract void drawImage(Image image, int x, int y, int z, int zslab, int width, int height, short bgcolix);
+ public abstract void drawImage(Image image, int x, int y, int z, int zslab, short bgcolix);
}
Modified: trunk/Jmol/src/org/jmol/export/Export3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/Export3D.java 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/export/Export3D.java 2008-08-11 13:02:36 UTC (rev 9704)
@@ -294,14 +294,13 @@
z, getColixArgb(colix), str, font3d);
}
- public void drawImage(Image image, int x, int y, int z, int zSlab, int width,
- int height, short bgcolix) {
+ public void drawImage(Image image, int x, int y, int z, int zSlab, short bgcolix) {
if (image == null || width == 0 || height == 0)
return;
if (isClippedZ(zSlab))
return;
z = Math.max(slab, z);
- exporter.plotImage(x, y, z, image, width, height, bgcolix);
+ exporter.plotImage(x, y, z, image, bgcolix);
}
//mostly public drawing methods -- add "public" if you need to
Modified: trunk/Jmol/src/org/jmol/export/_MayaExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_MayaExporter.java 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/export/_MayaExporter.java 2008-08-11 13:02:36 UTC (rev 9704)
@@ -229,7 +229,7 @@
}
- public void plotImage(int x, int y, int z, Image image, int width, int height, short bgcolix) {
+ public void plotImage(int x, int y, int z, Image image, short bgcolix) {
// TODO
}
Modified: trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2008-08-11 13:02:36 UTC (rev 9704)
@@ -629,9 +629,9 @@
output("// end text " + nText + ": " + text + "\n");
}
- public void plotImage(int x, int y, int z, Image image, int width, int height, short bgcolix) {
+ public void plotImage(int x, int y, int z, Image image, short bgcolix) {
output("// start image " + (++nImage) + "\n");
- g3d.plotImage(x, y, z, image, width, height, jmolRenderer, bgcolix);
+ g3d.plotImage(x, y, z, image, jmolRenderer, bgcolix);
output("// end image " + nImage + "\n");
}
// not needed:
Modified: trunk/Jmol/src/org/jmol/export/_VrmlExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_VrmlExporter.java 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/export/_VrmlExporter.java 2008-08-11 13:02:36 UTC (rev 9704)
@@ -240,7 +240,7 @@
}
- public void plotImage(int x, int y, int z, Image image, int width, int height, short bgcolix) {
+ public void plotImage(int x, int y, int z, Image image, short bgcolix) {
// TODO
}
Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2008-08-11 13:02:36 UTC (rev 9704)
@@ -351,6 +351,8 @@
setWidthHeight(antialiasThisFrame);
//setRectClip(clipX, clipY, clipWidth, clipHeight);
platform.obtainScreenBuffer();
+ if (backgroundImage != null)
+ plotImage(Integer.MIN_VALUE, 0, Integer.MIN_VALUE, backgroundImage, null, (short) 0);
}
private void releaseBuffers() {
@@ -490,6 +492,7 @@
}
private int backgroundArgb;
+ private Image backgroundImage;
public int bgcolor;
/**
@@ -502,8 +505,14 @@
bgcolor = argb;
backgroundArgb = argb + ((argb & 0xFF) == 0xFF ? -1 : 1);
platform.setBackground(backgroundArgb);
+ backgroundImage = null;
}
+ public void setBackgroundImage(Image image) {
+ backgroundImage = image;
+ }
+
+
/**
* controls greyscale rendering
* @param greyscaleMode Flag for greyscale rendering
@@ -1033,22 +1042,20 @@
antialiasThisFrame);
}
- public void drawImage(Image image, int x, int y, int z, int zSlab, int width, int height, short bgcolix) {
+ public void drawImage(Image image, int x, int y, int z, int zSlab, short bgcolix) {
if (image == null || width == 0 || height == 0)
return;
if (isClippedZ(zSlab))
return;
- plotImage(x, y, z, image, width, height, null, bgcolix);
+ plotImage(x, y, z, image, null, bgcolix);
}
- public void plotImage(int x, int y, int z, Image image, int width,
- int height, JmolRendererInterface jmolRenderer,
+ public void plotImage(int x, int y, int z, Image image, JmolRendererInterface jmolRenderer,
short bgcolix) {
setColix(bgcolix);
if (bgcolix == 0)
argbCurrent = 0;
- Text3D.plotImage(x, y, z, image, width, height, this, jmolRenderer,
- antialiasThisFrame, argbCurrent);
+ Text3D.plotImage(x, y, z, image, this, jmolRenderer, antialiasThisFrame, argbCurrent);
}
public void setFont(byte fid) {
Modified: trunk/Jmol/src/org/jmol/g3d/Text3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Text3D.java 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/g3d/Text3D.java 2008-08-11 13:02:36 UTC (rev 9704)
@@ -108,21 +108,33 @@
return textWidth;
}
- public static void plotImage(int x, int y, int z, Image image, int width,
- int height, Graphics3D g3d,
- JmolRendererInterface jmolRenderer,
- boolean antialias, int argbBackground) {
+ public static void plotImage(int x, int y, int z, Image image, Graphics3D g3d,
+ JmolRendererInterface jmolRenderer, boolean antialias,
+ int argbBackground) {
//System.out.println(x + " " + width + ", " + y + " " + height + " w/h " + g3d.width + " " + g3d.height + " " + g3d.isAntialiased());
- if (g3d.isAntialiased()) {
+ boolean isBackground = (x == Integer.MIN_VALUE);
+ int width = image.getWidth(null);
+ int height = image.getHeight(null);
+ if (isBackground) {
+ x = 0;
+ z = Integer.MAX_VALUE - 1;
+ width = g3d.width;
+ height = g3d.height;
+ } else if (x + width < 0 || x > g3d.width || y + height < 0 || y > g3d.height) {
+ return;
+ } else if (g3d.isAntialiased()) {
width += width;
height += height;
}
- if (x + width < 0 || x > g3d.width || y + height < 0 || y > g3d.height)
- return;
+
g3d.platform.checkOffscreenSize(width, height);
Graphics g = g3d.platform.gOffscreen;
g.clearRect(0,0,width,height);
- if (g3d.isAntialiased()) {
+ if (isBackground) {
+ g.drawImage(image, 0, 0, width, height, 0, 0, image.getWidth(null), image.getHeight(null), null);
+ width = g3d.width;
+ height = g3d.height;
+ } else if (g3d.isAntialiased()) {
g.drawImage(image, 0, 0, width, height, 0, 0, width >> 1, height >> 1, null);
} else {
g.drawImage(image, 0, 0, null);
@@ -136,21 +148,21 @@
return;
}
int[] buffer = (int[]) pixelGrabber.getPixels();
+ int bgcolor = (isBackground ? 0 : argbBackground == 0 ? buffer[0] : argbBackground);
if (jmolRenderer != null
|| (x < 0 || x + width > g3d.width || y < 0 || y + height > g3d.height))
- plotImageClipped(x, y, z, g3d, jmolRenderer, width, height, buffer, argbBackground);
+ plotImageClipped(x, y, z, g3d, jmolRenderer, width, height, buffer, bgcolor);
else
- plotImageUnClipped(x, y, z, g3d, width, height, buffer, argbBackground);
+ plotImageUnClipped(x, y, z, g3d, width, height, buffer, bgcolor);
return;
}
private static void plotImageClipped(int x, int y, int z, Graphics3D g3d,
JmolRendererInterface jmolRenderer,
int width, int height,
- int[] buffer, int argbBackground) {
+ int[] buffer, int bgcolor) {
if (jmolRenderer == null)
jmolRenderer = g3d;
- int bgcolor = (argbBackground == 0 ? buffer[0] : argbBackground);
for (int i = 0, offset = 0; i < height; i++) {
//System.out.println(Integer.toHexString(buffer[offset]));
for (int j = 0; j < width; j++) {
@@ -163,14 +175,13 @@
private static void plotImageUnClipped(int x, int y, int z, Graphics3D g3d,
int textWidth, int textHeight,
- int[] buffer, int argbBackground) {
+ int[] buffer, int bgcolor) {
int[] zbuf = g3d.zbuf;
int renderWidth = g3d.width;
int pbufOffset = y * renderWidth + x;
int i = 0;
int j = 0;
int offset = 0;
- int bgcolor = (argbBackground == 0 ? buffer[0] : argbBackground);
while (i < textHeight) {
//System.out.println(Integer.toHexString(buffer[offset]));
while (j < textWidth) {
Modified: trunk/Jmol/src/org/jmol/shape/Text.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Text.java 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/shape/Text.java 2008-08-11 13:02:36 UTC (rev 9704)
@@ -221,8 +221,7 @@
// now set x and y positions for text from (new?) box position
if (image != null) {
- g3d.drawImage(image, (int) boxX, (int) boxY, z, zSlab, (int) boxWidth,
- (int) boxHeight, bgcolix);
+ g3d.drawImage(image, (int) boxX, (int) boxY, z, zSlab, bgcolix);
} else {
// now write properly aligned text
Modified: trunk/Jmol/src/org/jmol/viewer/Compiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Compiler.java 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/viewer/Compiler.java 2008-08-11 13:02:36 UTC (rev 9704)
@@ -456,7 +456,7 @@
if (lookingAtString()) {
if (cchToken < 0)
return error(ERROR_endOfCommandUnexpected);
- String str = ((tokCommand == Token.load || tokCommand == Token.script)
+ String str = ((tokCommand == Token.load || tokCommand == Token.background || tokCommand == Token.script)
&& !iHaveQuotedString ? script.substring(ichToken + 1, ichToken
+ cchToken - 1) : getUnescapedStringLiteral());
addTokenToPrefix(new Token(Token.string, str));
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-11 13:02:36 UTC (rev 9704)
@@ -43,6 +43,7 @@
import org.jmol.modelset.Bond.BondSet;
+import java.awt.Image;
import java.io.*;
import java.util.Arrays;
import java.util.BitSet;
@@ -3572,6 +3573,21 @@
private void background(int i) throws ScriptException {
getToken(i);
int argb;
+ if (theTok == Token.image) {
+ // background IMAGE "xxxx.jpg"
+ checkLength(3);
+ if (isSyntaxCheck)
+ return;
+ Hashtable htParams = new Hashtable();
+ String file = parameterAsString(++i);
+ Object image = (Image) null;
+ if (!file.equalsIgnoreCase("none") && file.length() > 0)
+ image = viewer.getFileAsImage(file, htParams);
+ if (image instanceof String)
+ evalError((String) image);
+ viewer.setBackgroundImage((String) htParams.get("fullPathName"), (Image) image);
+ return;
+ }
if (isColorParam(i) || theTok == Token.none) {
argb = getArgbParamLast(i, true);
if (!isSyntaxCheck)
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-11 13:02:36 UTC (rev 9704)
@@ -3,6 +3,8 @@
version=11.6.RC5_dev
+# new feature: background IMAGE "filename"
+
# -----------------------------------------------------------------------------
#version=11.6.RC4
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-08-11 13:02:36 UTC (rev 9704)
@@ -572,7 +572,8 @@
boolean showMeasurements = true;
boolean zoomLarge = true; //false would be like Chime
boolean zShade = false;
-
+ String backgroundImageFileName;
+
//atoms and bonds
boolean bondModeOr = false;
@@ -676,6 +677,8 @@
if (objColors[i] != 0)
appendCmd(str, getObjectNameFromId(i) + "Color = \""
+ Escape.escapeColor(objColors[i]) + '"');
+ if (backgroundImageFileName != null)
+ appendCmd(str, "background IMAGE /*file*/" + Escape.escape(backgroundImageFileName));
str.append(getSpecularState());
if (stereoState != null)
appendCmd(str, "stereo" + stereoState);
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-10 19:48:31 UTC (rev 9703)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-11 13:02:36 UTC (rev 9704)
@@ -1191,11 +1191,17 @@
case StateManager.OBJ_BACKGROUND:
g3d.setBackgroundArgb(argb);
colorManager.setColixBackgroundContrast(argb);
+ global.backgroundImageFileName = null;
break;
}
global.setParameterValue(name + "Color", Escape.escapeColor(argb));
}
+ public void setBackgroundImage(String fileName, Image image) {
+ global.backgroundImageFileName = fileName;
+ g3d.setBackgroundImage(image);
+ }
+
int getObjectArgb(int objId) {
return global.objColors[objId];
}
@@ -6894,5 +6900,4 @@
}
return image;
}
-
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-11 13:45:34
|
Revision: 9705
http://jmol.svn.sourceforge.net/jmol/?rev=9705&view=rev
Author: hansonr
Date: 2008-08-11 13:45:19 +0000 (Mon, 11 Aug 2008)
Log Message:
-----------
version=11.6.RC5_dev # new feature: background IMAGE "filename"
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/JmolExportInterface.java
trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java
trunk/Jmol/src/org/jmol/export/Export3D.java
trunk/Jmol/src/org/jmol/export/_Exporter.java
trunk/Jmol/src/org/jmol/export/_MayaExporter.java
trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
trunk/Jmol/src/org/jmol/export/_VrmlExporter.java
trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
trunk/Jmol/src/org/jmol/viewer/FrameRenderer.java
Modified: trunk/Jmol/src/org/jmol/api/JmolExportInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolExportInterface.java 2008-08-11 13:02:36 UTC (rev 9704)
+++ trunk/Jmol/src/org/jmol/api/JmolExportInterface.java 2008-08-11 13:45:19 UTC (rev 9705)
@@ -99,4 +99,5 @@
abstract void renderEllipsoid(short colix, int x, int y, int z, int diameter,
double[] coef, Point3i[] selectedPoints);
+ abstract void renderBackground();
}
\ No newline at end of file
Modified: trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java 2008-08-11 13:02:36 UTC (rev 9704)
+++ trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java 2008-08-11 13:45:19 UTC (rev 9705)
@@ -322,5 +322,4 @@
public abstract void drawImage(Image image, int x, int y, int z, int zslab, short bgcolix);
-
}
Modified: trunk/Jmol/src/org/jmol/export/Export3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/Export3D.java 2008-08-11 13:02:36 UTC (rev 9704)
+++ trunk/Jmol/src/org/jmol/export/Export3D.java 2008-08-11 13:45:19 UTC (rev 9705)
@@ -85,6 +85,10 @@
// this.shapeRenderer = shapeRenderer;
}
+ public void renderBackground() {
+ exporter.renderBackground();
+ }
+
/**
* draws a screened circle ... every other dot is turned on
*
Modified: trunk/Jmol/src/org/jmol/export/_Exporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_Exporter.java 2008-08-11 13:02:36 UTC (rev 9704)
+++ trunk/Jmol/src/org/jmol/export/_Exporter.java 2008-08-11 13:45:19 UTC (rev 9705)
@@ -257,5 +257,5 @@
if (Graphics3D.isColixTranslucent(colix))
return new StringBuffer().append(translevel / 255f).toString();
return new StringBuffer().append(0f).toString();
- }
+ }
}
Modified: trunk/Jmol/src/org/jmol/export/_MayaExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_MayaExporter.java 2008-08-11 13:02:36 UTC (rev 9704)
+++ trunk/Jmol/src/org/jmol/export/_MayaExporter.java 2008-08-11 13:45:19 UTC (rev 9705)
@@ -234,4 +234,9 @@
}
+ public void renderBackground() {
+ // TODO
+
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2008-08-11 13:02:36 UTC (rev 9704)
+++ trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2008-08-11 13:45:19 UTC (rev 9705)
@@ -683,4 +683,9 @@
+ "," + tempP1.x + "," + tempP1.y + "," + tempP1.z + ")\n");
}
+ public void renderBackground() {
+ // VERY inefficient, but it works.
+ g3d.renderBackground(jmolRenderer);
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/export/_VrmlExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_VrmlExporter.java 2008-08-11 13:02:36 UTC (rev 9704)
+++ trunk/Jmol/src/org/jmol/export/_VrmlExporter.java 2008-08-11 13:45:19 UTC (rev 9705)
@@ -244,5 +244,10 @@
// TODO
}
+
+ public void renderBackground() {
+ // TODO
+
+ }
}
Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2008-08-11 13:02:36 UTC (rev 9704)
+++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2008-08-11 13:45:19 UTC (rev 9705)
@@ -492,7 +492,7 @@
}
private int backgroundArgb;
- private Image backgroundImage;
+ public Image backgroundImage;
public int bgcolor;
/**
@@ -2932,4 +2932,9 @@
return normix3d.getVector(normix);
}
+ public void renderBackground(JmolRendererInterface jmolRenderer) {
+ if (backgroundImage != null)
+ plotImage(Integer.MIN_VALUE, 0, Integer.MIN_VALUE, backgroundImage, jmolRenderer, (short) 0);
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/FrameRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FrameRenderer.java 2008-08-11 13:02:36 UTC (rev 9704)
+++ trunk/Jmol/src/org/jmol/viewer/FrameRenderer.java 2008-08-11 13:45:19 UTC (rev 9705)
@@ -58,6 +58,7 @@
if (logTime)
Logger.startTimer();
+ g3d.renderBackground(null);
for (int i = 0; i < JmolConstants.SHAPE_MAX && g3d.currentlyRendering(); ++i) {
Shape shape = modelSet.getShape(i);
@@ -119,6 +120,7 @@
exporter.getHeader();
g3dExport.setg3dExporter(g3d, exporter);
+ exporter.renderBackground();
for (int i = 0; i < JmolConstants.SHAPE_MAX; ++i) {
Shape shape = modelSet.getShape(i);
if (shape == null)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-12 22:18:02
|
Revision: 9712
http://jmol.svn.sourceforge.net/jmol/?rev=9712&view=rev
Author: hansonr
Date: 2008-08-12 22:17:55 +0000 (Tue, 12 Aug 2008)
Log Message:
-----------
version=11.6.RC5_dev bug fixes
# bug fix: set fontscaling with multiple echo texts/images at the same xyz location only scaling the first item
# bug fix: set echo xxxx 30 40
# bug fix: WAY more streamlined refreshing
# bug fix: createImage(), not getImage() in order to allow dynamic file change
# bug fix: halo size for antialiased display
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/JmolExportInterface.java
trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java
trunk/Jmol/src/org/jmol/export/Export3D.java
trunk/Jmol/src/org/jmol/export/_MayaExporter.java
trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
trunk/Jmol/src/org/jmol/export/_VrmlExporter.java
trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
trunk/Jmol/src/org/jmol/g3d/Text3D.java
trunk/Jmol/src/org/jmol/shape/Echo.java
trunk/Jmol/src/org/jmol/shape/HalosRenderer.java
trunk/Jmol/src/org/jmol/shape/Object2d.java
trunk/Jmol/src/org/jmol/shape/Text.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/RepaintManager.java
trunk/Jmol/src/org/jmol/viewer/StateManager.java
trunk/Jmol/src/org/jmol/viewer/StatusManager.java
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/api/JmolExportInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolExportInterface.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/api/JmolExportInterface.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -77,7 +77,8 @@
abstract void plotText(int x, int y, int z, int argb, String text, Font3D font3d);
- abstract void plotImage(int x, int y, int z, Image image, short bgcolix);
+ abstract void plotImage(int x, int y, int z, Image image, short bgcolix,
+ int width, int height);
// NOT IMPLEMENTED, but could be if needed:
Modified: trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -320,6 +320,6 @@
public abstract void renderEllipsoid(int x, int y, int z, int diameter, Matrix3f mToEllipsoidal, double[] coef, Matrix4f mDeriv, int selectedOctant, Point3i[] octantPoints);
- public abstract void drawImage(Image image, int x, int y, int z, int zslab, short bgcolix);
+ public abstract void drawImage(Image image, int x, int y, int z, int zslab, short bgcolix, int width, int height);
}
Modified: trunk/Jmol/src/org/jmol/export/Export3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/Export3D.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/export/Export3D.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -298,13 +298,14 @@
z, getColixArgb(colix), str, font3d);
}
- public void drawImage(Image image, int x, int y, int z, int zSlab, short bgcolix) {
+ public void drawImage(Image image, int x, int y, int z, int zSlab,
+ short bgcolix, int width, int height) {
if (image == null || width == 0 || height == 0)
return;
if (isClippedZ(zSlab))
return;
z = Math.max(slab, z);
- exporter.plotImage(x, y, z, image, bgcolix);
+ exporter.plotImage(x, y, z, image, bgcolix, width, height);
}
//mostly public drawing methods -- add "public" if you need to
Modified: trunk/Jmol/src/org/jmol/export/_MayaExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_MayaExporter.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/export/_MayaExporter.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -229,7 +229,7 @@
}
- public void plotImage(int x, int y, int z, Image image, short bgcolix) {
+ public void plotImage(int x, int y, int z, Image image, short bgcolix, int width, int height) {
// TODO
}
Modified: trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -629,9 +629,10 @@
output("// end text " + nText + ": " + text + "\n");
}
- public void plotImage(int x, int y, int z, Image image, short bgcolix) {
+ public void plotImage(int x, int y, int z, Image image, short bgcolix,
+ int width, int height) {
output("// start image " + (++nImage) + "\n");
- g3d.plotImage(x, y, z, image, jmolRenderer, bgcolix);
+ g3d.plotImage(x, y, z, image, jmolRenderer, bgcolix, width, height);
output("// end image " + nImage + "\n");
}
// not needed:
Modified: trunk/Jmol/src/org/jmol/export/_VrmlExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_VrmlExporter.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/export/_VrmlExporter.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -240,7 +240,8 @@
}
- public void plotImage(int x, int y, int z, Image image, short bgcolix) {
+ public void plotImage(int x, int y, int z, Image image, short bgcolix,
+ int width, int height) {
// TODO
}
Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -352,7 +352,7 @@
//setRectClip(clipX, clipY, clipWidth, clipHeight);
platform.obtainScreenBuffer();
if (backgroundImage != null)
- plotImage(Integer.MIN_VALUE, 0, Integer.MIN_VALUE, backgroundImage, null, (short) 0);
+ plotImage(Integer.MIN_VALUE, 0, Integer.MIN_VALUE, backgroundImage, null, (short) 0, 0, 0);
}
private void releaseBuffers() {
@@ -1042,20 +1042,22 @@
antialiasThisFrame);
}
- public void drawImage(Image image, int x, int y, int z, int zSlab, short bgcolix) {
+ public void drawImage(Image image, int x, int y, int z, int zSlab,
+ short bgcolix, int width, int height) {
if (image == null || width == 0 || height == 0)
return;
if (isClippedZ(zSlab))
return;
- plotImage(x, y, z, image, null, bgcolix);
+ plotImage(x, y, z, image, null, bgcolix, width, height);
}
public void plotImage(int x, int y, int z, Image image, JmolRendererInterface jmolRenderer,
- short bgcolix) {
+ short bgcolix, int width, int height) {
setColix(bgcolix);
if (bgcolix == 0)
argbCurrent = 0;
- Text3D.plotImage(x, y, z, image, this, jmolRenderer, antialiasThisFrame, argbCurrent);
+ Text3D.plotImage(x, y, z, image, this, jmolRenderer, antialiasThisFrame, argbCurrent,
+ width, height);
}
public void setFont(byte fid) {
@@ -2934,7 +2936,8 @@
public void renderBackground(JmolRendererInterface jmolRenderer) {
if (backgroundImage != null)
- plotImage(Integer.MIN_VALUE, 0, Integer.MIN_VALUE, backgroundImage, jmolRenderer, (short) 0);
+ plotImage(Integer.MIN_VALUE, 0, Integer.MIN_VALUE, backgroundImage,
+ jmolRenderer, (short) 0, 0, 0);
}
}
Modified: trunk/Jmol/src/org/jmol/g3d/Text3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Text3D.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/g3d/Text3D.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -95,9 +95,11 @@
int textWidth = text3d.width;
int textHeight = text3d.height;
int mapWidth = text3d.mapWidth;
- if (x + textWidth < 0 || x > g3d.width || y + textHeight < 0
- || y > g3d.height)
+ if (x + textWidth <= 0 || x >= g3d.width || y + textHeight <= 0
+ || y >= g3d.height)
return textWidth;
+ //TODO: text width/height are calculated 4x correct size here when antialiased.
+ // this is wasteful, as it requires drawing larger than necessary images
if (jmolRenderer != null ||
(x < 0 || x + textWidth > g3d.width || y < 0
|| y + textHeight > g3d.height))
@@ -110,35 +112,25 @@
public static void plotImage(int x, int y, int z, Image image, Graphics3D g3d,
JmolRendererInterface jmolRenderer, boolean antialias,
- int argbBackground) {
- //System.out.println(x + " " + width + ", " + y + " " + height + " w/h " + g3d.width + " " + g3d.height + " " + g3d.isAntialiased());
+ int argbBackground, int width, int height) {
boolean isBackground = (x == Integer.MIN_VALUE);
- int width = image.getWidth(null);
- int height = image.getHeight(null);
+ int width0 = image.getWidth(null);
+ int height0 = image.getHeight(null);
if (isBackground) {
x = 0;
z = Integer.MAX_VALUE - 1;
width = g3d.width;
height = g3d.height;
- } else if (x + width < 0 || x > g3d.width || y + height < 0 || y > g3d.height) {
- return;
} else if (g3d.isAntialiased()) {
width += width;
height += height;
}
-
+ if (x + width <= 0 || x >= g3d.width || y + height <= 0 || y >= g3d.height)
+ return;
g3d.platform.checkOffscreenSize(width, height);
Graphics g = g3d.platform.gOffscreen;
g.clearRect(0,0,width,height);
- if (isBackground) {
- g.drawImage(image, 0, 0, width, height, 0, 0, image.getWidth(null), image.getHeight(null), null);
- width = g3d.width;
- height = g3d.height;
- } else if (g3d.isAntialiased()) {
- g.drawImage(image, 0, 0, width, height, 0, 0, width >> 1, height >> 1, null);
- } else {
- g.drawImage(image, 0, 0, null);
- }
+ g.drawImage(image, 0, 0, width, height, 0, 0, width0, height0, null);
PixelGrabber pixelGrabber = new PixelGrabber(g3d.platform.imageOffscreen, 0, 0,
width, height, true);
try {
@@ -164,7 +156,6 @@
if (jmolRenderer == null)
jmolRenderer = g3d;
for (int i = 0, offset = 0; i < height; i++) {
- //System.out.println(Integer.toHexString(buffer[offset]));
for (int j = 0; j < width; j++) {
int argb = buffer[offset++];
if (argb != bgcolor && (argb & 0xFF000000) == 0xFF000000)
@@ -183,7 +174,6 @@
int j = 0;
int offset = 0;
while (i < textHeight) {
- //System.out.println(Integer.toHexString(buffer[offset]));
while (j < textWidth) {
if (z < zbuf[pbufOffset]) {
int argb = buffer[offset];
Modified: trunk/Jmol/src/org/jmol/shape/Echo.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Echo.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/shape/Echo.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -106,7 +106,6 @@
text.setTranslucent(currentTranslucentLevel, false);
if (currentBgTranslucentLevel != 0)
text.setTranslucent(currentBgTranslucentLevel, true);
-
}
currentObject = text;
return;
@@ -117,17 +116,9 @@
public String getShapeState() {
StringBuffer s = new StringBuffer("\n set echo off;\n");
- String lastFormat = "";
Enumeration e = objects.elements();
- while (e.hasMoreElements()) {
- Text t = (Text) e.nextElement();
- s.append(t.getState(true));
- String format = t.getState(false);
- if (format.equals(lastFormat))
- continue;
- lastFormat = format;
- s.append(format);
- }
+ while (e.hasMoreElements())
+ s.append(((Text) e.nextElement()).getState());
return s.toString();
}
}
Modified: trunk/Jmol/src/org/jmol/shape/HalosRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/HalosRenderer.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/shape/HalosRenderer.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -33,6 +33,7 @@
public class HalosRenderer extends ShapeRenderer {
+ boolean isAntialiased;
protected void render() {
Halos halos = (Halos) shape;
boolean selectDisplayTrue = viewer.getSelectionHaloEnabled();
@@ -40,6 +41,7 @@
.getShowHiddenSelectionHalos());
if (halos.mads == null && !selectDisplayTrue)
return;
+ isAntialiased = g3d.isAntialiased();
Atom[] atoms = modelSet.atoms;
BitSet bsSelected = (selectDisplayTrue ? viewer.getSelectionSet() : null);
for (int i = modelSet.getAtomCount(); --i >= 0;) {
@@ -75,7 +77,6 @@
void render1(Atom atom, short mad, short colix) {
int z = atom.screenZ;
int diameter = mad;
- int halowidth = 0;
if (diameter < 0) { //unsized selection
diameter = atom.screenDiameter;
if (diameter == 0) {
@@ -89,15 +90,21 @@
} else {
diameter = viewer.scaleToScreen(z, mad);
}
- halowidth = (diameter / 4);
- if (halowidth < 4)
- halowidth = 4;
- if (halowidth > 10)
- halowidth = 10;
- int haloDiameter = diameter + 2 * halowidth;
- if (haloDiameter <= 0)
+ float d = diameter;
+ if (isAntialiased)
+ d /= 2;
+ float haloDiameter = (d / 4);
+ if (haloDiameter < 4)
+ haloDiameter = 4;
+ if (haloDiameter > 10)
+ haloDiameter = 10;
+ haloDiameter = d + 2 * haloDiameter;
+ if (isAntialiased)
+ haloDiameter *= 2;
+ int haloWidth = (int) haloDiameter;
+ if (haloWidth <= 0)
return;
- g3d.fillScreenedCircleCentered(colix, haloDiameter, atom.screenX,
+ g3d.fillScreenedCircleCentered(colix, haloWidth, atom.screenX,
atom.screenY, atom.screenZ);
}
}
Modified: trunk/Jmol/src/org/jmol/shape/Object2d.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Object2d.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/shape/Object2d.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -355,12 +355,11 @@
}
- protected void setBoxOffsetsInWindow(float scale, float vMargin, float vTop) {
+ protected void setBoxOffsetsInWindow(float margin, float vMargin, float vTop) {
// not labels
// these coordinates are (0,0) in top left
// (user coordinates are (0,0) in bottom left)
- float margin = 5 * scale;
float bw = boxWidth + margin;
float x = boxX;
if (x + bw > windowWidth)
Modified: trunk/Jmol/src/org/jmol/shape/Text.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Text.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/shape/Text.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -64,7 +64,6 @@
short bgcolix, int x, int y, int z, int zSlab, int textAlign,
float scalePixelsPerMicron) {
this.scalePixelsPerMicron = scalePixelsPerMicron;
- //System.out.println("Text scalePixelsPerMicron=" + scalePixelsPerMicron);
this.viewer = null;
this.g3d = g3d;
isLabelOrHover = true;
@@ -123,7 +122,6 @@
if (font == null)
return;
fid = font.fid;
- //System.out.println("setFont fontSize/nominal now " + font.fontSize + "/" + font.fontSizeNominal);
getFontMetrics();
recalc();
}
@@ -148,8 +146,8 @@
protected void recalc() {
if (image != null) {
textWidth = textHeight = 0;
- boxWidth = image.getWidth(null);
- boxHeight = image.getHeight(null);
+ boxWidth = image.getWidth(null) * fontScale;
+ boxHeight = image.getHeight(null) * fontScale;
return;
}
if (text == null) {
@@ -168,8 +166,6 @@
textHeight = lines.length * lineHeight;
boxWidth = textWidth + (fontScale >= 2 ? 16 : 8);
boxHeight = textHeight + (fontScale >= 2 ? 16 : 8);
- //System.out.println("Text recalc fontScale,font.fontScale,font.fontScaleNominal="
- // +fontScale + " "+ font.fontSize + " "+ font.fontSizeNominal);
}
private void formatText() {
@@ -182,13 +178,11 @@
float imageFontScaling) {
if (text == null)
return;
- //System.out.println("render scalePixelsPerMicron=" + scalePixelsPerMicron + " imageFontScaling=" + imageFontScaling);
setWindow(g3d, scalePixelsPerMicron);
if (scalePixelsPerMicron != 0 && this.scalePixelsPerMicron != 0)
setFontScale(scalePixelsPerMicron / this.scalePixelsPerMicron);
else if (fontScale != imageFontScaling)
setFontScale(imageFontScaling);
-
if (doFormatText)
formatText();
@@ -208,11 +202,10 @@
// adjust positions if necessary
if (adjustForWindow)
- setBoxOffsetsInWindow(image == null ? fontScale : 0, isLabelOrHover ? 16 * fontScale
- + lineHeight : 0, boxY - textHeight);
+ setBoxOffsetsInWindow(image == null ? fontScale * 5 : 0, isLabelOrHover ? 16
+ * fontScale + lineHeight : 0, boxY - textHeight);
// draw the box if necessary
-
if (image == null && bgcolix != 0 && g3d.setColix(bgcolix))
showBox(g3d, colix, bgcolix, (int) boxX, (int) boxY, z + 2, zSlab,
(int) boxWidth, (int) boxHeight, fontScale, isLabelOrHover);
@@ -221,7 +214,8 @@
// now set x and y positions for text from (new?) box position
if (image != null) {
- g3d.drawImage(image, (int) boxX, (int) boxY, z, zSlab, bgcolix);
+ g3d.drawImage(image, (int) boxX, (int) boxY, z, zSlab, bgcolix,
+ (int) boxWidth, (int) boxHeight);
} else {
// now write properly aligned text
@@ -240,9 +234,6 @@
float x = x0;
float y = boxY + ascent + adj;
- //System.out.println("scale=" + fontScale + " boxwidth/height=" + boxWidth
- // + "/" + boxHeight + " ascent=" + ascent + " lineheight=" + lineHeight
- //+ " boxY=" + boxY + " adj=" + adj);
for (int i = 0; i < lines.length; i++) {
switch (align) {
case ALIGN_CENTER:
@@ -251,7 +242,6 @@
case ALIGN_RIGHT:
x = x0 - widths[i];
}
- //System.out.println(lines[i] + " text render font " + font.fid + " " + font.fontSize);
g3d.drawString(lines[i], font, (int) x, (int) y, z, zSlab);
y += lineHeight;
}
@@ -314,7 +304,7 @@
}
}
- public String getState(boolean isDefine) {
+ public String getState() {
StringBuffer s = new StringBuffer();
if (text == null || isLabelOrHover || target.equals("error"))
return "";
@@ -322,7 +312,7 @@
//set echo myecho x y
//echo .....
boolean isImage = (image != null);
- if (isDefine) {
+// if (isDefine) {
String strOff = null;
switch (valign) {
case VALIGN_XY:
@@ -363,21 +353,20 @@
if (modelIndex >= 0)
s.append(" set echo ").append(target).append(" model ").append(
viewer.getModelNumberDotted(modelIndex)).append(";\n");
- }
+// }
//isDefine and target==top: do all
//isDefine and target!=top: just start
//!isDefine and target==top: do nothing
//!isDefine and target!=top: do just this
//fluke because top is defined with default font
//in initShape(), so we MUST include its font def here
- if (isDefine != target.equals("top"))
- return s.toString();
+// if (isDefine != target.equals("top"))
+// return s.toString();
// these may not change much:
s.append(" " + Shape.getFontCommand("echo", font));
if (scalePixelsPerMicron > 0)
s.append(" " + (10000f / scalePixelsPerMicron)); // Angstroms per pixel
- s.append(";\n");
- s.append(" color echo");
+ s.append("; color echo");
if (Graphics3D.isColixTranslucent(colix))
s.append(" translucent " + Graphics3D.getColixTranslucencyLevel(colix));
s.append(" [x").append(g3d.getHexColorFromIndex(colix)).append("]");
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -8274,6 +8274,7 @@
if (statementLength == len)
return;
propertyName = "align";
+ propertyValue = null;
// set echo name xxx
if (statementLength == 4) {
if (isCenterParameter(3)) {
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -37,6 +37,7 @@
import java.net.URLEncoder;
import java.net.MalformedURLException;
import java.awt.Image;
+import java.awt.MediaTracker;
import java.awt.Toolkit;
import java.io.InputStream;
import java.io.BufferedInputStream;
@@ -340,14 +341,35 @@
Image image = null;
//try {
fullPathName = names[0].replace('\\', '/');
+ if (urlTypeIndex(fullPathName) >= 0)
+ try {
+ image = Toolkit.getDefaultToolkit().createImage(new URL(fullPathName));
+ } catch (Exception e) {
+ return "bad URL: " + fullPathName;
+ }
+ else
+ image = Toolkit.getDefaultToolkit().createImage(fullPathName);
try {
- if (urlTypeIndex(fullPathName) >= 0)
- image = Toolkit.getDefaultToolkit().getImage(new URL(fullPathName));
- else
- image = Toolkit.getDefaultToolkit().getImage(fullPathName);
- } catch (MalformedURLException e) {
- return "cannot create image from " + fullPathName;
+ MediaTracker mediaTracker = new MediaTracker(viewer.getAwtComponent());
+ mediaTracker.addImage(image, 0);
+ mediaTracker.waitForID(0);
+ /* SUN but here for malformed URL - can't trap
+Uncaught error fetching image:
+java.lang.NullPointerException
+ at sun.net.www.ParseUtil.toURI(Unknown Source)
+ at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
+ at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source)
+ at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
+ at sun.awt.image.URLImageSource.getDecoder(Unknown Source)
+ at sun.awt.image.InputStreamImageSource.doFetch(Unknown Source)
+ at sun.awt.image.ImageFetcher.fetchloop(Unknown Source)
+ at sun.awt.image.ImageFetcher.run(Unknown Source)
+ */
+ } catch (Exception e) {
+ return e.getMessage() + " opening " + fullPathName;
}
+ if (image.getWidth(null) < 1)
+ return "invalid or missing image " + fullPathName;
htParams.put("fullPathName", fullPathName);
return image;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-12 22:17:55 UTC (rev 9712)
@@ -3,6 +3,11 @@
version=11.6.RC5_dev
+# bug fix: set fontscaling with multiple echo texts/images at the same xyz location only scaling the first item
+# bug fix: set echo xxxx 30 40
+# bug fix: WAY more streamlined refreshing
+# bug fix: createImage(), not getImage() in order to allow dynamic file change
+# bug fix: halo size for antialiased display
# Addition of translation tags to webexport
# bug fix: write IMAGE broken for 11.6.RC2+
# bug fix: unnecessary refreshes removed from moveto/zoom with time 0
Modified: trunk/Jmol/src/org/jmol/viewer/RepaintManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/RepaintManager.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/viewer/RepaintManager.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -61,7 +61,6 @@
if (currentModelIndex != modelIndex) {
if (modelCount > 0) {
boolean fromDataFrame = viewer.isJmolDataFrame(currentModelIndex);
- //System.out.println("from state " + currentModelIndex + " to "+ modelIndex);
if (fromDataFrame)
viewer.setJmolDataFrame(null, -1, currentModelIndex);
if (currentModelIndex != -1)
@@ -427,22 +426,7 @@
int modelIndexNext = currentModelIndex + frameStep;
boolean isDone = (modelIndexNext > firstModelIndex
&& modelIndexNext > lastModelIndex || modelIndexNext < firstModelIndex
- && modelIndexNext < lastModelIndex);
-
-/*
- System.out.println("setAnimationRelative: " +
- " firstModelIndex=" + firstModelIndex +
- " displayModelIndex=" + currentModelIndex +
- " lastModelIndex=" + lastModelIndex +
- " currentDirection=" + currentDirection +
- " animationDirection=" + animationDirection +
- " direction=" + direction +
- " isDone="+isDone +
- " modelIndexNext=" + modelIndexNext +
- " modelCount=" + viewer.getModelCount() +
- " animationReplayMode=" + animationReplayMode +
- " animationDirection=" + animationDirection);
-*/
+ && modelIndexNext < lastModelIndex);
if (isDone) {
switch (animationReplayMode) {
case ANIMATION_ONCE:
@@ -516,7 +500,6 @@
if (sleepTime > 0)
Thread.sleep(sleepTime);
}
- //System.out.println(repaintPending + " frame " + currentModelIndex);
if (!isFirst && !repaintPending && !setAnimationNext()) {
Logger.debug("animation thread " + intThread + " exiting");
setAnimationOff(false);
@@ -526,29 +509,11 @@
targetTime += (1000 / animationFps);
sleepTime = targetTime
- (int) (System.currentTimeMillis() - timeBegin);
- //boolean autoFps = viewer.getAutoFps();
- //if (autoFps) {
- //System.out.println("requesting repaint for " + currentModelIndex);
- //requestRepaintAndWait();
- //} else
refresh();
sleepTime = targetTime
- (int) (System.currentTimeMillis() - timeBegin);
if (sleepTime > 0)
Thread.sleep(sleepTime);
- /*if (false && autoFps) {
- if (holdTime <= 0)
- holdTime = 10;
- int nHold = 0;
- //optimally we want 2 hold cycles
- while (repaintPending) {
- Thread.sleep(holdTime);
- nHold++;
- }
- holdTime *=(nHold - 1);
- if (nHold == 1)
- holdTime = holdTime / 2;
- } */
}
} catch (InterruptedException ie) {
Logger.debug("animation thread interrupted!");
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -619,7 +619,6 @@
boolean fontScaling = false;
boolean hideNameInPopup = false;
int hoverDelayMs = 500;
- boolean imageScaling = false;
boolean measurementLabels = true;
boolean messageStyleChime = false;
int pickingSpinRate = 10;
@@ -751,7 +750,7 @@
+ ";axesposition;axesmolecular;axesorientationrasmol;axesunitcell;axeswindow;axis1color;axis2color"
+ ";axis3color;backgroundcolor;backgroundmodel;bondsymmetryatoms;boundboxcolor;cameradepth"
+ ";debugscript;defaultlatttice;defaults;diffusepercent;exportdrivers"
- + ";fontscaling;imagescaling;language;loglevel;measureStyleChime"
+ + ";fontscaling;language;loglevel;measureStyleChime"
+ ";minimizationsteps;minimizationrefresh;minimizationcriterion;navigationmode"
+ ";perspectivedepth;visualrange;perspectivemodel;refreshing;rotationradius"
+ ";showaxes;showaxis1;showaxis2;showaxis3;showboundbox;showfrank;showunitcell"
@@ -1149,7 +1148,6 @@
setParameterValue("ellipsoidFill", ellipsoidFill);
setParameterValue("exportDrivers", JmolConstants.EXPORT_DRIVER_LIST);
setParameterValue("fontScaling", fontScaling);
- setParameterValue("imageScaling", imageScaling);
setParameterValue("forceAutoBond", forceAutoBond);
setParameterValue("greyscaleRendering", greyscaleRendering);
setParameterValue("hbondsBackbone", hbondsBackbone);
Modified: trunk/Jmol/src/org/jmol/viewer/StatusManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -260,10 +260,11 @@
int minSyncRepeatMs = 100;
boolean syncingScripts = false;
boolean syncingMouse = false;
+ boolean doSync() {
+ return (isSynced && drivingSync && !syncDisabled);
+ }
synchronized void setSync(String mouseCommand) {
- if (!isSynced || !drivingSync || syncDisabled)
- return;
if (syncingMouse) {
if (mouseCommand != null)
syncSend(mouseCommand, null);
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -1990,7 +1990,7 @@
elapsed = (int) (currentTime - startTime);
float t = (float) (elapsed % vibrationPeriodMs) / vibrationPeriodMs;
setVibrationT(t);
- viewer.refresh(0, "TransformationManager:VibrationThread:run()");
+ viewer.refresh(3, "TransformationManager:VibrationThread:run()");
} while (!isInterrupted());
} catch (Exception e) { //may be arithmetic %0/0
}
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-12 18:45:54 UTC (rev 9711)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-12 22:17:55 UTC (rev 9712)
@@ -525,14 +525,12 @@
}
void restoreModelOrientation(int modelIndex) {
- //System.out.println("resetoremodelorientation " + modelIndex);
StateManager.Orientation o = modelSet.getModelOrientation(modelIndex);
if (o != null)
o.restore(-1, true);
}
void restoreModelRotation(int modelIndex) {
- //System.out.println("resetoremodelrotate " + modelIndex);
StateManager.Orientation o = modelSet.getModelOrientation(modelIndex);
if (o != null)
o.restore(-1, false);
@@ -616,7 +614,7 @@
if (isJmolDataFrame())
return;
transformManager.setCenterAt(relativeTo, pt);
- refresh(0, "Viewer:setCenter(" + relativeTo + ")");
+ //refresh(0, "Viewer:setCenter(" + relativeTo + ")");
}
void setCenterBitSet(BitSet bsCenter, boolean doScale) {
@@ -629,7 +627,7 @@
if (isJmolDataFrame())
return;
transformManager.setNewRotationCenter(center, doScale);
- refresh(0, "Viewer:setCenterBitSet()");
+ //refresh(0, "Viewer:setCenterBitSet()");
}
void setNewRotationCenter(Point3f center) {
@@ -637,7 +635,7 @@
if (isJmolDataFrame())
return;
transformManager.setNewRotationCenter(center, true);
- refresh(0, "Viewer:setCenterBitSet()");
+ //refresh(0, "Viewer:setCenterBitSet()");
}
Point3f getNavigationCenter() {
@@ -901,25 +899,25 @@
void slabByPixels(int pixels) {
//MouseManager.mouseSinglePressDrag
transformManager.slabByPercentagePoints(pixels);
- refresh(0, "Viewer:slabByPixels()");
+ //refresh(0, "Viewer:slabByPixels()");
}
void depthByPixels(int pixels) {
//MouseManager.mouseDoublePressDrag
transformManager.depthByPercentagePoints(pixels);
- refresh(0, "Viewer:depthByPixels()");
+ //refresh(0, "Viewer:depthByPixels()");
}
void slabDepthByPixels(int pixels) {
//MouseManager.mouseSinglePressDrag
transformManager.slabDepthByPercentagePoints(pixels);
- refresh(0, "Viewer:slabDepthByPixels()");
+ //refresh(0, "Viewer:slabDepthByPixels()");
}
void slabToPercent(int percentSlab) {
//Eval.slab
transformManager.slabToPercent(percentSlab);
- refresh(0, "Viewer:slabToPercent()");
+ //refresh(0, "Viewer:slabToPercent()");
}
void slabInternal(Point4f plane, boolean isDepth) {
@@ -929,7 +927,7 @@
void depthToPercent(int percentDepth) {
//Eval.depth
transformManager.depthToPercent(percentDepth);
- refresh(0, "Viewer:depthToPercent()");
+ //refresh(0, "Viewer:depthToPercent()");
}
void setSlabDepthInternal(boolean isDepth) {
@@ -1123,7 +1121,7 @@
public void setVectorScale(float scale) {
global.setParameterValue("vectorScale", scale);
global.vectorScale = scale;
- refresh(0, "set vectorScale");
+ //refresh(0, "set vectorScale");
}
public float getDefaultDrawArrowScale() {
@@ -1133,7 +1131,7 @@
public void setDefaultDrawArrowScale(float scale) {
global.setParameterValue("defaultDrawArrowScale", scale);
global.defaultDrawArrowScale = scale;
- refresh(0, "set defaultDrawArrowScale");
+ //refresh(0, "set defaultDrawArrowScale");
}
float getVibrationScale() {
@@ -1191,7 +1189,7 @@
global.setParameterValue(name + "Color", Escape.escapeColor(argb));
}
- public void setBackgroundImage(String fileName, Image image) {
+ void setBackgroundImage(String fileName, Image image) {
global.backgroundImageFileName = fileName;
g3d.setBackgroundImage(image);
}
@@ -1404,7 +1402,7 @@
public void selectAll() {
//initializeModel
selectionManager.selectAll(false);
- refresh(0, "Viewer:selectAll()");
+ //refresh(0, "Viewer:selectAll()");
}
private boolean noneSelected;
@@ -1421,13 +1419,13 @@
//not used in this project; in jmolViewer interface, though
selectionManager.clearSelection(false);
global.setParameterValue("hideNotSelected", false);
- refresh(0, "Viewer:clearSelection()");
+ //refresh(0, "Viewer:clearSelection()");
}
public void setSelectionSet(BitSet set) {
//not used in this project; in jmolViewer interface, though
selectionManager.setSelectionSet(set);
- refresh(0, "Viewer:setSelectionSet()");
+ //refresh(0, "Viewer:setSelectionSet()");
}
void setSelectionSubset(BitSet subset) {
@@ -1944,7 +1942,7 @@
colorManager.clear();
evalVariables.clear();
//setRefreshing(true);
- refresh(0, "Viewer:clear()");
+ //refresh(0, "Viewer:clear()");
dataManager.clear();
System.gc();
}
@@ -2137,7 +2135,7 @@
void calcBoundBoxDimensions(BitSet bs) {
modelSet.calcBoundBoxDimensions(bs);
axesAreTainted = true;
- refresh(0, "set calcBoundBoxDimensions");
+ //refresh(0, "set calcBoundBoxDimensions");
}
BoxInfo getBoxInfo(BitSet bs) {
@@ -2721,7 +2719,7 @@
void clearAllMeasurements() {
//Eval only
setShapeProperty(JmolConstants.SHAPE_MEASURES, "clear", null);
- refresh(0, "Viewer:clearAllMeasurements()");
+ //refresh(0, "Viewer:clearAllMeasurements()");
}
public void clearMeasurements() {
@@ -2767,14 +2765,14 @@
//Eval
setShapeProperty(JmolConstants.SHAPE_MEASURES, isON ? "show" : "hide",
atomCountPlusIndices);
- refresh(0, "Viewer:showMeasurements()");
+ //refresh(0, "Viewer:showMeasurements()");
}
void hideMeasurements(boolean isOFF) {
//Eval
setShapeProperty(JmolConstants.SHAPE_MEASURES, "hideAll", Boolean
.valueOf(isOFF));
- refresh(0, "hideMeasurements()");
+ //refresh(0, "hideMeasurements()");
}
void toggleMeasurement(int[] atomCountPlusIndices, String strFormat) {
@@ -2859,7 +2857,7 @@
return;
}
repaintManager.resumeAnimation();
- refresh(0, "Viewer:resumeAnimation()");
+ //refresh(0, "Viewer:resumeAnimation()");
}
void pauseAnimation() {
@@ -2868,7 +2866,7 @@
return;
}
repaintManager.pauseAnimation();
- refresh(0, "Viewer:pauseAnimation()");
+ //refresh(0, "Viewer:pauseAnimation()");
}
void setAnimationRange(int modelIndex1, int modelIndex2) {
@@ -2887,26 +2885,28 @@
void setAnimationNext() {
//Eval
- if (repaintManager.setAnimationNext())
- refresh(0, "Viewer:setAnimationNext()");
+ repaintManager.setAnimationNext();
+ //if (repaintManager.setAnimationNext())
+ //refresh(0, "Viewer:setAnimationNext()");
}
void setAnimationPrevious() {
//Eval
- if (repaintManager.setAnimationPrevious())
- refresh(0, "Viewer:setAnimationPrevious()");
+ repaintManager.setAnimationPrevious();
+ //if (repaintManager.setAnimationPrevious())
+ //refresh(0, "Viewer:setAnimationPrevious()");
}
void setAnimationLast() {
//Eval
repaintManager.setAnimationLast();
- refresh(0, "Viewer:setAnimationLast()");
+ //refresh(0, "Viewer:setAnimationLast()");
}
void rewindAnimation() {
//Eval
repaintManager.rewindAnimation();
- refresh(0, "Viewer:rewindAnimation()");
+ //refresh(0, "Viewer:rewindAnimation()");
}
void setCurrentModelIndex(int modelIndex) {
@@ -3051,13 +3051,13 @@
*
*/
public void refresh(int mode, String strWhy) {
- // refresh(2 indicates this is a mouse motion -- not going through Eval script
+ // refresh(2) indicates this is a mouse motion -- not going through Eval script
// so we bypass Eval and mainline on the other viewer!
- if (mode >= 0)
+ // refresh(-1) is used in stateManager to force no refresh)
+ // refresh(3) is used by the vibration thread to ONLY do a repaint -- no syncing
+ if (mode > 0)
repaintManager.refresh();
- else
- mode = -mode;
- if (mode != 0)
+ if (mode % 3 != 0 && statusManager.doSync())
statusManager.setSync(mode == 2 ? strWhy : null);
}
@@ -3065,11 +3065,13 @@
if (!haveDisplay)
return;
repaintManager.requestRepaintAndWait();
- statusManager.setSync(null);
+ if (statusManager.doSync())
+ statusManager.setSync(null);
}
void setSync() {
- statusManager.setSync(null);
+ if (statusManager.doSync())
+ statusManager.setSync(null);
}
public void repaintView() {
@@ -3508,7 +3510,7 @@
}
public void pauseScriptExecution() {
- refresh(0, "pauseScriptExecution");
+ //refresh(0, "pauseScriptExecution");
eval.pauseExecution();
}
@@ -3606,8 +3608,6 @@
setShapeProperty(JmolConstants.SHAPE_LABELS, "label", strLabel);
}
- int n;
-
void togglePickingLabel(BitSet bs) {
//eval label toggle (atomset) and pickingManager
if (bs == null)
@@ -3616,7 +3616,7 @@
setShapeSize(JmolConstants.SHAPE_LABELS, 0, null);
modelSet.setShapeProperty(JmolConstants.SHAPE_LABELS, "toggleLabel", null,
bs);
- refresh(0, "Viewer:togglePickingLabel()");
+ //refresh(0, "Viewer:togglePickingLabel()");
}
BitSet getBitSetSelection() {
@@ -3638,7 +3638,7 @@
//above,
//Eval.configuration
modelSet.setShapeSize(shapeID, size, bsAtoms);
- refresh(0, "Viewer:setShapeSize(" + shapeID + "," + size + ")");
+ //refresh(0, "Viewer:setShapeSize(" + shapeID + "," + size + ")");
}
public void setShapeProperty(int shapeID, String propertyName, Object value) {
@@ -3654,7 +3654,7 @@
return; //not applicable
modelSet.setShapeProperty(shapeID, propertyName, value,
selectionManager.bsSelection);
- refresh(0, "Viewer:setShapeProperty()");
+ //refresh(0, "Viewer:setShapeProperty()");
}
void setShapeProperty(int shapeID, String propertyName, Object value,
@@ -3663,7 +3663,7 @@
if (shapeID < 0)
return; //not applicable
modelSet.setShapeProperty(shapeID, propertyName, value, bs);
- refresh(0, "Viewer:setShapeProperty()");
+ //refresh(0, "Viewer:setShapeProperty()");
}
void setShapePropertyArgb(int shapeID, String propertyName, int argb) {
@@ -4406,7 +4406,7 @@
//11.6.RC2//
if (key.equalsIgnoreCase("dotDensity")) {
global.dotDensity = value;
- refresh(0, "Viewer:setDotDensity");
+ //refresh(0, "Viewer:setDotDensity");
break;
}
@@ -4508,9 +4508,7 @@
break;
}
if (key.equalsIgnoreCase("pickingSpinRate")) {
- if (value < 1)
- value = 1;
- global.pickingSpinRate = value;
+ global.pickingSpinRate = (value < 1 ? 1 : value);
break;
}
if (key.equalsIgnoreCase("animationFps")) {
@@ -4575,11 +4573,6 @@
boolean notFound = false;
boolean doRepaint = true;
while (true) {
- //11.6.RC5
- if (key.equalsIgnoreCase("imageScaling")) {
- global.imageScaling = value;
- break;
- }
//11.5.52
if (key.equalsIgnoreCase("selectAllModels")) {
global.selectAllModels = value;
@@ -4781,12 +4774,12 @@
if (key.equalsIgnoreCase("slabEnabled")) {
//Eval.slab
transformManager.setSlabEnabled(value); //refresh?
