Revision: 5252
Author: hansonr
Date: 2006-06-28 18:58:57 -0700 (Wed, 28 Jun 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5252&view=rev
Log Message:
-----------
bob200603 10.x.16b polyhedra face/vertex limits return null indicating "too
complex"
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/viewer/Polyhedra.java
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Polyhedra.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Polyhedra.java 2006-06-28
23:30:26 UTC (rev 5251)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Polyhedra.java 2006-06-29
01:58:57 UTC (rev 5252)
@@ -234,9 +234,8 @@
}
}
- final static int MAX_VERTICES = 85;
- final static int MAX_POINTS = 256;
- final static int FACE_COUNT_MAX = 85;
+ final static int MAX_VERTICES = 80;
+ final static int FACE_COUNT_MAX = MAX_VERTICES - 3;
Atom[] otherAtoms = new Atom[MAX_VERTICES];
Polyhedron constructBondsPolyhedron(int atomIndex) {
Atom atom = frame.getAtomAt(atomIndex);
@@ -279,23 +278,9 @@
return validatePolyhedronNew(atom, otherAtomCount, otherAtoms);
}
- short[] normixesT = new short[FACE_COUNT_MAX];
- byte[] planesT = new byte[256];
+ short[] normixesT = new short[MAX_VERTICES];
+ byte[] planesT = new byte[MAX_VERTICES * 3];
-
- void setVisibilityFlags(BitSet bs) {
- /*
- * set all fixed objects visible; others based on model being displayed
note
- * that this is NOT done with atoms and bonds, because they have mads. When
- * you say "frame 0" it is just turning on all the mads.
- */
- for (int i = polyhedronCount; --i >= 0;) {
- Polyhedron p = polyhedrons[i];
- p.visibilityFlags = (p.visible && bs.get(p.centralAtom.modelIndex) ?
myVisibilityFlag : 0);
- }
- }
-
-
Polyhedron validatePolyhedronNew(Atom centralAtom, int vertexCount,
Atom[] otherAtoms) {
Vector3f normal = new Vector3f();
@@ -306,7 +291,7 @@
float distMax = 0;
float dAverage = 0;
- Point3f[] points = new Point3f[MAX_POINTS];
+ Point3f[] points = new Point3f[MAX_VERTICES * 3];
points[ptCenter] = centralAtom.point3f;
otherAtoms[ptCenter] = centralAtom;
for (int i = 0; i < ptCenter; i++) {
@@ -320,7 +305,7 @@
// here we are assuring that at least ONE face is drawn to
// all matching vertices
- while (!isOK) {
+ while (!isOK) {
distMax = dAverage * factor;
for (int i = 0; i < ptCenter; i++)
bs.set(i);
@@ -342,13 +327,15 @@
if (bs.get(i)) {
isOK = false;
factor *= 1.05f;
- System.out.println("maxFactor for "+ptCenter+ " atoms increased to "
+ factor
- + " in order to include " + otherAtoms[i].getIdentity());
+ System.out.println("Polyhedra maxFactor for " + ptCenter
+ + " atoms increased to " + factor + " in order to include "
+ + otherAtoms[i].getIdentity());
break;
}
}
- // simply define a face to be when all three distances
+ // start by defining a face to be when all three distances
// are < MAX_FACTOR * longest central
+ // but if a vertex is missed, then expand the range.
// collapsed trick is that introduce a "simple" atom
// near the center but not quite the center, so that our planes on
// either side of the facet don't overlap. We step out maxFactor * normal
@@ -365,6 +352,14 @@
continue;
g3d.getNormalFromCenter(points[ptCenter], points[i], points[j],
points[k], true, normal);
+ if (planeCount >= FACE_COUNT_MAX) {
+ System.out.println("Polyhedron error: maximum
face("+FACE_COUNT_MAX+")");
+ return null;
+ }
+ if (nPoints >= MAX_VERTICES) {
+ System.out.println("Polyhedron error: maximum vertex
count("+MAX_VERTICES+")");
+ return null;
+ }
if (isCollapsed) {
normal.scale(faceCenterOffset);
points[nPoints] = new Point3f(points[ptCenter]);
@@ -395,10 +390,9 @@
planesT[ipt++] = (byte) k;
normixesT[planeCount++] = g3d.getNormix(normal);
}
- if (planeCount == FACE_COUNT_MAX)
- break out;
}
}
+ //System.out.println("planeCount="+planeCount + " nPoints="+nPoints);
return new Polyhedron(centralAtom, nPoints, planeCount, otherAtoms,
normixesT, planesT);
}
@@ -431,4 +425,15 @@
}
}
+ void setVisibilityFlags(BitSet bs) {
+ /*
+ * set all fixed objects visible; others based on model being displayed
note
+ * that this is NOT done with atoms and bonds, because they have mads. When
+ * you say "frame 0" it is just turning on all the mads.
+ */
+ for (int i = polyhedronCount; --i >= 0;) {
+ Polyhedron p = polyhedrons[i];
+ p.visibilityFlags = (p.visible && bs.get(p.centralAtom.modelIndex) ?
myVisibilityFlag : 0);
+ }
+ }
}
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