From: Miguel <mig...@us...> - 2004-05-31 17:52:51
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Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20744/src/org/openscience/jmol/viewer Modified Files: JmolConstants.java Log Message: implemented purine & pyrimidine & fixed set definitions Index: JmolConstants.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/JmolConstants.java,v retrieving revision 1.133 retrieving revision 1.134 diff -u -r1.133 -r1.134 --- JmolConstants.java 30 May 2004 14:29:03 -0000 1.133 +++ JmolConstants.java 31 May 2004 17:52:12 -0000 1.134 @@ -31,7 +31,7 @@ // for now, just update this by hand // perhaps use ant filter later ... but mth doesn't like it :-( public final static String copyright = "(C) 2004 The Jmol Development Team"; - public final static String version = "10pre10f"; + public final static String version = "10pre10g"; public final static String cvsDate = "$Date$"; public final static String date = cvsDate.substring(7, 23); @@ -1854,7 +1854,7 @@ // // protein related // - // protein is pre-defined + // protein is hardwired "@amino _g>0 & _g<=23", "@acidic asp,glu", "@basic arg,his,lys", @@ -1887,19 +1887,17 @@ // // nucleic acid related - // nucleic, rna, and dna are hard-wired + // nucleic, dna, rna, purine, pyrimidine are hard-wired // - "@c _g=30,_g=31,_g=38,_g=39,_g>=61 & _g<=63", - "@g _g=26,_g=27,_g>=40 & _g<=46,_g>=55 & _g<=57", + "@c nucleic & within(group,_a=76)", + "@g nucleic & within(group,_a=79)", "@cg c,g", - "@a _g=24,_g=25,_g=36,_g=37,_g>=52 & _g<=54", - "@t _g=32,_g=33,_g>=64 & _g<=66", + "@a nucleic & within(group,_a=78)", + "@t nucleic & within(group,_a=77)", "@at a,t", - "@i _g=28,_g=29,_g>=58 & _g<=60", - "@u _g=34,_g=35,_g>=48 & _g<=51,_g>=67 & _g<=69", - - "@purine _g>=24 & _g<=29", - "@pyrimidine _g>=30 & _g<=35", + "@i nucleic & within(group,_a=75) & !t", + "@u nucleic & within(group,_a=74) & !t", + "@tu nucleic & within(group,_a=80)", // // solvent @@ -1912,10 +1910,10 @@ // // structure related // - "@alpha amino & _a=2", // rasmol doc says "approximately *.CA" - whatever? - "@backbone amino & _a<=4,nucleic & (_a>=9 & _a<=31)", - "@sidechain (protein,nucleic) & _a>=64", - "@base nucleic & _a>=64", + "@alpha _a=2", // rasmol doc says "approximately *.CA" - whatever? + "@backbone (protein,nucleic) & _a>0 & _a<=63", + "@sidechain (protein,nucleic) & !backbone", + "@base nucleic & !backbone", "@turn _structure=1", "@sheet _structure=2", |