From: <ha...@us...> - 2010-10-08 03:52:52
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Revision: 14427 http://jmol.svn.sourceforge.net/jmol/?rev=14427&view=rev Author: hansonr Date: 2010-10-08 03:52:46 +0000 (Fri, 08 Oct 2010) Log Message: ----------- dssp ! markings for carbonyl-oxygen-missing residues. Modified Paths: -------------- trunk/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java Modified: trunk/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java =================================================================== --- trunk/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java 2010-10-08 03:18:05 UTC (rev 14426) +++ trunk/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java 2010-10-08 03:52:46 UTC (rev 14427) @@ -715,8 +715,10 @@ if (labels[i] != null) { AminoPolymer ap = (AminoPolymer) bioPolymers[i]; sbSummary.append(ap.dumpSummary(labels[i])); - sb.append(ap.dumpTags("$.1: " + String.valueOf(labels[i]))); + sb.append(ap.dumpTags("$.1: " + String.valueOf(labels[i]), bsBad)); } + if (bsBad.nextSetBit(0) >= 0) + sb.append("\nNOTE: '!' indicates a residue that is missing a backbone carbonyl oxygen atom.\n"); sb.append("\n").append("SUMMARY:" + sbSummary); } @@ -832,7 +834,7 @@ if (reportOnly) { setTag(labels, bsTurn, 'T'); return dumpTags("$.5: " + line5 + "\n" + "$.4: " + line4 + "\n" + "$.3: " - + line3); + + line3, bsBad); } // if not calculate hbond, set the turn structure @@ -1261,7 +1263,7 @@ return sb.toString(); } - private String dumpTags(String lines) { + private String dumpTags(String lines, BitSet bsBad) { String prefix = monomers[0].getLeadAtom().getChainID() + "." + (bioPolymerIndexInModel + 1); lines = TextFormat.simpleReplace(lines, "$", prefix); @@ -1277,7 +1279,8 @@ sb.append(i % 100 == 0 ? "" + ((i / 100) % 100) : " "); sb1.append(i % 10 == 0 ? "" + ((i / 10) % 10) : " "); sb2.append(i % 10); - sb3.append(monomers[ii].getGroup1()); + sb3.append(bsBad.get(monomers[ii].leadAtomIndex) ? + '!' : monomers[ii].getGroup1()); } sb.append(sb1).append(sb2).append("\n"); sb.append(lines); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |