From: <ha...@us...> - 2008-08-30 13:31:24
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Revision: 9813 http://jmol.svn.sourceforge.net/jmol/?rev=9813&view=rev Author: hansonr Date: 2008-08-30 13:31:21 +0000 (Sat, 30 Aug 2008) Log Message: ----------- 11.6.RC12 VERSION Modified Paths: -------------- trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java trunk/Jmol/src/org/jmol/modelset/AtomCollection.java Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java =================================================================== --- trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java 2008-08-30 13:31:00 UTC (rev 9812) +++ trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java 2008-08-30 13:31:21 UTC (rev 9813) @@ -75,7 +75,6 @@ bonds = minBonds; this.angles = angles; this.torsions = torsions; - this.partialCharges = partialCharges; this.constraints = constraints; atomCount = atoms.length; bondCount = bonds.length; @@ -87,6 +86,7 @@ } if (!havePartialCharges) partialCharges = null; + this.partialCharges = partialCharges; } boolean haveParams() { Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java =================================================================== --- trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java 2008-08-30 13:31:00 UTC (rev 9812) +++ trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java 2008-08-30 13:31:21 UTC (rev 9813) @@ -711,12 +711,16 @@ switch (elemNo) { case 15: // P phi *= 84.4339; + break; case 33: // As phi *= 86.9735; + break; case 51: // Sb phi *= 87.7047; + break; case 83: // Bi phi *= 90.0; + break; } double cosPhi = Math.cos(phi); a0 = cosPhi * cosPhi; Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2008-08-30 13:31:00 UTC (rev 9812) +++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2008-08-30 13:31:21 UTC (rev 9813) @@ -1323,6 +1323,7 @@ for (int i = atomCount; --i >= 0;) if (atoms[i].isPurine()) bs.set(i); + return bs; case Token.pyrimidine: for (int i = atomCount; --i >= 0;) if (atoms[i].isPyrimidine()) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |