From: <ha...@us...> - 2008-02-07 18:18:59
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Revision: 8980 http://jmol.svn.sourceforge.net/jmol/?rev=8980&view=rev Author: hansonr Date: 2008-02-07 10:18:47 -0800 (Thu, 07 Feb 2008) Log Message: ----------- version=11.5.6 # bug fix: HETATM atoms not automatically bonded to nearby ATOM atoms Modified Paths: -------------- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-02-07 18:17:59 UTC (rev 8979) +++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-02-07 18:18:47 UTC (rev 8980) @@ -1900,8 +1900,8 @@ for (int i = atomCount; --i >= 0;) { boolean isAtomInSetA = (bsA == null || bsA.get(i)); boolean isAtomInSetB = (bsB == null || bsB.get(i)); - if (!isAtomInSetA && !isAtomInSetB || bsExclude != null - && bsExclude.get(i)) + if (!isAtomInSetA && !isAtomInSetB) + //|| bsExclude != null && bsExclude.get(i)) continue; Atom atom = atoms[i]; int modelIndex = atom.modelIndex; @@ -1930,8 +1930,10 @@ int atomIndexNear = atomNear.atomIndex; boolean isNearInSetA = (bsA == null || bsA.get(atomIndexNear)); boolean isNearInSetB = (bsB == null || bsB.get(atomIndexNear)); - if (!isNearInSetA && !isNearInSetB || bsExclude != null - && bsExclude.get(atomIndexNear)) + if (!isNearInSetA && !isNearInSetB + || bsExclude != null && bsExclude.get(atomIndexNear) + && bsExclude.get(i) //this line forces BOTH to be excluded in order to ignore bonding + ) continue; if (!(isAtomInSetA && isNearInSetB || isAtomInSetB && isNearInSetA)) continue; Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-02-07 18:17:59 UTC (rev 8979) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-02-07 18:18:47 UTC (rev 8980) @@ -1,5 +1,6 @@ version=11.5.6 +# bug fix: HETATM atoms not automatically bonded to nearby ATOM atoms # bug fix: setParameterValue("perspectiveDepth",perspectiveDepth); # bug fix: sets offset based on imageFontScaling, not overall font scaling This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |