From: <ha...@us...> - 2008-07-17 19:19:18
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Revision: 9609 http://jmol.svn.sourceforge.net/jmol/?rev=9609&view=rev Author: hansonr Date: 2008-07-17 19:17:59 +0000 (Thu, 17 Jul 2008) Log Message: ----------- version=11.5.48_dev quaternion arrows;connect aromatic auto # bug fix: quaternion derivative DRAW arrows placed on residue i+1 instead of residue i # bug fix: connect aromatic auto; select connected([bond type],...) Modified Paths: -------------- trunk/Jmol/src/org/jmol/modelset/Bond.java trunk/Jmol/src/org/jmol/modelset/BondCollection.java trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/modelset/Bond.java =================================================================== --- trunk/Jmol/src/org/jmol/modelset/Bond.java 2008-07-17 15:06:52 UTC (rev 9608) +++ trunk/Jmol/src/org/jmol/modelset/Bond.java 2008-07-17 19:17:59 UTC (rev 9609) @@ -246,7 +246,7 @@ } public boolean is(int bondType) { - return (order & ~JmolConstants.BOND_NEW) != bondType; + return (order & ~JmolConstants.BOND_NEW) == bondType; } } Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2008-07-17 15:06:52 UTC (rev 9608) +++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2008-07-17 19:17:59 UTC (rev 9609) @@ -520,7 +520,7 @@ for (int i = bondCount; --i >= 0;) if (bsBonds == null || bsBonds.get(i)) { bond = bonds[i]; - if (bond.is(JmolConstants.BOND_AROMATIC) + if (!bond.is(JmolConstants.BOND_AROMATIC) || bsAromaticDouble.get(i) || bsAromaticSingle.get(i)) continue; if (!assignAromaticDouble(bond)) Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java =================================================================== --- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2008-07-17 15:06:52 UTC (rev 9608) +++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2008-07-17 19:17:59 UTC (rev 9609) @@ -639,7 +639,7 @@ // helices and sheets are missed // (in terms of assigning structure from quaternions). Atom atemp = a; - a = aprev; + monomer = (Monomer) (a = aprev).getGroup(); aprev = atemp; // save this dq as dq' dqprev = dq; @@ -675,7 +675,6 @@ : p instanceof NucleicPolymer ? ((NucleicMonomer) monomer).getQuaternionFrameCenter(qtype) : new Point3f()); - if (isDraw) { if (bsSelected != null && !bsSelected.get(a.getAtomIndex())) continue; @@ -712,7 +711,7 @@ new Point3f[] { ptCenter } }); if (qtype == 'n' && isAmino) strExtra += TextFormat.sprintf(" %10.5p %10.5p %10.5p", - new Object[] { new Point3f[] { ((AminoMonomer) a.getGroup()) + new Object[] { new Point3f[] { ((AminoMonomer) monomer) .getNitrogenHydrogenPoint() } }); } if (pdbATOM == null) Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-17 15:06:52 UTC (rev 9608) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-17 19:17:59 UTC (rev 9609) @@ -3,8 +3,10 @@ version=11.5.48_dev +# bug fix: quaternion derivative DRAW arrows placed on residue i+1 instead of residue i +# bug fix: connect aromatic auto; select connected([bond type],...) # bug fix: queue thread termination when applets are off screen -# bug fix: sheetsmoothing not consistent among structures in multi-chain systems +# bug fix : sheetsmoothing not consistent among structures in multi-chain systems # bug fix: messages not sent to messageCallback # code: simpler matrix-->quaternion code # bug fix: 11.5.47 shows oddly sized arrow for very first rendering This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |