From: <ha...@us...> - 2011-08-17 16:26:30
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Revision: 15978 http://jmol.svn.sourceforge.net/jmol/?rev=15978&view=rev Author: hansonr Date: 2011-08-17 16:26:24 +0000 (Wed, 17 Aug 2011) Log Message: ----------- version=12.2.RC5 # bug fix: "$phosphorus pentoxide" label %[shape] indicates AX4E not AX4 hybridization on phosphorus Modified Paths: -------------- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2011-08-17 14:37:25 UTC (rev 15977) +++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2011-08-17 16:26:24 UTC (rev 15978) @@ -1882,6 +1882,7 @@ int _90 = 0; int _120 = 1; int _180 = 2; + int n120_atom0 = 0; for (int i = 0; i < nAttached - 1; i++) for (int j = i + 1; j < nAttached; j++) { float angle = Measure @@ -1891,6 +1892,8 @@ typePtrs[itype][ntypes[itype]] = n; ntypes[itype]++; angles[n++] = new int[] { i, j }; + if (i == 0 && itype == _120) + n120_atom0++; } // categorization is done simply by listing // the number of 90, 120, and 180 angles. @@ -1912,31 +1915,33 @@ return "bent"; case 111: case 201: - return "T-shaped";// -- AX3E or AX3E2 or AX3E3"; + return "T-shaped";// -- AX3E or AX3E2 or AX3E3 case 30: case 120: case 210: case 300: if (Math.abs(Measure.computeTorsion(attached[0], atom, attached[1], attached[2], true)) > 162) - return "trigonal planar";// -- AX3"; - return "trigonal pyramidal";// -- AX3E"; + return "trigonal planar";// -- AX3 + return "trigonal pyramidal";// -- AX3E case 330: - return "uncapped trigonal pyramid";// -- AX4E"; + // may just have a rather distorted tetrahedron, as in "$phosphorus pentoxide" + // in that case, each atom will have 1 or 3 120o angles, not 0 or 2, as in trigonal pyramid + return (n120_atom0 % 2 == 1 ? "tetrahedral" : "uncapped trigonal pyramid");// -- AX4 or AX4E case 60: case 150: case 240: - return "tetrahedral";// -- AX4"; + return "tetrahedral";// -- AX4 case 402: - return "square planar";// -- AX4E2"; + return "square planar";// -- AX4E2 case 411: case 501: - return "see-saw";// -- AX4E"; + return "see-saw";// -- AX4E case 631: - return "trigonal bipyramidal";// -- AX5"; + return "trigonal bipyramidal";// -- AX5 case 802: - return "uncapped square pyramid";// -- AX5E"; + return "uncapped square pyramid";// -- AX5E case 1203: - return "octahedral";// -- AX6"; + return "octahedral";// -- AX6 } } Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-08-17 14:37:25 UTC (rev 15977) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-08-17 16:26:24 UTC (rev 15978) @@ -3,6 +3,7 @@ version=12.2.RC5 +# bug fix: "$phosphorus pentoxide" label %[shape] indicates AX4E not AX4 hybridization on phosphorus # new feature: set isosurfaceKey ON|OFF # -- creates a vertical hoverable key on the left # -- only the most recent and visible isosurface This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |