Revision: 5255
Author: hansonr
Date: 2006-06-29 21:43:18 -0700 (Thu, 29 Jun 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5255&view=rev
Log Message:
-----------
bob200603 isosurface lobes minor fix; removing unreferenced but erroneous #FFFF
in one atom function
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/viewer/Atom.java
branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Atom.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Atom.java 2006-06-30
03:14:13 UTC (rev 5254)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Atom.java 2006-06-30
04:43:18 UTC (rev 5255)
@@ -262,8 +262,7 @@
}
int getBondedAtomIndex(int bondIndex) {
- return bonds[bondIndex].getOtherAtom(this).atomIndex & 0xFFFF;
- //BH: why & 0xFFFF ?
+ return bonds[bondIndex].getOtherAtom(this).atomIndex;
}
/*
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-06-30
03:14:13 UTC (rev 5254)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-06-30
04:43:18 UTC (rev 5255)
@@ -146,6 +146,8 @@
boolean isAnisotropic;
boolean isEccentric;
float eccentricityScale;
+ float eccentricityRatio;
+
float scale;
Matrix3f eccentricityMatrix;
Matrix3f eccentricityMatrixInverse;
@@ -539,6 +541,7 @@
float c = (scale > 0 ? scale : info.w < 0 ? 1f : ecc.length());
eccentricityScale = c;
float fab_c = Math.abs(info.w);
+ eccentricityRatio = fab_c;
if (fab_c > 1)
eccentricityScale *= fab_c;
ecc.normalize();
@@ -3322,10 +3325,10 @@
psi_Znuc = 6;
if (center.x == Float.MAX_VALUE)
center.set(0, 0, 0);
- float radius = lobe_sizeAngstroms / 2f * eccentricityScale;
+ float radius = lobe_sizeAngstroms * eccentricityRatio * eccentricityScale;
setVoxelRange(0, -radius, radius, lobe_ptsPerAngstrom, lobe_gridMax);
setVoxelRange(1, -radius, radius, lobe_ptsPerAngstrom, lobe_gridMax);
- setVoxelRange(2, 0, radius * 4.5f, lobe_ptsPerAngstrom, lobe_gridMax);
+ setVoxelRange(2, 0, radius / eccentricityRatio * 2.25f,
lobe_ptsPerAngstrom, lobe_gridMax);
jvxlFileHeader = "lobe \nn="
+ psi_n
+ ", l="
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