From: <ha...@us...> - 2012-06-17 17:21:50
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Revision: 17316 http://jmol.svn.sourceforge.net/jmol/?rev=17316&view=rev Author: hansonr Date: 2012-06-17 17:21:43 +0000 (Sun, 17 Jun 2012) Log Message: ----------- version=12.3.32_dev # bug fix: color for hbonds/ssbonds backbone incorrect # new feature: load "$$xxxxx" loads 2D version, not 3D (used for JmolData connection with JME) # -- two &'s drops "&get3d=True" from NCI call Modified Paths: -------------- trunk/Jmol/src/org/jmol/shape/SticksRenderer.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/shape/SticksRenderer.java =================================================================== --- trunk/Jmol/src/org/jmol/shape/SticksRenderer.java 2012-06-17 17:21:14 UTC (rev 17315) +++ trunk/Jmol/src/org/jmol/shape/SticksRenderer.java 2012-06-17 17:21:43 UTC (rev 17316) @@ -98,9 +98,13 @@ } } + private Atom atomA0; + private Atom atomB0; + private void renderBond() { - atomA = bond.getAtom1(); - atomB = bond.getAtom2(); + atomA = atomA0 = bond.getAtom1(); + atomB = atomB0 = bond.getAtom2(); + int order = bond.order & ~JmolEdge.BOND_NEW; if (bondsBackbone) { if (ssbondsBackbone && (order & JmolEdge.BOND_SULFUR_MASK) != 0) { @@ -133,14 +137,14 @@ (g3d.isClippedZ(atomA.screenZ) || g3d.isClippedZ(atomB.screenZ))) return; } - colixA = atomA.getColix(); - colixB = atomB.getColix(); + colixA = atomA0.getColix(); + colixB = atomB0.getColix(); if (((colix = bond.getColix()) & Graphics3D.OPAQUE_MASK) == Graphics3D.USE_PALETTE) { colix = (short) (colix & ~Graphics3D.OPAQUE_MASK); colixA = Graphics3D.getColixInherited((short) (colix | viewer - .getColixAtomPalette(atomA, EnumPalette.CPK.id)), colixA); + .getColixAtomPalette(atomA0, EnumPalette.CPK.id)), colixA); colixB = Graphics3D.getColixInherited((short) (colix | viewer - .getColixAtomPalette(atomB, EnumPalette.CPK.id)), colixB); + .getColixAtomPalette(atomB0, EnumPalette.CPK.id)), colixB); } else { colixA = Graphics3D.getColixInherited(colix, colixA); colixB = Graphics3D.getColixInherited(colix, colixB); Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-06-17 17:21:14 UTC (rev 17315) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-06-17 17:21:43 UTC (rev 17316) @@ -5,6 +5,7 @@ version=12.3.32_dev +# bug fix: color for hbonds/ssbonds backbone incorrect # new feature: load "$$xxxxx" loads 2D version, not 3D (used for JmolData connection with JME) # -- two &'s drops "&get3d=True" from NCI call This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |