From: Miguel <mig...@us...> - 2004-05-31 17:52:29
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Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20744/src/org/openscience/jmol/viewer/script Modified Files: Eval.java Token.java Log Message: implemented purine & pyrimidine & fixed set definitions Index: Eval.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script/Eval.java,v retrieving revision 1.158 retrieving revision 1.159 diff -u -r1.158 -r1.159 --- Eval.java 29 May 2004 14:54:22 -0000 1.158 +++ Eval.java 31 May 2004 17:52:13 -0000 1.159 @@ -813,6 +813,12 @@ case Token.rna: stack[sp++] = getRnaSet(); break; + case Token.purine: + stack[sp++] = getPurineSet(); + break; + case Token.pyrimidine: + stack[sp++] = getPyrimidineSet(); + break; case Token.y: case Token.amino: case Token.backbone: @@ -985,6 +991,24 @@ return bsRna; } + BitSet getPurineSet() { + Frame frame = viewer.getFrame(); + BitSet bsPurine = new BitSet(); + for (int i = viewer.getAtomCount(); --i >= 0; ) + if (frame.getAtomAt(i).isPurine()) + bsPurine.set(i); + return bsPurine; + } + + BitSet getPyrimidineSet() { + Frame frame = viewer.getFrame(); + BitSet bsPyrimidine = new BitSet(); + for (int i = viewer.getAtomCount(); --i >= 0; ) + if (frame.getAtomAt(i).isPyrimidine()) + bsPyrimidine.set(i); + return bsPyrimidine; + } + /* BitSet getResidueSet(String strResidue) { Frame frame = viewer.getFrame(); Index: Token.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script/Token.java,v retrieving revision 1.67 retrieving revision 1.68 diff -u -r1.67 -r1.68 --- Token.java 29 May 2004 14:54:22 -0000 1.67 +++ Token.java 31 May 2004 17:52:20 -0000 1.68 @@ -316,16 +316,18 @@ final static int jmol = misc | 33; final static int displacement = misc | 34; - final static int amino = predefinedset | 0; - final static int hetero = predefinedset | 1 | setparam; - final static int hydrogen = predefinedset | 2 | setparam; - final static int selected = predefinedset | 3 | showparam; - final static int solvent = predefinedset | 4 | setparam; - final static int sidechain = predefinedset | 5; - final static int protein = predefinedset | 6; - final static int nucleic = predefinedset | 7; - final static int dna = predefinedset | 8; - final static int rna = predefinedset | 9; + final static int amino = predefinedset | 0; + final static int hetero = predefinedset | 1 | setparam; + final static int hydrogen = predefinedset | 2 | setparam; + final static int selected = predefinedset | 3 | showparam; + final static int solvent = predefinedset | 4 | setparam; + final static int sidechain = predefinedset | 5; + final static int protein = predefinedset | 6; + final static int nucleic = predefinedset | 7; + final static int dna = predefinedset | 8; + final static int rna = predefinedset | 9; + final static int purine = predefinedset | 10; + final static int pyrimidine = predefinedset | 11; final static Token tokenOn = new Token(on, 1, "on"); final static Token tokenAll = new Token(all, "all"); @@ -574,6 +576,8 @@ "nucleic", new Token(nucleic, "nucleic"), "dna", new Token(dna, "dna"), "rna", new Token(rna, "rna"), + "purine", new Token(purine, "purine"), + "pyrimidine", new Token(pyrimidine, "pyrimidine"), "mode", new Token(mode, "mode"), "direction", new Token(direction, "direction"), |