- refresh(0, "Viewer:setSlabEnabled");
+ //refresh(0, "Viewer:setSlabEnabled");
break;
}
if (key.equalsIgnoreCase("zoomEnabled")) {
transformManager.setZoomEnabled(value);
- refresh(1, "Viewer:setZoomEnabled()");
+ //refresh(0, "Viewer:setZoomEnabled()");
break;
}
if (key.equalsIgnoreCase("highResolution")) {
@@ -4840,12 +4833,12 @@
}
if (key.equalsIgnoreCase("showMultipleBonds")) {
global.showMultipleBonds = value;
- refresh(0, "Viewer:setShowMultipleBonds()");
+ //refresh(0, "Viewer:setShowMultipleBonds()");
break;
}
if (key.equalsIgnoreCase("showHiddenSelectionHalos")) {
global.showHiddenSelectionHalos = value;
- refresh(0, "Viewer:setShowHiddenSelectionHalos()");
+ //refresh(0, "Viewer:setShowHiddenSelectionHalos()");
break;
}
if (key.equalsIgnoreCase("windowCentered")) {
@@ -4886,7 +4879,7 @@
}
if (key.equalsIgnoreCase("greyscaleRendering")) {
g3d.setGreyscaleMode(global.greyscaleRendering = value);
- refresh(0, "Viewer:setGreyscaleRendering()");
+ //refresh(0, "Viewer:setGreyscaleRendering()");
break;
}
if (key.equalsIgnoreCase("measurementLabels")) {
@@ -5028,7 +5021,7 @@
return false;
if (doRepaint) {
setTainted(true);
- refresh(0, "viewer.setBooleanProperty");
+ //refresh(0, "viewer.setBooleanProperty");
}
return true;
}
@@ -5055,10 +5048,6 @@
return global.fontScaling;
}
- public boolean getImageScaling() {
- return global.imageScaling;
- }
-
void showParameter(String key, boolean ifNotSet, int nMax) {
String sv = "" + global.getParameterEscaped(key, nMax);
if (ifNotSet || sv.indexOf("<not set>") < 0)
@@ -5161,7 +5150,7 @@
//app preferences dialog
global.setParameterValue("perspectiveDepth", perspectiveDepth);
transformManager.setPerspectiveDepth(perspectiveDepth);
- refresh(0, "Viewer:setPerspectiveDepth()");
+ //refresh(0, "Viewer:setPerspectiveDepth()");
}
public void setAxesOrientationRasmol(boolean TF) {
@@ -5193,7 +5182,7 @@
void setAxesScale(float scale) {
global.axesScale = scale;
axesAreTainted = true;
- refresh(0, "set axesScale");
+ //refresh(0, "set axesScale");
}
public Point3f[] getAxisPoints() {
@@ -5403,7 +5392,7 @@
modelSet.deleteAllBonds();
modelSet.autoBond(null, null, null, null);
addStateScript("connect;", false, true);
- refresh(0, "Viewer:rebond()");
+ //refresh(0, "Viewer:rebond()");
}
void setPdbConectBonding(boolean isAuto) {
@@ -5418,7 +5407,7 @@
return;
}
addStateScript("connect PDB;", false, true);
- refresh(0, "Viewer:setPdbConnectBonding()");
+ //refresh(0, "Viewer:setPdbConnectBonding()");
}
// //////////////////////////////////////////////////////////////
@@ -5468,7 +5457,7 @@
void setModeMultipleBond(byte modeMultipleBond) {
//not implemented
global.modeMultipleBond = modeMultipleBond;
- refresh(0, "Viewer:setModeMultipleBond()");
+ //refresh(0, "Viewer:setModeMultipleBond()");
}
*/
@@ -5486,7 +5475,7 @@
//setBooleanProperty
global.setParameterValue("showHydrogens", TF);
global.showHydrogens = TF;
- refresh(0, "Viewer:setShowHydrogens()");
+ //refresh(0, "Viewer:setShowHydrogens()");
}
public boolean getShowHydrogens() {
@@ -5545,7 +5534,7 @@
//setbooleanProperty
global.setParameterValue("showMeasurements", TF);
global.showMeasurements = TF;
- refresh(0, "setShowMeasurements()");
+ //refresh(0, "setShowMeasurements()");
}
public boolean getShowMeasurements() {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-13 23:36:03
|
Revision: 9729
http://jmol.svn.sourceforge.net/jmol/?rev=9729&view=rev
Author: hansonr
Date: 2008-08-13 23:35:59 +0000 (Wed, 13 Aug 2008)
Log Message:
-----------
version=11.6.RC7_dev
# bug fix: adaptation for malformed PDB files (HEADER with nothing following it)
# bug fix: more language localization in webexport
# new feature: applet message regarding help and command entry
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
trunk/Jmol/src/org/jmol/applet/Console.java
trunk/Jmol/src/org/jmol/applet/Jmol.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2008-08-13 21:21:16 UTC (rev 9728)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2008-08-13 23:35:59 UTC (rev 9729)
@@ -236,6 +236,8 @@
}
private void header() {
+ if (lineLength < 8)
+ return;
if (lineLength >= 66)
atomSetCollection.setCollectionName(line.substring(62, 66));
if (lineLength > 50)
Modified: trunk/Jmol/src/org/jmol/applet/Console.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Console.java 2008-08-13 21:21:16 UTC (rev 9728)
+++ trunk/Jmol/src/org/jmol/applet/Console.java 2008-08-13 23:35:59 UTC (rev 9729)
@@ -131,8 +131,12 @@
}
protected void addHelpMenuBar(JMenuBar menuBar) {
- String menuKey = "help";
- JMenu m0 = createMenu(menuKey);
+ //JMenu m0 = createMenu("Help");
+ JMenu m0 = newJMenu("Help");
+ JMenuItem item = new JMenuItem("Search...");
+ item.addActionListener(this);
+ item.setName("help ?search=?");
+ m0.add(item);
if (m0 == null)
return;
addHelpItems(m0, "commands", "command");
@@ -248,8 +252,8 @@
//menu.addMenuListener(display.getMenuListener());
- JMenuItem mi = createMenuItem("Help");
- menu.add(mi);
+ //JMenuItem mi = createMenuItem("Help");
+ //menu.add(mi);
return menu;
}
Modified: trunk/Jmol/src/org/jmol/applet/Jmol.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jmol.java 2008-08-13 21:21:16 UTC (rev 9728)
+++ trunk/Jmol/src/org/jmol/applet/Jmol.java 2008-08-13 23:35:59 UTC (rev 9729)
@@ -511,8 +511,11 @@
}
void consoleMessage(String message) {
- if (jvm12 != null)
+ if (jvm12 != null) {
jvm12.consoleMessage(message);
+ if (message == null)
+ jvm12.consoleMessage(GT._("Messages will appear here. Enter commands in the box below. Click the console Help menu item for on-line help, which will appear in a new browser window."));
+ }
sendJsTextareaStatus(message);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-13 21:21:16 UTC (rev 9728)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-13 23:35:59 UTC (rev 9729)
@@ -3,7 +3,9 @@
version=11.6.RC7_dev
+# bug fix: adaptation for malformed PDB files (HEADER with nothing following it)
# bug fix: more language localization in webexport
+# new feature: applet message regarding help and command entry
# -----------------------------------------------------------------------------
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-14 03:18:01
|
Revision: 9730
http://jmol.svn.sourceforge.net/jmol/?rev=9730&view=rev
Author: hansonr
Date: 2008-08-14 03:17:56 +0000 (Thu, 14 Aug 2008)
Log Message:
-----------
version=11.6.RC7_dev structure command
# bug fix: structure helix|sheet|turn|none {atomExpression} was undocumented and had state issues
# bug fix: set echo myecho ON was not implemented
# new feature: set echo myecho HIDDEN
# new feature: set echo myecho DISPLAY (same as ON)
# new feature: set echo all; set echo HIDDEN/DISPLAY
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/Model.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/modelsetbio/ProteinStructure.java
trunk/Jmol/src/org/jmol/shape/Echo.java
trunk/Jmol/src/org/jmol/shape/EchoRenderer.java
trunk/Jmol/src/org/jmol/shape/Object2d.java
trunk/Jmol/src/org/jmol/shape/TextShape.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2008-08-13 23:35:59 UTC (rev 9729)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2008-08-14 03:17:56 UTC (rev 9730)
@@ -924,10 +924,6 @@
return group.getProteinStructureID();
}
- public int setProteinStructureType(byte type, int indexCurrent) {
- return group.setProteinStructureType(type, indexCurrent);
- }
-
public short getGroupID() {
return group.groupID;
}
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2008-08-13 23:35:59 UTC (rev 9729)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2008-08-14 03:17:56 UTC (rev 9730)
@@ -256,19 +256,6 @@
}
}
- public void setProteinType(BitSet bs, byte iType) {
- int monomerIndexCurrent = -1;
- int iLast = -1;
- for (int i = 0; i < atomCount; i++)
- if (bs.get(i)) {
- if (iLast != i - 1)
- monomerIndexCurrent = -1;
- iLast = i;
- monomerIndexCurrent = atoms[i].setProteinStructureType(iType,
- monomerIndexCurrent);
- }
- }
-
protected float getRadiusVdwJmol(Atom atom) {
return JmolConstants.getVanderwaalsMar(atom.getElementNumber(),
JmolConstants.VDW_JMOL) / 1000f;
Modified: trunk/Jmol/src/org/jmol/modelset/Model.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Model.java 2008-08-13 23:35:59 UTC (rev 9729)
+++ trunk/Jmol/src/org/jmol/modelset/Model.java 2008-08-14 03:17:56 UTC (rev 9730)
@@ -174,13 +174,19 @@
}
}
+ boolean structureTainted;
void calculateStructures() {
+ structureTainted = modelSet.proteinStructureTainted = true;
for (int i = bioPolymerCount; --i >= 0; ) {
bioPolymers[i].clearStructures();
bioPolymers[i].calculateStructures();
}
}
+ public boolean isStructureTainted() {
+ return structureTainted;
+ }
+
void setConformation(BitSet bsConformation) {
for (int i = bioPolymerCount; --i >= 0; )
bioPolymers[i].setConformation(bsConformation, nAltLocs);
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-08-13 23:35:59 UTC (rev 9729)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-08-14 03:17:56 UTC (rev 9730)
@@ -74,6 +74,7 @@
for (int j = 0; j < m.chainCount; j++)
m.chains[j].setModelSet(m.modelSet);
stateScripts = modelSet.stateScripts;
+ proteinStructureTainted = modelSet.proteinStructureTainted;
thisStateModel = -1;
}
super.merge(modelSet);
@@ -541,6 +542,20 @@
propagateSecondaryStructure();
}
+ public void setProteinType(BitSet bs, byte iType) {
+ int monomerIndexCurrent = -1;
+ int iLast = -1;
+ for (int i = 0; i < atomCount; i++)
+ if (bs.get(i)) {
+ if (iLast != i - 1)
+ monomerIndexCurrent = -1;
+ iLast = i;
+ monomerIndexCurrent = atoms[i].group.setProteinStructureType(iType,
+ monomerIndexCurrent);
+ proteinStructureTainted = models[atoms[i].modelIndex].structureTainted = true;
+ }
+ }
+
private void freezeModels() {
for (int iModel = modelCount; --iModel >= 0;) {
Model m = models[iModel];
@@ -990,7 +1005,7 @@
if (ctype != 'R')
remark += " quaternionFrame = \"" + qtype + "\"";
remark += "\nREMARK 6 Jmol Version " + Viewer.getJmolVersion();
- remark += "\n\n" + getProteinStructureState(bsAtoms, ctype == 'R');
+ remark += "\n\n" + getProteinStructureState(bsAtoms, false, ctype == 'R');
return remark + s;
}
@@ -2100,7 +2115,10 @@
//////////// state definition ///////////
- public String getProteinStructureState(BitSet bsAtoms, boolean needPhiPsi) {
+ boolean proteinStructureTainted = false;
+
+ public String getProteinStructureState(BitSet bsAtoms, boolean taintedOnly,
+ boolean needPhiPsi) {
BitSet bs = null;
StringBuffer cmd = new StringBuffer();
StringBuffer sbTurn = new StringBuffer();
@@ -2120,8 +2138,20 @@
int nHelix = 0;
int nTurn = 0;
int nSheet = 0;
+ BitSet bsTainted = null;
+ if (taintedOnly) {
+ if (!proteinStructureTainted)
+ return "";
+ bsTainted = new BitSet();
+ for (int i = 0; i < atomCount; i++)
+ if (models[atoms[i].modelIndex].isStructureTainted())
+ bsTainted.set(i);
+ bsTainted.set(atomCount);
+ }
for (int i = 0; i <= atomCount; i++)
if (i == atomCount || bsAtoms == null || bsAtoms.get(i)) {
+ if (taintedOnly && !bsTainted.get(i))
+ continue;
id = Integer.MIN_VALUE;
if (i == atomCount || (id = atoms[i].getProteinStructureID()) != lastId) {
if (bs != null) {
@@ -2133,11 +2163,9 @@
int iModel = atoms[iLastAtom].modelIndex;
cmd.append(" structure ").append(
JmolConstants.getProteinStructureName(itype)).append(" ")
- .append(Escape.escape(bs))
- .append(" \t# model=")
- .append(getModelNumberDotted(iModel))
- .append(" & (").append(res1).append(" - ").append(res2)
- .append(");\n");
+ .append(Escape.escape(bs)).append(" \t# model=").append(
+ getModelNumberDotted(iModel)).append(" & (").append(
+ res1).append(" - ").append(res2).append(");\n");
} else {
String str;
int nx;
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-13 23:35:59 UTC (rev 9729)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-14 03:17:56 UTC (rev 9730)
@@ -647,8 +647,9 @@
setModelVisibility();
- //unnecessary. Removed in 11.5.35
- //commands.append(getProteinStructureState(null, false));
+ //unnecessary. Removed in 11.5.35 -- oops!
+
+ commands.append(getProteinStructureState(null, true, false));
for (int i = 0; i < JmolConstants.SHAPE_MAX; ++i) {
Shape shape = shapes[i];
Modified: trunk/Jmol/src/org/jmol/modelsetbio/ProteinStructure.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/ProteinStructure.java 2008-08-13 23:35:59 UTC (rev 9729)
+++ trunk/Jmol/src/org/jmol/modelsetbio/ProteinStructure.java 2008-08-14 03:17:56 UTC (rev 9730)
@@ -44,8 +44,7 @@
final Vector3f vectorProjection = new Vector3f();
Point3f[] segments;
int uniqueID;
- //Point3f center;
-
+
ProteinStructure(AlphaPolymer apolymer, byte type,
int monomerIndex, int monomerCount) {
uniqueID = ++globalSerialID;
Modified: trunk/Jmol/src/org/jmol/shape/Echo.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Echo.java 2008-08-13 23:35:59 UTC (rev 9729)
+++ trunk/Jmol/src/org/jmol/shape/Echo.java 2008-08-14 03:17:56 UTC (rev 9730)
@@ -27,6 +27,7 @@
import org.jmol.util.Logger;
import org.jmol.g3d.*;
+import java.awt.Image;
import java.util.BitSet;
import java.util.Enumeration;
@@ -71,6 +72,34 @@
// continue on to Object2d setting
}
+ if ("image" == propertyName) {
+ Image image = (Image) value;
+ if (currentObject == null) {
+ if (isAll) {
+ Enumeration e = objects.elements();
+ while (e.hasMoreElements())
+ ((Text) e.nextElement()).setImage(image);
+ }
+ return;
+ }
+ ((Text) currentObject).setImage(image);
+ return;
+ }
+
+ if ("hidden" == propertyName) {
+ boolean isHidden = ((Boolean)value).booleanValue();
+ if (currentObject == null) {
+ if (isAll) {
+ Enumeration e = objects.elements();
+ while (e.hasMoreElements())
+ ((Text) e.nextElement()).hidden = isHidden;
+ }
+ return;
+ }
+ ((Text) currentObject).hidden = isHidden;
+ return;
+ }
+
if (Object2d.setProperty(propertyName, value, currentObject))
return;
@@ -117,8 +146,12 @@
public String getShapeState() {
StringBuffer s = new StringBuffer("\n set echo off;\n");
Enumeration e = objects.elements();
- while (e.hasMoreElements())
- s.append(((Text) e.nextElement()).getState());
+ while (e.hasMoreElements()) {
+ Text t = (Text) e.nextElement();
+ s.append(t.getState());
+ if (t.hidden)
+ s.append(" set echo " + t.target + " hidden;\n");
+ }
return s.toString();
}
}
Modified: trunk/Jmol/src/org/jmol/shape/EchoRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/EchoRenderer.java 2008-08-13 23:35:59 UTC (rev 9729)
+++ trunk/Jmol/src/org/jmol/shape/EchoRenderer.java 2008-08-14 03:17:56 UTC (rev 9730)
@@ -38,7 +38,7 @@
imageFontScaling = viewer.getImageFontScaling();
while (e.hasMoreElements()) {
Text t = (Text)e.nextElement();
- if (!t.visible)
+ if (!t.visible || t.hidden)
continue;
if (t.valign == Object2d.VALIGN_XYZ) {
viewer.transformPoint(t.xyz, pt);
Modified: trunk/Jmol/src/org/jmol/shape/Object2d.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Object2d.java 2008-08-13 23:35:59 UTC (rev 9729)
+++ trunk/Jmol/src/org/jmol/shape/Object2d.java 2008-08-14 03:17:56 UTC (rev 9730)
@@ -58,8 +58,9 @@
protected boolean adjustForWindow;
protected float boxWidth, boxHeight, boxX, boxY;
- public int modelIndex = -1;
- public boolean visible = true;
+ int modelIndex = -1;
+ boolean visible = true;
+ boolean hidden = false;
protected final float[] boxXY = new float[2];
@@ -385,7 +386,7 @@
}
public boolean checkObjectClicked(int x, int y, BitSet bsVisible) {
- if (modelIndex >= 0 && !bsVisible.get(modelIndex))
+ if (modelIndex >= 0 && !bsVisible.get(modelIndex) || hidden)
return false;
if (g3d.isAntialiased()) {
x <<= 1;
@@ -397,6 +398,7 @@
}
public static boolean setProperty(String propertyName, Object value, Object2d currentObject) {
+
if ("script" == propertyName) {
if (currentObject != null)
currentObject.setScript((String) value);
Modified: trunk/Jmol/src/org/jmol/shape/TextShape.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/TextShape.java 2008-08-13 23:35:59 UTC (rev 9729)
+++ trunk/Jmol/src/org/jmol/shape/TextShape.java 2008-08-14 03:17:56 UTC (rev 9730)
@@ -28,7 +28,6 @@
import org.jmol.g3d.*;
-import java.awt.Image;
import java.util.BitSet;
import java.util.Enumeration;
@@ -42,21 +41,6 @@
Logger.debug("TextShape.setProperty(" + propertyName + "," + value + ")");
}
- if ("image" == propertyName) {
- Image image = (Image) value;
- if (currentObject == null) {
- if (isAll) {
- Enumeration e = objects.elements();
- while (e.hasMoreElements())
- ((Text) e.nextElement()).setImage(image);
- }
- return;
- }
- ((Text) currentObject).setImage(image);
- return;
- }
-
-
if ("text" == propertyName) {
String text = (String) value;
if (currentObject == null) {
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-13 23:35:59 UTC (rev 9729)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-14 03:17:56 UTC (rev 9730)
@@ -8226,6 +8226,15 @@
echoShapeActive = false;
propertyName = "allOff";
break;
+ case Token.hidden:
+ propertyName = "hidden";
+ propertyValue = Boolean.TRUE;
+ break;
+ case Token.on:
+ case Token.display:
+ propertyName = "hidden";
+ propertyValue = Boolean.FALSE;
+ break;
case Token.none:
echoShapeActive = false;
//fall through
@@ -8285,6 +8294,15 @@
case Token.off:
propertyName = "off";
break;
+ case Token.display:
+ case Token.on:
+ propertyName = "hidden";
+ propertyValue = Boolean.FALSE;
+ break;
+ case Token.hidden:
+ propertyName = "hidden";
+ propertyValue = Boolean.TRUE;
+ break;
case Token.model:
int modelIndex = modelNumberParameter(4);
if (isSyntaxCheck)
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-13 23:35:59 UTC (rev 9729)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-14 03:17:56 UTC (rev 9730)
@@ -3,6 +3,11 @@
version=11.6.RC7_dev
+# bug fix: structure helix|sheet|turn|none {atomExpression} was undocumented and had state issues
+# bug fix: set echo myecho ON was not implemented
+# new feature: set echo myecho HIDDEN
+# new feature: set echo myecho DISPLAY (same as ON)
+# new feature: set echo all; set echo HIDDEN/DISPLAY
# bug fix: adaptation for malformed PDB files (HEADER with nothing following it)
# bug fix: more language localization in webexport
# new feature: applet message regarding help and command entry
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-13 23:35:59 UTC (rev 9729)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-14 03:17:56 UTC (rev 9730)
@@ -2560,7 +2560,7 @@
String getProteinStructureState() {
return modelSet.getProteinStructureState(selectionManager.bsSelection,
- false);
+ false, false);
}
public String getCoordinateState(BitSet bsSelected) {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-16 18:58:50
|
Revision: 9742
http://jmol.svn.sourceforge.net/jmol/?rev=9742&view=rev
Author: hansonr
Date: 2008-08-16 18:58:44 +0000 (Sat, 16 Aug 2008)
Log Message:
