From: <ha...@us...> - 2010-10-08 05:28:38
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Revision: 14429 http://jmol.svn.sourceforge.net/jmol/?rev=14429&view=rev Author: hansonr Date: 2010-10-08 05:28:32 +0000 (Fri, 08 Oct 2010) Log Message: ----------- version=12.1.14 # bug fix: loading a multi-structure PDB file with CONECT bonding may not autobond (2q3t) Modified Paths: -------------- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java trunk/Jmol/src/org/jmol/modelset/ModelSet.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java =================================================================== --- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2010-10-08 05:26:46 UTC (rev 14428) +++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2010-10-08 05:28:32 UTC (rev 14429) @@ -943,9 +943,11 @@ for (int i = baseModelIndex; i < modelCount; atomIndex += modelAtomCount, i++) { modelAtomCount = models[i].bsAtoms.cardinality(); int modelBondCount = getModelAuxiliaryInfoInt(i, "initialBondCount"); - if (modelBondCount < 0) + + boolean modelIsPDB = models[i].isPDB; + if (modelBondCount < 0) { modelBondCount = bondCount; - boolean modelIsPDB = models[i].isPDB; + } boolean modelHasSymmetry = getModelAuxiliaryInfoBoolean(i, "hasSymmetry"); // check for PDB file with fewer than one bond per every two atoms Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java =================================================================== --- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2010-10-08 05:26:46 UTC (rev 14428) +++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2010-10-08 05:28:32 UTC (rev 14429) @@ -450,8 +450,9 @@ continue; } int nConnect = vConnect.size(); + setModelAuxiliaryInfo(i, "initialBondCount", Integer.valueOf(nConnect)); int[] atomInfo = (int[]) getModelAuxiliaryInfo(i, "PDB_CONECT_firstAtom_count_max"); - int firstAtom = atomInfo[0] + baseAtomIndex; + int firstAtom = atomInfo[0] + baseAtomIndex; int atomMax = firstAtom + atomInfo[1]; int max = atomInfo[2]; int[] serialMap = new int[max + 1]; Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-10-08 05:26:46 UTC (rev 14428) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-10-08 05:28:32 UTC (rev 14429) @@ -3,6 +3,7 @@ version=12.1.14 +# bug fix: loading a multi-structure PDB file with CONECT bonding may not autobond (2q3t) # new feature: "xxxx"%9999 == "to upper case"; "xXxX"%-9999 == "to lower case" # bug fix: undocumented save STRUCTURE not working for initial structure state # code: removal of unnecessary structure class in ModelCollection This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |