Revision: 5251
Author: hansonr
Date: 2006-06-28 16:30:26 -0700 (Wed, 28 Jun 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5251&view=rev
Log Message:
-----------
bob200603 10.x.16a feature modification for polyhedra definition
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
22:11:51 UTC (rev 5250)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Polyhedra.java 2006-06-28
23:30:26 UTC (rev 5251)
@@ -253,7 +253,7 @@
break;
otherAtoms[bondCount++] = otherAtom;
}
- if (bondCount < 2 || nBonds > 0 && nBonds != bondCount)
+ if (bondCount < 3 || nBonds > 0 && nBonds != bondCount)
return null;
return validatePolyhedronNew(atom, bondCount, otherAtoms);
}
@@ -274,7 +274,7 @@
break;
otherAtoms[otherAtomCount++] = other;
}
- if (otherAtomCount < 2 || nBonds > 0 && nBonds != otherAtomCount)
+ if (otherAtomCount < 3 || nBonds > 0 && nBonds != otherAtomCount)
return null;
return validatePolyhedronNew(atom, otherAtomCount, otherAtoms);
}
@@ -304,16 +304,49 @@
int ptCenter = vertexCount;
int nPoints = ptCenter + 1;
float distMax = 0;
+ float dAverage = 0;
Point3f[] points = new Point3f[MAX_POINTS];
points[ptCenter] = centralAtom.point3f;
otherAtoms[ptCenter] = centralAtom;
for (int i = 0; i < ptCenter; i++) {
points[i] = otherAtoms[i].point3f;
- distMax += points[ptCenter].distance(points[i]);
+ dAverage += points[ptCenter].distance(points[i]);
}
- distMax = distMax / ptCenter * maxFactor;
-
+ dAverage = dAverage / ptCenter;
+ float factor = maxFactor;
+ BitSet bs = new BitSet(ptCenter);
+ boolean isOK = (dAverage == 0);
+ // here we are assuring that at least ONE face is drawn to
+ // all matching vertices
+
+ while (!isOK) {
+ distMax = dAverage * factor;
+ for (int i = 0; i < ptCenter; i++)
+ bs.set(i);
+ for (int i = 0; i < ptCenter - 2; i++)
+ for (int j = i + 1; j < ptCenter - 1; j++) {
+ if (points[i].distance(points[j]) > distMax)
+ continue;
+ for (int k = j + 1; k < ptCenter; k++) {
+ if (points[i].distance(points[k]) > distMax
+ || points[j].distance(points[k]) > distMax)
+ continue;
+ bs.clear(i);
+ bs.clear(j);
+ bs.clear(k);
+ }
+ }
+ isOK = true;
+ for (int i = 0; i < ptCenter; i++)
+ 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());
+ break;
+ }
+ }
// simply define a face to be when all three distances
// are < MAX_FACTOR * longest central
// collapsed trick is that introduce a "simple" atom
@@ -322,8 +355,7 @@
// also needed: consideration for faces involving more than three atoms
- out:
- for (int i = 0; i < ptCenter - 2; i++)
+ out: for (int i = 0; i < ptCenter - 2; i++)
for (int j = i + 1; j < ptCenter - 1; j++) {
if (points[i].distance(points[j]) > distMax)
continue;
@@ -331,7 +363,7 @@
if (points[i].distance(points[k]) > distMax
|| points[j].distance(points[k]) > distMax)
continue;
- g3d.getNormalFromCenter(points[ptCenter], points[i], points[j],
+ g3d.getNormalFromCenter(points[ptCenter], points[i], points[j],
points[k], true, normal);
if (isCollapsed) {
normal.scale(faceCenterOffset);
@@ -341,14 +373,14 @@
planesT[ipt++] = (byte) nPoints;
planesT[ipt++] = (byte) j;
planesT[ipt++] = (byte) k;
- g3d.getNormalFromCenter(points[i], points[ptCenter],
- points[j], points[k], false, normal);
+ g3d.getNormalFromCenter(points[i], points[ptCenter], points[j],
+ points[k], false, normal);
normixesT[planeCount++] = g3d.getNormix(normal);
planesT[ipt++] = (byte) i;
planesT[ipt++] = (byte) nPoints;
planesT[ipt++] = (byte) k;
- g3d.getNormalFromCenter(points[j], points[i],
- points[ptCenter], points[k], false, normal);
+ g3d.getNormalFromCenter(points[j], points[i], points[ptCenter],
+ points[k], false, normal);
normixesT[planeCount++] = g3d.getNormix(normal);
planesT[ipt++] = (byte) i;
planesT[ipt++] = (byte) j;
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