-----------
version=11.6.RC8_dev direct applet-applet communication
# new feature: script APPLET appletName "some script"
# --allows direct inter-applet communication independent of set SYNC
# --appletName can be * (all applets), > (other applets), . (this applet),
# or an applet name such as "jmolApplet0" or just the extension "0"
# --for *, the current applet always reports LAST
# new feature: x = script("some script", "appletName")
# --same as above
# --in addition, allows retrieval of information from another applet
# for example:
#
# x = script("print getProperty(\"modelInfo.modelCount\")","B")
#
# gets the number of models loaded in applet jmolAppletB.
#
# x = script("show orientation moveto","jmolApplet2")
#
# gets the current orientation of applet jmolApplet2.
#
# xList = script("print getProperty(\"appletInfo.fullName\").split(\"__\")[1] + \":\" + script(\"show rotation\").trim()","*")
#
# gets a new-line-separated list of rotational quaternions for all applets with applet names.
#
#
# new feature: print getProperty("modelInfo.models[3].file") syntax
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/applet/Jmol.java
trunk/Jmol/src/org/jmol/applet/JmolAppletRegistry.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StatusManager.java
trunk/Jmol/src/org/jmol/viewer/Token.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/applet/Jmol.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jmol.java 2008-08-16 18:17:54 UTC (rev 9741)
+++ trunk/Jmol/src/org/jmol/applet/Jmol.java 2008-08-16 18:58:44 UTC (rev 9742)
@@ -186,7 +186,7 @@
String language;
String menuStructure;
-
+
public void init() {
htmlName = getParameter("name");
syncId = getParameter("syncId");
@@ -1032,7 +1032,7 @@
showStatusAndConsole(strInfo, toConsole);
break;
case JmolConstants.CALLBACK_SYNC:
- sendSyncScript(doCallback, strInfo, (String) data[2]);
+ sendScript(strInfo, (String) data[2], true, doCallback);
return;
}
if (!doCallback || !mayScript)
@@ -1118,6 +1118,10 @@
}
public String eval(String strEval) {
+ // may be appletName\1script
+ int pt = strEval.indexOf("\1");
+ if (pt >= 0)
+ return sendScript(strEval.substring(pt + 1), strEval.substring(0, pt), false, false);
if (strEval.startsWith("_GET_MENU"))
return (jmolpopup == null ? "" : jmolpopup.getMenu("Jmol version " + Viewer.getJmolVersion() + "|" + strEval));
if(!haveDocumentAccess)
@@ -1241,32 +1245,46 @@
jvm12.showConsole(showConsole);
}
- private void sendSyncScript(boolean doCallback, String script, String appletName) {
- Vector apps = JmolAppletRegistry.findApplets(appletName, syncId, fullName);
- if (doCallback)
+ private String sendScript(String script, String appletName, boolean isSync,
+ boolean doCallback) {
+ if (doCallback) {
script = notifySync(script);
- if (apps == null || apps.size() == 0) {
- if (!doCallback)
- Logger.error(fullName + " couldn't find applet " + appletName);
- return;
+ // if the notified JavaScript function returns "" or 0, then
+ // we do NOT continue to notify the other applets
+ if (script == null || script.length() == 0 || script.equals("0"))
+ return "";
}
- // if the notified JavaScript function returns 0, then
- // we do NOT continue to notify the other applet
- if (script == null || script.length() == 0)
- return;
- for (int i = 0; i < apps.size(); i++) {
- String theApplet = (String)apps.elementAt(i);
- JmolAppletInterface app = (JmolAppletInterface)JmolAppletRegistry.htRegistry.get(theApplet);
+ Vector apps = JmolAppletRegistry
+ .findApplets(appletName, syncId, fullName);
+ int nApplets = apps.size();
+ if (nApplets == 0) {
+ if (!appletName.equals("*")) {
+ if (!doCallback)
+ Logger.error(fullName + " couldn't find applet " + appletName);
+ }
+ return "";
+ }
+ StringBuffer sb = (isSync ? null : new StringBuffer());
+ for (int i = 0; i < nApplets; i++) {
+ String theApplet = (String) apps.elementAt(i);
+ JmolAppletInterface app = (JmolAppletInterface) JmolAppletRegistry.htRegistry
+ .get(theApplet);
if (Logger.debugging)
- Logger.debug(fullName + " sending to " + theApplet + ": "
- + script);
+ Logger.debug(fullName + " sending to " + theApplet + ": " + script);
try {
- app.syncScript(script);
+ if (isSync)
+ app.syncScript(script);
+ else
+ sb.append(app.scriptWait(script, "output")).append("\n");
} catch (Exception e) {
- Logger.error(htmlName + " couldn't send to " + theApplet + ": "
- + script + ": " + e);
- }
+ String msg = htmlName + " couldn't send to " + theApplet + ": "
+ + script + ": " + e;
+ Logger.error(msg);
+ if (!isSync)
+ sb.append(msg);
+ }
}
+ return (isSync ? "" : sb.toString());
}
public Hashtable getRegistryInfo() {
Modified: trunk/Jmol/src/org/jmol/applet/JmolAppletRegistry.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/JmolAppletRegistry.java 2008-08-16 18:17:54 UTC (rev 9741)
+++ trunk/Jmol/src/org/jmol/applet/JmolAppletRegistry.java 2008-08-16 18:58:44 UTC (rev 9742)
@@ -151,24 +151,26 @@
Logger.error("unable to find target:" + targetName);
}
- synchronized public static Vector findApplets(String appletName, String mySyncId,
- String excludeName) {
- if (appletName != null && appletName.indexOf("__") < 0)
- appletName += "__" + mySyncId + "__";
+ synchronized public static Vector findApplets(String appletName,
+ String mySyncId,
+ String excludeName) {
+ String ext = "__" + mySyncId + "__";
Vector apps = new Vector();
- if (appletName != null && htRegistry.containsKey(appletName)) {
- apps.addElement(appletName);
- return apps;
+ if (appletName.equals("*") || appletName.equals(">")) {
+ Enumeration keys = htRegistry.keys();
+ while (keys.hasMoreElements()) {
+ appletName = (String) keys.nextElement();
+ if (!appletName.equals(excludeName) && appletName.indexOf(ext) > 0)
+ apps.addElement(appletName);
+ }
+ } else {
+ if (appletName.indexOf("__") < 0)
+ appletName += ext;
+ if (!htRegistry.containsKey(appletName))
+ appletName = "jmolApplet" + appletName;
+ if (!appletName.equals(excludeName) && htRegistry.containsKey(appletName))
+ apps.addElement(appletName);
}
- Enumeration keys = htRegistry.keys();
- while (keys.hasMoreElements()) {
- String theApplet = (String) keys.nextElement();
- if (excludeName != null && theApplet.equals(excludeName))
- continue;
- if (appletName == null && theApplet.indexOf("__" + mySyncId + "__") > 0
- || theApplet.equals(appletName))
- apps.addElement(theApplet);
- }
return apps;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-16 18:17:54 UTC (rev 9741)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-16 18:58:44 UTC (rev 9742)
@@ -903,7 +903,6 @@
if (token == null)
continue;
switch (token.tok) {
-
case Token.elseif:
case Token.ifcmd:
case Token.whilecmd:
@@ -974,9 +973,9 @@
case Token.rotate:
rotate(false, false);
break;
+ case Token.javascript:
case Token.script:
- case Token.javascript:
- script(token.tok == Token.javascript);
+ script(token.tok);
break;
case Token.function:
function();
@@ -4463,7 +4462,7 @@
if (errMsg != null && !isScriptCheck) {
if (errMsg.indexOf("file recognized as a script file:") >= 0) {
viewer.addLoadScript("-");
- script(false);
+ script(Token.script);
return;
}
evalError(errMsg);
@@ -5070,57 +5069,74 @@
"getSpinAxis:" + axisID);
}
- private void script(boolean isJavaScript) throws ScriptException {
- if (isJavaScript) {
- checkLength(2);
- if (!isSyntaxCheck)
- viewer.eval(parameterAsString(1));
- return;
- }
- if (getToken(1).tok != Token.string)
- error(ERROR_filenameExpected);
+ private void script(int tok) throws ScriptException {
+ boolean loadCheck = true;
+ boolean isCheck = false;
int lineNumber = 0;
int pc = 0;
int lineEnd = 0;
int pcEnd = 0;
int i = 2;
- String filename = parameterAsString(1);
- String theScript = null;
- if (filename.equalsIgnoreCase("inline")) {
- theScript = parameterExpression(2, 0, "_script", false).toString();
- i = iToken + 1;
+ String filename = null;
+ String theScript = parameterAsString(1);
+ if (tok == Token.javascript) {
+ checkLength(2);
+ if (!isSyntaxCheck)
+ viewer.eval(theScript);
+ return;
}
- boolean loadCheck = true;
- boolean isCheck = false;
- String option = optParameterAsString(i);
- if (option.equalsIgnoreCase("check")) {
- isCheck = true;
- option = optParameterAsString(++i);
+ if (theScript.equalsIgnoreCase("applet")) {
+ // script APPLET x "....."
+ String appID = parameterAsString(2);
+ theScript = parameterExpression(3, 0, "_script", false).toString();
+ checkLength(iToken + 1);
+ if (isSyntaxCheck)
+ return;
+ if (appID.length() == 0 || appID.equals("all"))
+ appID = "*";
+ if (!appID.equals(".")) {
+ viewer.eval(appID + "\1" + theScript);
+ if (!appID.equals("*"))
+ return;
+ }
+ } else {
+ if (getToken(1).tok != Token.string)
+ error(ERROR_filenameExpected);
+ filename = theScript;
+ if (filename.equalsIgnoreCase("inline")) {
+ theScript = parameterExpression(2, 0, "_script", false).toString();
+ i = iToken + 1;
+ }
+ String option = optParameterAsString(i);
+ if (option.equalsIgnoreCase("check")) {
+ isCheck = true;
+ option = optParameterAsString(++i);
+ }
+ if (option.equalsIgnoreCase("noload")) {
+ loadCheck = false;
+ option = optParameterAsString(++i);
+ }
+ if (option.equalsIgnoreCase("line") || option.equalsIgnoreCase("lines")) {
+ i++;
+ lineEnd = lineNumber = Math.max(intParameter(i++), 0);
+ if (checkToken(i))
+ if (getToken(i++).tok == Token.minus)
+ lineEnd = (checkToken(i) ? intParameter(i++) : 0);
+ else
+ error(ERROR_invalidArgument);
+ } else if (option.equalsIgnoreCase("command")
+ || option.equalsIgnoreCase("commands")) {
+ i++;
+ pc = Math.max(intParameter(i++) - 1, 0);
+ pcEnd = pc + 1;
+ if (checkToken(i))
+ if (getToken(i++).tok == Token.minus)
+ pcEnd = (checkToken(i) ? intParameter(i++) : 0);
+ else
+ error(ERROR_invalidArgument);
+ }
+ checkLength(i);
}
- if (option.equalsIgnoreCase("noload")) {
- loadCheck = false;
- option = optParameterAsString(++i);
- }
- if (option.equalsIgnoreCase("line") || option.equalsIgnoreCase("lines")) {
- i++;
- lineEnd = lineNumber = Math.max(intParameter(i++), 0);
- if (checkToken(i))
- if (getToken(i++).tok == Token.minus)
- lineEnd = (checkToken(i) ? intParameter(i++) : 0);
- else
- error(ERROR_invalidArgument);
- } else if (option.equalsIgnoreCase("command")
- || option.equalsIgnoreCase("commands")) {
- i++;
- pc = Math.max(intParameter(i++) - 1, 0);
- pcEnd = pc + 1;
- if (checkToken(i))
- if (getToken(i++).tok == Token.minus)
- pcEnd = (checkToken(i) ? intParameter(i++) : 0);
- else
- error(ERROR_invalidArgument);
- }
- checkLength(i);
if (isSyntaxCheck && !isScriptCheck)
return;
if (isScriptCheck)
@@ -12054,7 +12070,7 @@
return evaluateWrite(args);
case Token.script:
case Token.javascript:
- return evaluateScript(args, tok == Token.javascript);
+ return evaluateScript(args, tok);
case Token.within:
return evaluateWithin(args);
case Token.getproperty:
@@ -12585,18 +12601,32 @@
return addX(write(args));
}
- private boolean evaluateScript(Token[] args, boolean isJavaScript)
+ private boolean evaluateScript(Token[] args, int tok)
throws ScriptException {
- if (args.length != 1)
+ if (tok == Token.javascript && args.length != 1 || args.length == 0
+ || args.length > 2)
return false;
if (isSyntaxCheck)
return addX("");
String s = Token.sValue(args[0]);
- if (isJavaScript)
- return addX(viewer.eval(s));
StringBuffer sb = new StringBuffer();
- runScript(s, sb);
- return addX(sb.toString());
+ switch (tok) {
+ case Token.script:
+ String appID = (args.length == 2 ? Token.sValue(args[1]) : ".");
+ //options include * > . or an appletID with or without "jmolApplet"
+ if (!appID.equals("."))
+ sb.append(viewer.eval(appID + "\1" + s));
+ if (appID.equals(".") || appID.equals("*"))
+ runScript(s, sb);
+ break;
+ case Token.javascript:
+ sb.append(viewer.eval(s));
+ break;
+ }
+ s = sb.toString();
+ float f;
+ return (Float.isNaN(f = Parser.parseFloatStrict(s)) ? addX(s) : s
+ .indexOf(".") >= 0 ? addX(f) : addX(Parser.parseInt(s)));
}
private boolean evaluateData(Token[] args) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-16 18:17:54 UTC (rev 9741)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-16 18:58:44 UTC (rev 9742)
@@ -3,7 +3,30 @@
version=11.6.RC8_dev
-# new feature: print getProperty("modelinfo.models[3].file") syntax
+# new feature: script APPLET appletName "some script"
+# --allows direct inter-applet communication independent of set SYNC
+# --appletName can be * (all applets), > (other applets), . (this applet),
+# or an applet name such as "jmolApplet0" or just the extension "0"
+# --for *, the current applet always reports LAST
+# new feature: x = script("some script", "appletName")
+# --same as above
+# --in addition, allows retrieval of information from another applet
+# for example:
+#
+# x = script("print getProperty(\"modelInfo.modelCount\")","B")
+#
+# gets the number of models loaded in applet jmolAppletB.
+#
+# x = script("show orientation moveto","jmolApplet2")
+#
+# gets the current orientation of applet jmolApplet2.
+#
+# xList = script("print getProperty(\"appletInfo.fullName\").split(\"__\")[1] + \":\" + script(\"show rotation\").trim()","*")
+#
+# gets a new-line-separated list of rotational quaternions for all applets with applet names.
+#
+#
+# new feature: print getProperty("modelInfo.models[3].file") syntax
# -----------------------------------------------------------------------------
Modified: trunk/Jmol/src/org/jmol/viewer/StatusManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2008-08-16 18:17:54 UTC (rev 9741)
+++ trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2008-08-16 18:58:44 UTC (rev 9742)
@@ -81,6 +81,7 @@
Hashtable messageQueue = new Hashtable();
int statusPtr = 0;
static int MAXIMUM_QUEUE_LENGTH = 16;
+ StringBuffer outputBuffer;
StatusManager(Viewer viewer) {
this.viewer = viewer;
@@ -194,6 +195,8 @@
synchronized void setScriptEcho(String strEcho, boolean isScriptQueued) {
if (strEcho == null) return;
setStatusChanged("scriptEcho", 0, strEcho, false);
+ if (outputBuffer != null)
+ outputBuffer.append(strEcho);
if (jmolStatusListener != null)
jmolStatusListener.notifyCallback(JmolConstants.CALLBACK_ECHO, new Object[] { "", strEcho,
new Integer(isScriptQueued ? 1 : 0) });
@@ -267,9 +270,9 @@
synchronized void setSync(String mouseCommand) {
if (syncingMouse) {
if (mouseCommand != null)
- syncSend(mouseCommand, null);
+ syncSend(mouseCommand, "*");
} else if (!syncingScripts)
- syncSend("!" + viewer.getMoveToText(minSyncRepeatMs / 1000f), null);
+ syncSend("!" + viewer.getMoveToText(minSyncRepeatMs / 1000f), "*");
}
synchronized void popupMenu(int x, int y) {
@@ -376,7 +379,7 @@
messageQueue.put(statusName, statusRecordSet);
}
- synchronized Vector getStatusChanged(String statusNameList) {
+ synchronized Object getStatusChanged(String statusNameList) {
/*
* returns a Vector of statusRecordSets, one per status type,
* where each statusRecordSet is itself a vector of vectors:
@@ -387,6 +390,15 @@
*
*/
Vector msgList = new Vector();
+ if (statusNameList.equals("output")) {
+ if (outputBuffer == null) {
+ outputBuffer = new StringBuffer();
+ return "";
+ }
+ String s = outputBuffer.toString();
+ outputBuffer = null;
+ return s;
+ }
if (setStatusList(statusNameList)) return msgList;
Enumeration e = messageQueue.keys();
int n = 0;
Modified: trunk/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Token.java 2008-08-16 18:17:54 UTC (rev 9741)
+++ trunk/Jmol/src/org/jmol/viewer/Token.java 2008-08-16 18:58:44 UTC (rev 9742)
@@ -517,11 +517,10 @@
final static int load = 1 | 1 << 9 | mathfunc | command;
final static int substructure = 2 | 1 << 9 | mathfunc;
- final static int script = 3 | 1 << 9 | mathfunc | command;
- final static int javascript = 4 | 1 << 9 | mathfunc | implicitStringCommand;
- final static int sin = 5 | 1 << 9 | mathfunc;
- final static int cos = 6 | 1 << 9 | mathfunc;
- final static int sqrt = 7 | 1 << 9 | mathfunc;
+ final static int javascript = 3 | 1 << 9 | mathfunc | implicitStringCommand;
+ final static int sin = 4 | 1 << 9 | mathfunc;
+ final static int cos = 5 | 1 << 9 | mathfunc;
+ final static int sqrt = 6 | 1 << 9 | mathfunc;
// ___.xxx(a)
@@ -543,6 +542,7 @@
final static int random = 1 | 2 << 9 | mathfunc;
final static int data = 2 | 2 << 9 | mathfunc | command;
final static int cross = 3 | 2 << 9 | mathfunc;
+ final static int script = 4 | 2 << 9 | mathfunc | command;
// ___.xxx(a,b)
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-16 18:17:54 UTC (rev 9741)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-16 18:58:44 UTC (rev 9742)
@@ -3055,7 +3055,9 @@
// refresh(2) indicates this is a mouse motion -- not going through Eval script
// so we bypass Eval and mainline on the other viewer!
