Revision: 20401
http://sourceforge.net/p/jmol/code/20401
Author: hansonr
Date: 2015-03-23 13:22:47 +0000 (Mon, 23 Mar 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.13_2015.03.23"
bug fix: isosurface solvent will fail if max volume is smaller than cavity max
even though not cavity
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2015-03-23
13:22:00 UTC (rev 20400)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2015-03-23
13:22:47 UTC (rev 20401)
@@ -472,19 +472,19 @@
BS bsAll = new BS();
BS[] bsSurfaces = meshData.getSurfaceSet();
BS[] bsSources = null;
- double[] volumes = (double[]) (isPocket ? null :
- MeshData.calculateVolumeOrArea(meshData, Integer.MIN_VALUE, false,
false));
- float minVolume = (float)(1.5 * Math.PI * Math.pow(sr, 3));
+ double[] volumes = (double[]) (isPocket ? null : MeshData
+ .calculateVolumeOrArea(meshData, Integer.MIN_VALUE, false, false));
+ float minVolume = (isCavity ? (float) (1.5 * Math.PI * Math.pow(sr, 3))
: 0);
double maxVolume = 0;
boolean maxIsNegative = false;
if (volumes != null && !isCavity)
- for (int i = 0; i < meshData.nSets; i++) {
- double v = volumes[i];
- if (Math.abs(v) > maxVolume) {
- maxVolume = Math.abs(v);
- maxIsNegative = (v < 0);
+ for (int i = 0; i < meshData.nSets; i++) {
+ double v = volumes[i];
+ if (Math.abs(v) > maxVolume) {
+ maxVolume = Math.abs(v);
+ maxIsNegative = (v < 0);
+ }
}
- }
double factor = (maxIsNegative ? -1 : 1);
// added this factor business to account for situations where
// the first volume recorded is negative, but later, larger volumes,
@@ -776,20 +776,26 @@
this.pS = P3.newP(pS);
}
-// protected void dump() {
-// P3 ptA = atomXyz[ia];
-// P3 ptB = atomXyz[ib];
-// P3 ptC = atomXyz[ic];
-// String color = "red";
-// String label = "f"+ ia + "_" + ib + "_" + ic + "_";
-// dumpLine(ptA, ptB, label, color);
-// dumpLine(ptB, ptC, label, color);
-// dumpLine(ptC, ptA, label, color);
-// dumpLine2(pS, ptA, label, solventRadius, color, "white");
-// dumpLine2(pS, ptB, label, solventRadius, color, "white");
-// dumpLine2(pS, ptC, label, solventRadius, color, "white");
-// }
+ protected void dump() {
+ P3 ptA = atomXyz[ia];
+ P3 ptB = atomXyz[ib];
+ P3 ptC = atomXyz[ic];
+ String color = "red";
+ String label = "f"+ ia + "_" + ib + "_" + ic + "_";
+ sg.log("draw ID \"x" + label + (nTest++) + "\" "
+ + P3.newP(ptA)
+ + " " + P3.newP(ptB)
+ + " " + P3.newP(ptC)
+ + " color " + color);
+ //dumpLine(ptA, ptB, label, color);
+ //dumpLine(ptB, ptC, label, color);
+ //dumpLine(ptC, ptA, label, color);
+ //dumpLine2(pS, ptA, label, sr, color, "white");
+ //dumpLine2(pS, ptB, label, sr, color, "white");
+ //dumpLine2(pS, ptC, label, sr, color, "white");
+ }
+
@Override
public String toString() {
return ia + "_" + ib + "_" + ic + "_" + pS;
@@ -827,9 +833,12 @@
if ((f = validateFace(ia, ib, ic, edge, ptS1)) != null) {
vFaces.addLast(f);
isOK = true;
+ f.dump();
}
if ((f = validateFace(ia, ib, ic, edge, ptS2)) != null) {
vFaces.addLast(f);
+ if (!isOK)
+ f.dump();
isOK = true;
}
if (isOK) {
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
2015-03-23 13:22:00 UTC (rev 20400)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
2015-03-23 13:22:47 UTC (rev 20401)
@@ -5,7 +5,7 @@
@Override
protected void readSurfaceData(boolean isMapData) throws Exception {
initializeSurfaceData();
- voxelData = new float[nPointsX][nPointsY][nPointsZ];
+ newVoxelDataCube();
getPeriodicVoxels();
if (params.extendGrid != 0) {
int[] n = new int[3];
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-03-23 13:22:00 UTC
(rev 20400)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-03-23 13:22:47 UTC
(rev 20401)
@@ -14,8 +14,12 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.13_2015.03.21"
+Jmol.___JmolVersion="14.3.13_2015.03.23"
+bug fix: isosurface solvent will fail if max volume is smaller than cavity max
even though not cavity
+
+JmolVersion="14.3.13_2015.03.21"
+
bug fix: JmolVersion="14.3.13_2015.03.20b" broke JSmol due to error in coding
URL.js
JmolVersion="14.3.13_2015.03.20b"
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