// refresh(-1) is used in stateManager to force no repaint)
- // refresh(3) is used by operations to ONLY do a repaint -- no syncing
+ // refresh(3) is used by operations to ONLY do a repaint -- no syncing
+ if (repaintManager == null)
+ return;
if (mode > 0)
repaintManager.refresh();
if (mode % 3 != 0 && statusManager.doSync())
@@ -3393,6 +3395,7 @@
/// direct no-queue use:
public String scriptWait(String strScript) {
+ System.out.println("Viewer scriptWait1 " + htmlName + " " + strScript + " ");
scriptManager.waitForQueue();
boolean doTranslateTemp = GT.getDoTranslate();
GT.setDoTranslate(false);
@@ -3404,6 +3407,7 @@
}
public Object scriptWaitStatus(String strScript, String statusList) {
+ System.out.println("Viewer scriptWait2 " + htmlName + " " + strScript);
scriptManager.waitForQueue();
boolean doTranslateTemp = GT.getDoTranslate();
GT.setDoTranslate(false);
@@ -3415,6 +3419,7 @@
public Object evalStringWaitStatus(String returnType, String strScript,
String statusList) {
+ System.out.println("Viewer scriptWait3 " + htmlName + " " + strScript);
scriptManager.waitForQueue();
return evalStringWaitStatus(returnType, strScript, statusList, false,
false, false);
@@ -3850,7 +3855,7 @@
statusManager.setStatusScriptStarted(iscript, script);
}
- Vector getStatusChanged(String statusNameList) {
+ Object getStatusChanged(String statusNameList) {
return statusManager.getStatusChanged(statusNameList);
}
@@ -6317,14 +6322,15 @@
}
public void syncScript(String script, String applet) {
- boolean isAll = ("*".equals(applet));
- boolean allButMe = (">".equals(applet));
- boolean disableSend = ("~".equals(applet));
- boolean justMe = disableSend || (".".equals(applet));
+ // * : all applets
+ // > : all OTHER applets
+ // . : just me
+ // ~ : disable send (just me)
+ boolean disableSend = "~".equals(applet);
//null same as ">" -- "all others"
- if (!justMe) {
- statusManager.syncSend(script, (isAll || allButMe ? null : applet));
- if (!isAll)
+ if (!disableSend && !".".equals(applet)) {
+ statusManager.syncSend(script, applet);
+ if (!"*".equals(applet))
return;
}
if (script.equalsIgnoreCase("on")) {
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|
|
From: <ha...@us...> - 2008-08-17 04:46:34
|
Revision: 9748
http://jmol.svn.sourceforge.net/jmol/?rev=9748&view=rev
Author: hansonr
Date: 2008-08-17 04:46:32 +0000 (Sun, 17 Aug 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-08-17 00:28:07 UTC (rev 9747)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-08-17 04:46:32 UTC (rev 9748)
@@ -1032,8 +1032,8 @@
models[modelDataIndex].defaultRotationRadius = (type
.startsWith("ramachandran") ? 260 : 12);
model.dataFrames.put(type, new Integer(modelDataIndex));
- }
- if (type.indexOf(" ") > 0 && type.indexOf("deriv") < 0) { //generic quaternion
+ }
+ if (type.startsWith("quaternion") && type.indexOf("deriv") < 0) { //generic quaternion
type = type.substring(0, type.indexOf(" "));
model.dataFrames.put(type, new Integer(modelDataIndex));
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-17 00:28:07 UTC (rev 9747)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-17 04:46:32 UTC (rev 9748)
@@ -3,6 +3,7 @@
version=11.6.RC8
+# bug fix: ramachandran / ramachandran r navigation problem
# code: Minor refactoring and pruning.
# --- Core applet now 715K (JmolApplet0.jar + _Core, _Jars, _Main, _Popup, and _Viewer)
# code: Pre-Jmol.js button controls removed, saving about 10K
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|
|
From: <ha...@us...> - 2008-08-17 05:03:17
|
Revision: 9749
http://jmol.svn.sourceforge.net/jmol/?rev=9749&view=rev
Author: hansonr
Date: 2008-08-17 05:03:13 +0000 (Sun, 17 Aug 2008)
Log Message:
-----------
quaternion scaling problem
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-08-17 04:46:32 UTC (rev 9748)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-08-17 05:03:13 UTC (rev 9749)
@@ -1029,8 +1029,6 @@
model.dataFrames = new Hashtable();
models[modelDataIndex].dataSourceFrame = modelIndex;
models[modelDataIndex].jmolFrameType = type;
- models[modelDataIndex].defaultRotationRadius = (type
- .startsWith("ramachandran") ? 260 : 12);
model.dataFrames.put(type, new Integer(modelDataIndex));
}
if (type.startsWith("quaternion") && type.indexOf("deriv") < 0) { //generic quaternion
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-17 04:46:32 UTC (rev 9748)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-08-17 05:03:13 UTC (rev 9749)
@@ -4576,6 +4576,7 @@
break;
}
runScript(script);
+ viewer.setRotationRadius(isQuaternion ? 12.5f : 260f, true);
viewer.loadShape(JmolConstants.SHAPE_ECHO);
showString("frame " + viewer.getModelNumberDotted(modelCount - 1) + " created: "
+ type);
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|
|
From: <ha...@us...> - 2008-08-20 02:38:03
|
Revision: 9754
http://jmol.svn.sourceforge.net/jmol/?rev=9754&view=rev
Author: hansonr
Date: 2008-08-20 02:38:00 +0000 (Wed, 20 Aug 2008)
Log Message:
-----------
version=11.6.RC9_dev # bug fix: print $planeA - capital letters in a draw name disallow finding it.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/shape/MeshCollection.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/shape/MeshCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/MeshCollection.java 2008-08-19 17:13:53 UTC (rev 9753)
+++ trunk/Jmol/src/org/jmol/shape/MeshCollection.java 2008-08-20 02:38:00 UTC (rev 9754)
@@ -406,15 +406,17 @@
if (JmolConstants.PREVIOUS_MESH_ID.equals(thisID))
return (previousMeshID == null ? meshCount - 1
: getIndexFromName(previousMeshID));
- if (TextFormat.isWild(thisID))
+ if (TextFormat.isWild(thisID)) {
+ thisID = thisID.toLowerCase();
for (int i = meshCount; --i >= 0;) {
if (meshes[i] != null
&& TextFormat.isMatch(meshes[i].thisID, thisID, true, true))
return i;
}
+ }
else
for (int i = meshCount; --i >= 0;) {
- if (meshes[i] != null && thisID.equals(meshes[i].thisID))
+ if (meshes[i] != null && thisID.equalsIgnoreCase(meshes[i].thisID))
return i;
}
return -1;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-19 17:13:53 UTC (rev 9753)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-20 02:38:00 UTC (rev 9754)
@@ -3,7 +3,7 @@
version=11.6.RC9_dev
-# SVN TEST
+# bug fix: print $planeA - capital letters in a draw name disallow finding it.
# -----------------------------------------------------------------------------
#version=11.6.RC8
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|
|
From: <ha...@us...> - 2008-08-20 06:17:51
|
Revision: 9755
http://jmol.svn.sourceforge.net/jmol/?rev=9755&view=rev
Author: hansonr
Date: 2008-08-20 06:17:47 +0000 (Wed, 20 Aug 2008)
Log Message:
-----------
11.6.RC9 VERSION
# new feature: getProperty PointGroupInfo
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2008-08-20 02:38:00 UTC (rev 9754)
+++ trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2008-08-20 06:17:47 UTC (rev 9755)
@@ -19,7 +19,8 @@
public abstract String getPointGroupName();
public abstract String getPointGroupInfo(int modelIndex, boolean asDraw,
- String type, int index, float scale);
+ String type, int index, float scale,
+ Hashtable info);
public abstract void setSpaceGroup(boolean doNormalize);
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-20 02:38:00 UTC (rev 9754)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-20 06:17:47 UTC (rev 9755)
@@ -425,19 +425,25 @@
}
public String calculatePointGroup(BitSet bsAtoms) {
- return calculatePointGroupForFirstModel(bsAtoms, true, false, false, null, 0, 0);
+ return calculatePointGroupForFirstModel(bsAtoms, true, false, false, null, 0, 0, null);
}
+ public Hashtable getPointGroupInfo(BitSet bsAtoms) {
+ Hashtable info = new Hashtable();
+ calculatePointGroupForFirstModel(bsAtoms, false, true, false, null, 0, 0, info);
+ return info;
+ }
+
public String getPointGroupAsString(BitSet bsAtoms, boolean asDraw,
String type, int index, float scale) {
- return calculatePointGroupForFirstModel(bsAtoms, false, true, asDraw, type, index, scale);
+ return calculatePointGroupForFirstModel(bsAtoms, false, true, asDraw, type, index, scale, null);
}
private String calculatePointGroupForFirstModel(BitSet bsAtoms,
boolean forceNew,
boolean doAll,
boolean asDraw, String type,
- int index, float scale) {
+ int index, float scale, Hashtable info) {
int modelIndex = viewer.getCurrentModelIndex();
int iAtom = BitSetUtil.firstSetBit(bsAtoms);
if (modelIndex < 0 && iAtom >= 0)
@@ -466,7 +472,7 @@
if (doAll)
return (modelCount > 1 ? "frame " + getModelNumberDotted(modelIndex)
+ "; " : "")
- + symmetry.getPointGroupInfo(modelIndex, asDraw, type, index, scale);
+ + symmetry.getPointGroupInfo(modelIndex, asDraw, type, index, scale, info);
return symmetry.getPointGroupName();
}
@@ -789,5 +795,6 @@
super.deleteAtoms(-1, 0, 0, null, null);
return bsDeleted;
}
+
}
Modified: trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-20 02:38:00 UTC (rev 9754)
+++ trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-20 06:17:47 UTC (rev 9755)
@@ -25,6 +25,9 @@
package org.jmol.symmetry;
import java.util.BitSet;
+import java.util.Hashtable;
+import java.util.Vector;
+
import javax.vecmath.Point3f;
import javax.vecmath.Vector3f;
@@ -120,7 +123,8 @@
private int nAtoms;
private float radius;
private float distanceTolerance = 0.2f;
- private float linearTolerance = 0.99f; // 8 degrees
+ private float linearTolerance = 8f;
+ private float cosTolerance = 0.99f; // 8 degrees
private String name = "C_1?";
private Operation principalAxis = new Operation(null);
private Operation principalPlane = new Operation(null);
@@ -138,7 +142,8 @@
PointGroup(Atom[] atomset, BitSet bsAtoms, boolean haveVibration,
float distanceTolerance, float linearTolerance) {
this.distanceTolerance = distanceTolerance;
- this.linearTolerance = (float) (Math.cos(linearTolerance / 180 * Math.PI));
+ this.linearTolerance = linearTolerance;
+ cosTolerance = (float) (Math.cos(linearTolerance / 180 * Math.PI));
Point3f[] atoms;
if ((atoms = getAtoms(atomset, bsAtoms)) == null) {
@@ -419,12 +424,12 @@
private boolean isParallel(Vector3f v1, Vector3f v2) {
// note -- these MUST be unit vectors
- return (Math.abs(v1.dot(v2)) >= linearTolerance);
+ return (Math.abs(v1.dot(v2)) >= cosTolerance);
}
private boolean isPerpendicular(Vector3f v1, Vector3f v2) {
// note -- these MUST be unit vectors
- return (Math.abs(v1.dot(v2)) <= 1 - linearTolerance);
+ return (Math.abs(v1.dot(v2)) <= 1 - cosTolerance);
}
int maxElement = 0;
@@ -801,6 +806,7 @@
int type;
int order;
int index;
+ int typeIndex;
Vector3f normalOrAxis;
Operation() {
@@ -844,7 +850,7 @@
}
String getInfo(int modelIndex, boolean asDraw, String type, int index,
- float scaleFactor) {
+ float scaleFactor, Hashtable info) {
Vector3f v = new Vector3f();
Operation op;
if (scaleFactor == 0)
@@ -855,7 +861,7 @@
nType[axes[i][j].type][0]++;
StringBuffer sb = new StringBuffer("# " + nAtoms + " atoms\n");
if (asDraw) {
- boolean haveType = (type.length() > 0);
+ boolean haveType = (type != null && type.length() > 0);
boolean anyProperAxis = (type.equalsIgnoreCase("Cn"));
boolean anyImproperAxis = (type.equalsIgnoreCase("Sn"));
sb.append("set perspectivedepth off;\n");
@@ -931,9 +937,10 @@
sb.append(", nSn=" + nType[OPERATION_IMPROPER_AXIS][0]);
sb.append(": ");
for (int i = maxAxis; --i >= 2;)
- if (nAxes[i] > 0)
- sb.append(" n" + (i < firstProper ? "S" : "C") + (i % firstProper)
- + "=" + nAxes[i]);
+ if (nAxes[i] > 0) {
+ String s = " n" + (i < firstProper ? "S" : "C") + (i % firstProper);
+ sb.append(s + "=" + nAxes[i]);
+ }
sb.append(";\n");
} else {
int n = 0;
@@ -942,19 +949,30 @@
if (nAxes[i] > 0) {
n = nUnique[i];
String label = axes[i][0].getLabel();
+ if (info != null)
+ info.put("n" + label, new Integer(nAxes[i]));
sb.append("\n\n" + name + "\tn" + label + "\t" + nAxes[i] + "\t" + n);
n *= nAxes[i];
nTotal += n;
nType[axes[i][0].type][1] += n;
+ Vector vinfo = (info == null ? null : new Vector());
for (int j = 0; j < nAxes[i]; j++) {
+ axes[i][j].typeIndex = j + 1;
+ if (vinfo != null) {
+ vinfo.add(axes[i][j].normalOrAxis);
+ }
sb.append("\n" + name + "\t" + label + "_" + (j + 1) + "\t"
+ axes[i][j].normalOrAxis);
}
+ if (info != null)
+ info.put(label, vinfo);
}
}
if (haveInversionCenter) {
nTotal++;
sb.append("\n\n" + name + "\tCi\t" + Escape.escape(center));
+ if (info != null)
+ info.put("Ci", center);
}
sb.append("\n");
sb.append("\n" + name + "\ttype\tnType\tnUnique");
@@ -977,6 +995,25 @@
sb.append(name + "\t\tTOTAL\t");
TextFormat.rFill(sb, " ", nTotal + "\n");
+
+ if (info != null) {
+ info.put("name", name);
+ info.put("nAtoms", new Integer(nAtoms));
+ info.put("nTotal", new Integer(nTotal));
+ info.put("nCi", new Integer(haveInversionCenter ? 1 : 0));
+ info.put("nCs", new Integer(nAxes[0]));
+ info.put("nCn", new Integer(nType[OPERATION_PROPER_AXIS][0]));
+ info.put("nSn", new Integer(nType[OPERATION_IMPROPER_AXIS][0]));
+ info.put("distanceTolerance", new Float(distanceTolerance));
+ info.put("linearTolerance", new Float(linearTolerance));
+ info.put("detail", sb.toString().replace('\n', ';'));
+ if (principalAxis.index > 0)
+ info.put("principalAxis", principalAxis.getLabel() + "["
+ + principalAxis.typeIndex + "]");
+ if (principalPlane.index > 0)
+ info.put("principalPlane", principalPlane.getLabel() + "["
+ + principalPlane.typeIndex + "]");
+ }
}
return sb.toString();
}
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2008-08-20 02:38:00 UTC (rev 9754)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2008-08-20 06:17:47 UTC (rev 9755)
@@ -83,8 +83,9 @@
return pointGroup.getName();
}
- public String getPointGroupInfo(int modelIndex, boolean asDraw, String type, int index, float scale) {
- return pointGroup.getInfo(modelIndex, asDraw, type, index, scale);
+ public String getPointGroupInfo(int modelIndex, boolean asDraw, String type,
+ int index, float scale, Hashtable info) {
+ return pointGroup.getInfo(modelIndex, asDraw, type, index, scale, info);
}
// SpaceGroup methods
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-20 02:38:00 UTC (rev 9754)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-20 06:17:47 UTC (rev 9755)
@@ -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=11.6.RC9_dev
+version=11.6.RC9
+# new feature: getProperty PointGroupInfo
+# bug fix: show pointgroup draw null pointer exception
# bug fix: print $planeA - capital letters in a draw name disallow finding it.
# -----------------------------------------------------------------------------
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2008-08-20 02:38:00 UTC (rev 9754)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2008-08-20 06:17:47 UTC (rev 9755)
@@ -80,6 +80,7 @@
"evaluate" , "<expression>", "",
"menu" , "<type>", "current",
"minimizationInfo", "", "",
+ "PointGroupInfo" , atomExpression, "(visible)",
};
private final static int PROP_APPLET_INFO = 0;
@@ -118,7 +119,8 @@
private final static int PROP_EVALUATE = 28;
private final static int PROP_MENU = 29;
private final static int PROP_MINIMIZATION_INFO = 30;
- private final static int PROP_COUNT = 31;
+ private final static int PROP_POINTGROUP_INFO = 31;
+ private final static int PROP_COUNT = 32;
//// static methods used by Eval and Viewer ////
@@ -354,6 +356,8 @@
return viewer.getShapeInfo();
case PROP_STATE_INFO:
return viewer.getStateInfo(myParam.toString());
+ case PROP_POINTGROUP_INFO:
+ return viewer.getPointGroupInfo(myParam);
case PROP_TRANSFORM_INFO:
return viewer.getMatrixRotate();
case PROP_DATA_INFO:
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-20 02:38:00 UTC (rev 9754)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-20 06:17:47 UTC (rev 9755)
@@ -6516,6 +6516,10 @@
return modelSet.calculatePointGroup(selectionManager.bsSelection);
}
+ public Hashtable getPointGroupInfo(Object atomExpression) {
+ return modelSet.getPointGroupInfo(getAtomBitSet(atomExpression));
+ }
+
public String getPointGroupAsString(boolean asDraw, String type, int index,
float scale) {
return modelSet.getPointGroupAsString(selectionManager.bsSelection, asDraw,
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-20 13:11:16
|
Revision: 9756
http://jmol.svn.sourceforge.net/jmol/?rev=9756&view=rev
Author: hansonr
Date: 2008-08-20 13:11:10 +0000 (Wed, 20 Aug 2008)
Log Message:
-----------
version=11.6.RC9 # code: more efficient return of point group information and calculation
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2008-08-20 06:17:47 UTC (rev 9755)
+++ trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2008-08-20 13:11:10 UTC (rev 9756)
@@ -11,16 +11,18 @@
public interface SymmetryInterface {
- public abstract void setPointGroup(Atom[] atomset, BitSet bsAtoms,
+ public abstract SymmetryInterface setPointGroup(
+ SymmetryInterface pointGroupPrevious,
+ Atom[] atomset, BitSet bsAtoms,
boolean haveVibration,
float distanceTolerance,
float linearTolerance);
public abstract String getPointGroupName();
- public abstract String getPointGroupInfo(int modelIndex, boolean asDraw,
- String type, int index, float scale,
- Hashtable info);
+ public abstract Object getPointGroupInfo(int modelIndex, boolean asDraw,
+ boolean asInfo, String type,
+ int index, float scale);
public abstract void setSpaceGroup(boolean doNormalize);
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-08-20 06:17:47 UTC (rev 9755)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-08-20 13:11:10 UTC (rev 9756)
@@ -1339,8 +1339,10 @@
atoms[i].add(center);
} else {
ptTemp.add(atoms[i]);
+ System.out.println((Point3f)atoms[i]);
matTemp.transform(atoms[i]);
ptTemp.sub(atoms[i]);
+ System.out.println((Point3f)atoms[i]);
}
taint(i, TAINT_COORD);
n++;
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-20 06:17:47 UTC (rev 9755)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-20 13:11:10 UTC (rev 9756)
@@ -425,25 +425,27 @@
}
public String calculatePointGroup(BitSet bsAtoms) {
- return calculatePointGroupForFirstModel(bsAtoms, true, false, false, null, 0, 0, null);
+ return (String) calculatePointGroupForFirstModel(bsAtoms, false,
+ false, false, null, 0, 0);
}
public Hashtable getPointGroupInfo(BitSet bsAtoms) {
- Hashtable info = new Hashtable();
- calculatePointGroupForFirstModel(bsAtoms, false, true, false, null, 0, 0, info);
- return info;
+ return (Hashtable) calculatePointGroupForFirstModel(bsAtoms, false,
+ false, true, null, 0, 0);
}
public String getPointGroupAsString(BitSet bsAtoms, boolean asDraw,
String type, int index, float scale) {
- return calculatePointGroupForFirstModel(bsAtoms, false, true, asDraw, type, index, scale, null);
+ return (String) calculatePointGroupForFirstModel(bsAtoms, true,
+ asDraw, false, type, index, scale);
}
- private String calculatePointGroupForFirstModel(BitSet bsAtoms,
- boolean forceNew,
+ SymmetryInterface pointGroup;
+ private Object calculatePointGroupForFirstModel(BitSet bsAtoms,
boolean doAll,
- boolean asDraw, String type,
- int index, float scale, Hashtable info) {
+ boolean asDraw,
+ boolean asInfo, String type,
+ int index, float scale) {
int modelIndex = viewer.getCurrentModelIndex();
int iAtom = BitSetUtil.firstSetBit(bsAtoms);
if (modelIndex < 0 && iAtom >= 0)
@@ -466,14 +468,18 @@
Object obj = getShapeProperty(JmolConstants.SHAPE_VECTORS, "mad", iAtom);
boolean haveVibration = (obj != null && ((Integer) obj).intValue() != 0 || viewer
.isVibrationOn());
- SymmetryInterface symmetry = (SymmetryInterface) Interface.getOptionInterface("symmetry.Symmetry");
- symmetry.setPointGroup(atoms, bs, haveVibration,
+ SymmetryInterface symmetry = (SymmetryInterface) Interface
+ .getOptionInterface("symmetry.Symmetry");
+ pointGroup = symmetry.setPointGroup(pointGroup, atoms, bs, haveVibration,
viewer.getPointGroupTolerance(0), viewer.getPointGroupTolerance(1));
- if (doAll)
- return (modelCount > 1 ? "frame " + getModelNumberDotted(modelIndex)
- + "; " : "")
- + symmetry.getPointGroupInfo(modelIndex, asDraw, type, index, scale, info);
- return symmetry.getPointGroupName();
+ if (!doAll && !asInfo)
+ return pointGroup.getPointGroupName();
+ Object ret = pointGroup.getPointGroupInfo(modelIndex, asDraw, asInfo, type,
+ index, scale);
+ if (asInfo)
+ return ret;
+ return (modelCount > 1 ? "frame " + getModelNumberDotted(modelIndex) + "; "
+ : "") + ret;
}
private BitSet modelsOf(BitSet bsAtoms, BitSet bsAllAtoms) {
Modified: trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-20 06:17:47 UTC (rev 9755)
+++ trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-20 13:11:10 UTC (rev 9756)
@@ -139,27 +139,48 @@
final private Point3f center = new Point3f();
- PointGroup(Atom[] atomset, BitSet bsAtoms, boolean haveVibration,
- float distanceTolerance, float linearTolerance) {
+ private Point3f[] atoms;
+ private int[] elements;
+
+ public static PointGroup getPointGroup(PointGroup pgLast, Atom[] atomset,
+ BitSet bsAtoms, boolean haveVibration,
+ float distanceTolerance,
+ float linearTolerance) {
+ PointGroup pg = new PointGroup();
+ return (pg.set(pgLast, atomset, bsAtoms, haveVibration, distanceTolerance,
+ linearTolerance) ? pg : pgLast);
+ }
+
+ private PointGroup() {
+ }
+
+ public boolean isEqual(PointGroup pg) {
+ if (pg == null)
+ return false;
+ if (this.linearTolerance != pg.linearTolerance
+ || this.distanceTolerance != pg.distanceTolerance
+ || this.nAtoms != pg.nAtoms)
+ return false;
+ for (int i = 0; i < nAtoms; i++) {
+ // real floating == 0 here because they must be IDENTICAL POSITIONS
+ if (elements[i] != pg.elements[i] || atoms[i].distance(pg.atoms[i]) != 0)
+ return false;
+ }
+ return true;
+ }
+
+ private boolean set(PointGroup pgLast, Atom[] atomset, BitSet bsAtoms,
+ boolean haveVibration, float distanceTolerance, float linearTolerance) {
this.distanceTolerance = distanceTolerance;
this.linearTolerance = linearTolerance;
cosTolerance = (float) (Math.cos(linearTolerance / 180 * Math.PI));
-
- Point3f[] atoms;
- if ((atoms = getAtoms(atomset, bsAtoms)) == null) {
+ if (!getAtomsAndElements(atomset, bsAtoms)) {
Logger.error("Too many atoms for point group calculation");
name = "point group not determined -- atomCount > " + ATOM_COUNT_MAX
+ " -- select fewer atoms and try again.";
- return;
+ return true;
}
- int[] elements = new int[atoms.length];
- int n = 0;
- for (int i = atomset.length; --i >= 0;)
- if (bsAtoms.get(i)) {
- int bondIndex = 1 + Math.max(3, atomset[i].getCovalentBondCount());
- elements[n++] = atomset[i].getElementNumber() * bondIndex;
- }
- getElementArrays(atoms, elements);
+ getElementCounts();
if (haveVibration) {
Point3f[] atomVibs = new Point3f[atoms.length];
for (int i = atoms.length; --i >= 0;) {
@@ -170,7 +191,9 @@
}
atoms = atomVibs;
}
- findInversionCenter(atoms, elements);
+ if (isEqual(pgLast))
+ return false;
+ findInversionCenter();
if (isLinear(atoms)) {
if (haveInversionCenter) {
@@ -185,17 +208,17 @@
axes[0] = new Operation[1];
principalPlane = axes[0][nAxes[0]++] = new Operation(vTemp);
}
- return;
+ return true;
}
axes[0] = new Operation[15];
int nPlanes = 0;
- findCAxes(atoms, elements);
- nPlanes = findPlanes(atoms, elements);
- findAdditionalAxes(nPlanes, atoms, elements);
+ findCAxes();
+ nPlanes = findPlanes();
+ findAdditionalAxes(nPlanes);
/* flow chart contribution of Dean Johnston */
- n = getHighestOrder();
+ int n = getHighestOrder();
if (nAxes[c3] > 1) {
// must be Ix, Ox, or Tx
if (nAxes[c5] > 1) {
@@ -226,11 +249,11 @@
if (n < 2) {
if (nPlanes == 1) {
name = "Cs";
- return;
+ return true;
}
if (haveInversionCenter) {
name = "Ci";
- return;
+ return true;
}
name = "C1";
} else if ((n % 2) == 1 && nAxes[c2] > 0 || (n % 2) == 0 && nAxes[c2] > 1) {
@@ -280,6 +303,7 @@
name = "C" + n + "h";
}
}
+ return true;
}
private Operation setPrincipalAxis(int n, int nPlanes) {
@@ -324,17 +348,20 @@
}
private final static int ATOM_COUNT_MAX = 100;
- private Atom[] getAtoms(Atom[] atomset, BitSet bsAtoms) {
+ private boolean getAtomsAndElements(Atom[] atomset, BitSet bsAtoms) {
int atomCount = BitSetUtil.cardinalityOf(bsAtoms);
if (atomCount > ATOM_COUNT_MAX)
- return null;
- Atom[] atoms = new Atom[atomCount];
- if (atomCount == 0)
- return atoms;
+ return false;
+ Point3f[] atoms = this.atoms = new Point3f[atomCount];
+ elements = new int[atomCount];
+ if (atomCount == 0)
+ return true;
nAtoms = 0;
for (int i = BitSetUtil.length(bsAtoms); --i >= 0;)
if (bsAtoms.get(i)) {
- atoms[nAtoms] = atomset[i];
+ atoms[nAtoms] = new Point3f(atomset[i]);
+ int bondIndex = 1 + Math.max(3, atomset[i].getCovalentBondCount());
+ elements[nAtoms] = atomset[i].getElementNumber() * bondIndex;
center.add(atoms[nAtoms++]);
}
center.scale(1f / nAtoms);
@@ -344,19 +371,18 @@
centerAtomIndex = i;
radius = Math.max(radius, r);
}
- return atoms;
+ return true;
}
- private void findInversionCenter(Point3f[] atoms, int[] elements) {
- haveInversionCenter = checkOperation(atoms, elements, null, center, -1);
+ private void findInversionCenter() {
+ haveInversionCenter = checkOperation(null, center, -1);
if (haveInversionCenter) {
axes[1] = new Operation[1];
axes[1][0] = new Operation();
}
}
- private boolean checkOperation(Point3f[] atoms, int[] elements, Quaternion q,
- Point3f center, int iOrder) {
+ private boolean checkOperation(Quaternion q, Point3f center, int iOrder) {
Point3f pt = new Point3f();
int nFound = 0;
boolean isInversion = (iOrder < firstProper);
@@ -435,7 +461,7 @@
int maxElement = 0;
int[] eCounts;
- private void getElementArrays(Point3f[] atoms, int[] elements) {
+ private void getElementCounts() {
for (int i = atoms.length; --i >= 0;) {
int e1 = elements[i];
if (e1 > maxElement)
@@ -443,10 +469,10 @@
}
eCounts = new int[++maxElement];
for (int i = atoms.length; --i >= 0;)
- eCounts[elements[i]]++;
+ eCounts[elements[i]]++;
}
- private int findCAxes(Point3f[] atoms, int[] elements) {
+ private int findCAxes() {
Vector3f v1 = new Vector3f();
Vector3f v2 = new Vector3f();
Vector3f v3 = new Vector3f();
@@ -474,12 +500,12 @@
v1.normalize();
v2.normalize();
if (isParallel(v1, v2)) {
- getAllAxes(v1, atoms, elements);
+ getAllAxes(v1);
continue;
}
if (nAxes[c2] < axesMaxN[c2]) {
v3.set(pt);
- getAllAxes(v3, atoms, elements);
+ getAllAxes(v3);
}
// look for the axis perpendicular to the A -- 0 -- B plane
@@ -491,7 +517,7 @@
continue;
if (nAxes[iOrder] < axesMaxN[iOrder]) {
v3.cross(v1, v2);
- checkAxisOrder(atoms, elements, iOrder, v3, center);
+ checkAxisOrder(iOrder, v3, center);
}
}
}
@@ -515,7 +541,7 @@
v3.add(vs[k]);
if (v3.length() < 1.0)
continue;
- checkAxisOrder(atoms, elements, c3, v3, center);
+ checkAxisOrder(c3, v3, center);
}
// Now check for triples of elements that will define
@@ -549,15 +575,15 @@
v1.normalize();
v2.normalize();
v3.cross(v1, v2);
- getAllAxes(v3, atoms, elements);
-// checkAxisOrder(atoms, elements, 3, v3, center);
+ getAllAxes(v3);
+// checkAxisOrder(3, v3, center);
pt.set(atoms[i]);
pt.add(atoms[j]);
pt.add(atoms[k]);
v1.set(pt);
v1.normalize();
if (!isParallel(v1, v3))
- getAllAxes(v1, atoms, elements);
+ getAllAxes(v1);
if (nAxes[c5] == axesMaxN[c5])
break out;
}
@@ -594,17 +620,17 @@
v1.set(vs[i]);
v1.sub(vs[j]);
}
- checkAxisOrder(atoms, elements, c2, v1, center);
+ checkAxisOrder(c2, v1, center);
}
return getHighestOrder();
}
- private void getAllAxes(Vector3f v3, Point3f[] atoms, int[] elements) {
+ private void getAllAxes(Vector3f v3) {
for (int o = c2; o < maxAxis; o++)
if (nAxes[o] < axesMaxN[o])
- checkAxisOrder(atoms, elements, o, v3, center);
+ checkAxisOrder(o, v3, center);
}
private int getHighestOrder() {
@@ -620,8 +646,7 @@
return n;
}
- private boolean checkAxisOrder(Point3f[] atoms, int[] elements, int iOrder,
- Vector3f v, Point3f center) {
+ private boolean checkAxisOrder(int iOrder, Vector3f v, Point3f center) {
switch (iOrder) {
case c8:
if (nAxes[c3] > 0)
@@ -646,35 +671,35 @@
if (haveAxis(iOrder, v))
return false;
Quaternion q = new Quaternion(v, (iOrder < firstProper ? 180 : 0) + 360 / (iOrder % firstProper));
- if (!checkOperation(atoms, elements, q, center, iOrder))
+ if (!checkOperation(q, center, iOrder))
return false;
addAxis(iOrder, v);
// check for Sn:
switch (iOrder) {
case c2:
- checkAxisOrder(atoms, elements, s4, v, center);//D2d, D4h, D6d
+ checkAxisOrder(s4, v, center);//D2d, D4h, D6d
break;
case c3:
- checkAxisOrder(atoms, elements, s3, v, center);//C3h, D3h
+ checkAxisOrder(s3, v, center);//C3h, D3h
if (haveInversionCenter)
addAxis(s6, v);
break;
case c4:
addAxis(c2, v);
- checkAxisOrder(atoms, elements, s4, v, center);//D2d, D4h, D6d
- checkAxisOrder(atoms, elements, s8, v, center);//D4d
+ checkAxisOrder(s4, v, center);//D2d, D4h, D6d
+ checkAxisOrder(s8, v, center);//D4d
break;
case c5:
- checkAxisOrder(atoms, elements, s5, v, center); //C5h, D5h
+ checkAxisOrder(s5, v, center); //C5h, D5h
if (haveInversionCenter)
addAxis(s10, v);
break;
case c6:
addAxis(c2, v);
addAxis(c3, v);
- checkAxisOrder(atoms, elements, s3, v, center);//C6h, D6h
- checkAxisOrder(atoms, elements, s6, v, center);//C6h, D6h
- checkAxisOrder(atoms, elements, s12, v, center);//D6d
+ checkAxisOrder(s3, v, center);//C6h, D6h
+ checkAxisOrder(s6, v, center);//C6h, D6h
+ checkAxisOrder(s12, v, center);//D6d
break;
case c8:
//note -- D8d would have a S16 axis. This will not be found.
@@ -705,7 +730,7 @@
return false;
}
- private int findPlanes(Point3f[] atoms, int[] elements) {
+ private int findPlanes() {
Point3f pt = new Point3f();
Vector3f v1 = new Vector3f();
Vector3f v2 = new Vector3f();
@@ -734,7 +759,7 @@
if (!isParallel(v1, v2)) {
v3.cross(v1, v2);
v3.normalize();
- nPlanes = getPlane(nPlanes, v3, atoms, elements, center);
+ nPlanes = getPlane(nPlanes, v3, center);
}
// second, look for planes perpendicular to the A -- B line
@@ -742,7 +767,7 @@
v3.set(a2);
v3.sub(a1);
v3.normalize();
- nPlanes = getPlane(nPlanes, v3, atoms, elements, center);
+ nPlanes = getPlane(nPlanes, v3, center);
if (nPlanes == axesMaxN[0])
return nPlanes;
}
@@ -752,21 +777,19 @@
if (haveAxes)
for (int i = c2; i < maxAxis; i++)
for (int j = 0; j < nAxes[i]; j++)
- nPlanes = getPlane(nPlanes, axes[i][j].normalOrAxis, atoms, elements,
- center);
+ nPlanes = getPlane(nPlanes, axes[i][j].normalOrAxis, center);
return nPlanes;
}
- private int getPlane(int nPlanes, Vector3f v3, Point3f[] atoms,
- int[] elements, Point3f center2) {
+ private int getPlane(int nPlanes, Vector3f v3, Point3f center2) {
if (!haveAxis(0, v3)
- && checkOperation(atoms, elements, new Quaternion(v3, 180), center,
+ && checkOperation(new Quaternion(v3, 180), center,
-1))
axes[0][nAxes[0]++] = new Operation(v3);
return nAxes[0];
}
- private void findAdditionalAxes(int nPlanes, Point3f[] atoms, int[] elements) {
+ private void findAdditionalAxes(int nPlanes) {
Operation[] planes = axes[0];
int Cn = 0;
@@ -775,10 +798,10 @@
&& nAxes[Cn] == 0) {
// cross pairs of plane normals. We don't need many.
vTemp.cross(planes[0].normalOrAxis, planes[1].normalOrAxis);
- if (!checkAxisOrder(atoms, elements, Cn, vTemp, center)
+ if (!checkAxisOrder(Cn, vTemp, center)
&& nPlanes > 2) {
vTemp.cross(planes[1].normalOrAxis, planes[2].normalOrAxis);
- checkAxisOrder(atoms, elements, Cn - 1, vTemp, center);
+ checkAxisOrder(Cn - 1, vTemp, center);
}
}
if (nAxes[c2] == 0 && nPlanes > 2) {
@@ -786,7 +809,7 @@
for (int i = 0; i < nPlanes - 1; i++) {
for (int j = i + 1; j < nPlanes; j++) {
vTemp.add(planes[1].normalOrAxis, planes[2].normalOrAxis);
- if (checkAxisOrder(atoms, elements, c2, vTemp, center))
+ if (checkAxisOrder(c2, vTemp, center))
System.out.println("found a C2 axis by adding plane normals");
}
}
@@ -849,8 +872,15 @@
}
}
- String getInfo(int modelIndex, boolean asDraw, String type, int index,
- float scaleFactor, Hashtable info) {
+ String drawInfo;
+ String drawType = "";
+ Hashtable info;
+ String textInfo;
+
+ Object getInfo(int modelIndex, boolean asDraw, boolean asInfo, String type,
+ int index, float scaleFactor) {
+ if (asInfo)
+ info = new Hashtable();
Vector3f v = new Vector3f();
Operation op;
if (scaleFactor == 0)
@@ -862,6 +892,7 @@
StringBuffer sb = new StringBuffer("# " + nAtoms + " atoms\n");
if (asDraw) {
boolean haveType = (type != null && type.length() > 0);
+ drawType = (haveType ? type : "");
boolean anyProperAxis = (type.equalsIgnoreCase("Cn"));
boolean anyImproperAxis = (type.equalsIgnoreCase("Sn"));
sb.append("set perspectivedepth off;\n");
@@ -942,38 +973,43 @@
sb.append(s + "=" + nAxes[i]);
}
sb.append(";\n");
- } else {
- int n = 0;
- int nTotal = 1;
- for (int i = maxAxis; --i >= 0;) {
- if (nAxes[i] > 0) {
- n = nUnique[i];
- String label = axes[i][0].getLabel();
- if (info != null)
- info.put("n" + label, new Integer(nAxes[i]));
- sb.append("\n\n" + name + "\tn" + label + "\t" + nAxes[i] + "\t" + n);
- n *= nAxes[i];
- nTotal += n;
- nType[axes[i][0].type][1] += n;
- Vector vinfo = (info == null ? null : new Vector());
- for (int j = 0; j < nAxes[i]; j++) {
- axes[i][j].typeIndex = j + 1;
- if (vinfo != null) {
- vinfo.add(axes[i][j].normalOrAxis);
- }
- sb.append("\n" + name + "\t" + label + "_" + (j + 1) + "\t"
- + axes[i][j].normalOrAxis);
+ drawInfo = sb.toString();
+ return drawInfo;
+ }
+ int n = 0;
+ int nTotal = 1;
+ for (int i = maxAxis; --i >= 0;) {
+ if (nAxes[i] > 0) {
+ n = nUnique[i];
+ String label = axes[i][0].getLabel();
+ if (info != null)
+ info.put("n" + label, new Integer(nAxes[i]));
+ sb.append("\n\n" + name + "\tn" + label + "\t" + nAxes[i] + "\t" + n);
+ n *= nAxes[i];
+ nTotal += n;
+ nType[axes[i][0].type][1] += n;
+ Vector vinfo = (info == null ? null : new Vector());
+ for (int j = 0; j < nAxes[i]; j++) {
+ axes[i][j].typeIndex = j + 1;
+ if (vinfo != null) {
+ vinfo.add(axes[i][j].normalOrAxis);
}
- if (info != null)
- info.put(label, vinfo);
+ sb.append("\n" + name + "\t" + label + "_" + (j + 1) + "\t"
+ + axes[i][j].normalOrAxis);
}
+ if (info != null)
+ info.put(label, vinfo);
}
- if (haveInversionCenter) {
- nTotal++;
+ }
+ if (haveInversionCenter) {
+ nTotal++;
+ if (info == null)
sb.append("\n\n" + name + "\tCi\t" + Escape.escape(center));
- if (info != null)
- info.put("Ci", center);
- }
+ else
+ info.put("Ci", center);
+ }
+
+ if (info == null) {
sb.append("\n");
sb.append("\n" + name + "\ttype\tnType\tnUnique");
sb.append("\n" + name + "\tE\t 1\t 1");
@@ -995,26 +1031,23 @@
sb.append(name + "\t\tTOTAL\t");
TextFormat.rFill(sb, " ", nTotal + "\n");
-
- if (info != null) {
- info.put("name", name);
- info.put("nAtoms", new Integer(nAtoms));
- info.put("nTotal", new Integer(nTotal));
- info.put("nCi", new Integer(haveInversionCenter ? 1 : 0));
- info.put("nCs", new Integer(nAxes[0]));
- info.put("nCn", new Integer(nType[OPERATION_PROPER_AXIS][0]));
- info.put("nSn", new Integer(nType[OPERATION_IMPROPER_AXIS][0]));
- info.put("distanceTolerance", new Float(distanceTolerance));
- info.put("linearTolerance", new Float(linearTolerance));
- info.put("detail", sb.toString().replace('\n', ';'));
- if (principalAxis.index > 0)
- info.put("principalAxis", principalAxis.getLabel() + "["
- + principalAxis.typeIndex + "]");
- if (principalPlane.index > 0)
- info.put("principalPlane", principalPlane.getLabel() + "["
- + principalPlane.typeIndex + "]");
- }
+ textInfo = sb.toString();
+ return textInfo;
}
- return sb.toString();
+ info.put("name", name);
+ info.put("nAtoms", new Integer(nAtoms));
+ info.put("nTotal", new Integer(nTotal));
+ info.put("nCi", new Integer(haveInversionCenter ? 1 : 0));
+ info.put("nCs", new Integer(nAxes[0]));
+ info.put("nCn", new Integer(nType[OPERATION_PROPER_AXIS][0]));
+ info.put("nSn", new Integer(nType[OPERATION_IMPROPER_AXIS][0]));
+ info.put("distanceTolerance", new Float(distanceTolerance));
+ info.put("linearTolerance", new Float(linearTolerance));
+ info.put("detail", sb.toString().replace('\n', ';'));
+ if (principalAxis.index > 0)
+ info.put("principalAxis", principalAxis.normalOrAxis);
+ if (principalPlane.index > 0)
+ info.put("principalPlane", principalPlane.normalOrAxis);
+ return info;
}
}
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2008-08-20 06:17:47 UTC (rev 9755)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2008-08-20 13:11:10 UTC (rev 9756)
@@ -72,20 +72,32 @@
// as that will invalidate the Jar file modularization
}
- public void setPointGroup(Atom[] atomset, BitSet bsAtoms,
- boolean haveVibration, float distanceTolerance,
- float linearTolerance) {
- pointGroup = new PointGroup(atomset, bsAtoms, haveVibration,
+ public SymmetryInterface setPointGroup(SymmetryInterface siLast,
+ Atom[] atomset, BitSet bsAtoms,
+ boolean haveVibration,
+ float distanceTolerance,
+ float linearTolerance) {
+ pointGroup = PointGroup.getPointGroup(siLast == null ? null
+ : ((Symmetry) siLast).pointGroup, atomset, bsAtoms, haveVibration,
distanceTolerance, linearTolerance);
+ return this;
}
public String getPointGroupName() {
return pointGroup.getName();
}
- public String getPointGroupInfo(int modelIndex, boolean asDraw, String type,
- int index, float scale, Hashtable info) {
- return pointGroup.getInfo(modelIndex, asDraw, type, index, scale, info);
+ public Object getPointGroupInfo(int modelIndex, boolean asDraw,
+ boolean asInfo, String type, int index,
+ float scale) {
+ if (!asDraw && !asInfo && pointGroup.textInfo != null)
+ return pointGroup.textInfo;
+ else if (asDraw && pointGroup.drawInfo != null
+ && pointGroup.drawType.equals(type))
+ return pointGroup.drawInfo;
+ else if (asInfo && pointGroup.info != null)
+ return pointGroup.info;
+ return pointGroup.getInfo(modelIndex, asDraw, asInfo, type, index, scale);
}
// SpaceGroup methods
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-20 06:17:47 UTC (rev 9755)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-20 13:11:10 UTC (rev 9756)
@@ -3,6 +3,7 @@
version=11.6.RC9
+# code: more efficient return of point group information and calculation
# new feature: getProperty PointGroupInfo
# bug fix: show pointgroup draw null pointer exception
# bug fix: print $planeA - capital letters in a draw name disallow finding it.
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|
|
From: <ha...@us...> - 2008-08-22 14:00:35
|
Revision: 9760
http://jmol.svn.sourceforge.net/jmol/?rev=9760&view=rev
Author: hansonr
Date: 2008-08-22 14:00:28 +0000 (Fri, 22 Aug 2008)
Log Message:
-----------
11.6.RC10 VERSION
# bug fix -- draw pointgroup, write pointgroup draw
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-21 20:28:23 UTC (rev 9759)
+++ trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2008-08-22 14:00:28 UTC (rev 9760)
@@ -48,7 +48,7 @@
*
*/
-public class PointGroup {
+class PointGroup {
private final static int[] axesMaxN = new int[] {
15, // used for plane count
@@ -142,7 +142,7 @@
private Point3f[] atoms;
private int[] elements;
- public static PointGroup getPointGroup(PointGroup pgLast, Atom[] atomset,
+ static PointGroup getPointGroup(PointGroup pgLast, Atom[] atomset,
BitSet bsAtoms, boolean haveVibration,
float distanceTolerance,
float linearTolerance) {
@@ -154,7 +154,7 @@
private PointGroup() {
}
- public boolean isEqual(PointGroup pg) {
+ private boolean isEqual(PointGroup pg) {
if (pg == null)
return false;
if (this.linearTolerance != pg.linearTolerance
@@ -892,7 +892,7 @@
StringBuffer sb = new StringBuffer("# " + nAtoms + " atoms\n");
if (asDraw) {
boolean haveType = (type != null && type.length() > 0);
- drawType = (haveType ? type : "");
+ drawType = type = (haveType ? type : "");
boolean anyProperAxis = (type.equalsIgnoreCase("Cn"));
boolean anyImproperAxis = (type.equalsIgnoreCase("Sn"));
sb.append("set perspectivedepth off;\n");
@@ -1050,4 +1050,9 @@
info.put("principalPlane", principalPlane.normalOrAxis);
return info;
}
+
+ boolean isDrawType(String type) {
+ return (drawInfo != null && drawType.equals(type == null ? "" : type));
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2008-08-21 20:28:23 UTC (rev 9759)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2008-08-22 14:00:28 UTC (rev 9760)
@@ -92,8 +92,7 @@
float scale) {
if (!asDraw && !asInfo && pointGroup.textInfo != null)
return pointGroup.textInfo;
- else if (asDraw && pointGroup.drawInfo != null
- && pointGroup.drawType.equals(type))
+ else if (asDraw && pointGroup.isDrawType(type))
return pointGroup.drawInfo;
else if (asInfo && pointGroup.info != null)
return pointGroup.info;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-21 20:28:23 UTC (rev 9759)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-22 14:00:28 UTC (rev 9760)
@@ -3,6 +3,8 @@
version=11.6.RC10
+# bug fix -- draw pointgroup, write pointgroup draw
+
# -----------------------------------------------------------------------------
#version=11.6.RC9
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|
|
From: <ha...@us...> - 2008-08-22 21:16:00
|
Revision: 9761
http://jmol.svn.sourceforge.net/jmol/?rev=9761&view=rev
Author: hansonr
Date: 2008-08-22 21:15:55 +0000 (Fri, 22 Aug 2008)
Log Message:
-----------
version=11.6.RC10 # bug fix -- draw pointgroup, write pointgroup draw
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/shape/Measures.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PickingManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/shape/Measures.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Measures.java 2008-08-22 14:00:28 UTC (rev 9760)
+++ trunk/Jmol/src/org/jmol/shape/Measures.java 2008-08-22 21:15:55 UTC (rev 9761)
@@ -226,6 +226,8 @@
}
public Object getProperty(String property, int index) {
+ if ("pending".equals(property))
+ return measurementPending;
if ("count".equals(property))
return new Integer(measurementCount);
if ("countPlusIndices".equals(property))
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-22 14:00:28 UTC (rev 9760)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-22 21:15:55 UTC (rev 9761)
@@ -4,6 +4,7 @@
version=11.6.RC10
# bug fix -- draw pointgroup, write pointgroup draw
+# bug fix -- set picking spin, also compatibility of set picking spin and doing measurements
# -----------------------------------------------------------------------------
Modified: trunk/Jmol/src/org/jmol/viewer/PickingManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PickingManager.java 2008-08-22 14:00:28 UTC (rev 9760)
+++ trunk/Jmol/src/org/jmol/viewer/PickingManager.java 2008-08-22 21:15:55 UTC (rev 9761)
@@ -184,15 +184,14 @@
viewer.script("zoomTo " + Escape.escape(ptClicked));
return;
case JmolConstants.PICKING_SPIN:
- if (viewer.getSpinOn()) {
+ if (viewer.getSpinOn() || viewer.getPendingMeasurement() != null) {
+ resetMeasurement();
viewer.script("spin off");
return;
}
if (measurementQueued.getCount() >= 2)
resetMeasurement();
int queuedAtomCount = measurementQueued.getCount();
- if (queuedAtomCount < 2)
- return;
if (queuedAtomCount == 1) {
if (ptClicked == null) {
if (measurementQueued.getAtomIndex(1) == atomIndex)
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-22 14:00:28 UTC (rev 9760)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-22 21:15:55 UTC (rev 9761)
@@ -2726,6 +2726,10 @@
measurementPending);
}
+ MeasurementPending getPendingMeasurement() {
+ return (MeasurementPending) getShapeProperty(JmolConstants.SHAPE_MEASURES, "pending");
+ }
+
void clearAllMeasurements() {
//Eval only
setShapeProperty(JmolConstants.SHAPE_MEASURES, "clear", null);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-27 16:28:00
|
Revision: 9776
http://jmol.svn.sourceforge.net/jmol/?rev=9776&view=rev
Author: hansonr
Date: 2008-08-27 16:27:57 +0000 (Wed, 27 Aug 2008)
Log Message:
-----------
version=11.6.RC11 # bug fix: super/subscripts with antialiasdisplay
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/g3d/Text3D.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/g3d/Text3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Text3D.java 2008-08-27 15:50:01 UTC (rev 9775)
+++ trunk/Jmol/src/org/jmol/g3d/Text3D.java 2008-08-27 16:27:57 UTC (rev 9776)
@@ -78,6 +78,7 @@
JmolRendererInterface jmolRenderer, boolean antialias) {
if (text.length() == 0)
return 0;
+ System.out.println(x + " " + y + " " + text);
if (text.indexOf("<su") >= 0)
return plotByCharacter(x, y, z, argb, text, font3d, g3d, jmolRenderer,
antialias);
@@ -95,6 +96,7 @@
int textWidth = text3d.width;
int textHeight = text3d.height;
int mapWidth = text3d.mapWidth;
+ System.out.println ("mapWidth = " + mapWidth);
if (x + textWidth <= 0 || x >= g3d.width || y + textHeight <= 0
|| y >= g3d.height)
return textWidth;
@@ -199,11 +201,11 @@
int len = text.length();
int suboffset = (int)(font3d.fontMetrics.getHeight() * 0.25);
int supoffset = -(int)(font3d.fontMetrics.getHeight() * 0.3);
- if (antialias) {
+/* if (antialias) {
suboffset <<= 1;
supoffset <<= 1;
}
- for (int i = 0; i < len; i++) {
+*/ for (int i = 0; i < len; i++) {
if (text.charAt(i) == '<') {
if (i + 4 < len && text.substring(i, i + 5).equals("<sub>")) {
i += 4;
@@ -226,9 +228,13 @@
continue;
}
}
- w += plot(x + w, y, z, argb, text.substring(i, i + 1), font3d,
+ int width = plot(x + w, y, z, argb, text.substring(i, i + 1), font3d,
g3d, jmolRenderer, antialias);
+ if (antialias) // this is a hack
+ width >>= 1;
+ w += width;
}
+ System.out.println("w=" + w);
return w;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-27 15:50:01 UTC (rev 9775)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-27 16:27:57 UTC (rev 9776)
@@ -3,8 +3,8 @@
version=11.6.RC11
+# bug fix: super/subscripts with antialiasdisplay
# translation: menu items in console
-
# bug fix: web export / language
# bug fix: draw pointgroup C2 2 not distinguished from draw pointgroup C2 1
# bug fix: d2 point groups cause null pointer exception due to missing principal axis
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-27 16:44:35
|
Revision: 9777
http://jmol.svn.sourceforge.net/jmol/?rev=9777&view=rev
Author: hansonr
Date: 2008-08-27 16:44:32 +0000 (Wed, 27 Aug 2008)
Log Message:
-----------
version=11.6.RC11 # bug fix: echo IMAGE and antialiasdisplay
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/g3d/Text3D.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/g3d/Text3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Text3D.java 2008-08-27 16:27:57 UTC (rev 9776)
+++ trunk/Jmol/src/org/jmol/g3d/Text3D.java 2008-08-27 16:44:32 UTC (rev 9777)
@@ -124,8 +124,8 @@
width = g3d.width;
height = g3d.height;
} else if (g3d.isAntialiased()) {
- width += width;
- height += height;
+ //width += width;
+ //height += height;
}
if (x + width <= 0 || x >= g3d.width || y + height <= 0 || y >= g3d.height)
return;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-27 16:27:57 UTC (rev 9776)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-27 16:44:32 UTC (rev 9777)
@@ -3,6 +3,7 @@
version=11.6.RC11
+# bug fix: echo IMAGE and antialiasdisplay
# bug fix: super/subscripts with antialiasdisplay
# translation: menu items in console
# bug fix: web export / language
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|
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