From: <ha...@us...> - 2007-05-05 15:23:01
|
Revision: 7585 http://svn.sourceforge.net/jmol/?rev=7585&view=rev Author: hansonr Date: 2007-05-05 08:23:00 -0700 (Sat, 05 May 2007) Log Message: ----------- 11.1.32 fix for PdbReader failing on short HET lines. Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2007-05-05 15:20:21 UTC (rev 7584) +++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2007-05-05 15:23:00 UTC (rev 7585) @@ -494,13 +494,13 @@ void het() { if (htHetero == null) htHetero = new Hashtable(); + if (line.length() < 30) + return; String groupName = parseToken(line, 7, 10); - String hetName = line.substring(30, 70).trim(); - String htName = (String) htHetero.get(groupName); - if (htName != null) + if (htHetero.contains(groupName)) return; + String hetName = line.substring(30, Math.min(line.length(),70)).trim(); htHetero.put(groupName, hetName); - //Logger.debug("het: "+groupName); } void hetnam() { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-05-05 15:23:45
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Revision: 7586 http://svn.sourceforge.net/jmol/?rev=7586&view=rev Author: hansonr Date: 2007-05-05 08:23:44 -0700 (Sat, 05 May 2007) Log Message: ----------- 11.1.32 fix for PdbReader failing on short HET lines. Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2007-05-05 15:23:00 UTC (rev 7585) +++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2007-05-05 15:23:44 UTC (rev 7586) @@ -492,10 +492,10 @@ } void het() { + if (line.length() < 30) + return; if (htHetero == null) htHetero = new Hashtable(); - if (line.length() < 30) - return; String groupName = parseToken(line, 7, 10); if (htHetero.contains(groupName)) return; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-05-05 15:26:43
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Revision: 7587 http://svn.sourceforge.net/jmol/?rev=7587&view=rev Author: hansonr Date: 2007-05-05 08:26:42 -0700 (Sat, 05 May 2007) Log Message: ----------- 11.1.32 fix for PdbReader failing on short HET lines. Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2007-05-05 15:23:44 UTC (rev 7586) +++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2007-05-05 15:26:42 UTC (rev 7587) @@ -499,7 +499,7 @@ String groupName = parseToken(line, 7, 10); if (htHetero.contains(groupName)) return; - String hetName = line.substring(30, Math.min(line.length(),70)).trim(); + String hetName = parseTrimmed(line, 30, 70); htHetero.put(groupName, hetName); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-05-14 13:27:07
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Revision: 7691 http://svn.sourceforge.net/jmol/?rev=7691&view=rev Author: hansonr Date: 2007-05-14 06:27:05 -0700 (Mon, 14 May 2007) Log Message: ----------- 11.1.39 bug fix for PDB files not supplying information about residues for the popup menu. Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2007-05-14 12:42:30 UTC (rev 7690) +++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2007-05-14 13:27:05 UTC (rev 7691) @@ -169,6 +169,7 @@ return atomSetCollection; } + int atomCount; void atom() { boolean isHetero = line.startsWith("HETATM"); char charAlternateLocation = line.charAt(16); @@ -253,7 +254,7 @@ atom.insertionCode = JmolAdapter.canonizeInsertionCode(insertionCode); atom.radius = radius; atomSetCollection.addAtom(atom); - if (atom.atomIndex == 0) + if (atomCount++ == 0) atomSetCollection.setAtomSetAuxiliaryInfo("isPDB", Boolean.TRUE); // note that values are +1 in this serial map serialMap[serial] = atomSetCollection.getAtomCount(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2008-04-28 07:21:10
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Revision: 9331 http://jmol.svn.sourceforge.net/jmol/?rev=9331&view=rev Author: hansonr Date: 2008-04-28 00:21:07 -0700 (Mon, 28 Apr 2008) Log Message: ----------- version=11.5.32 # new feature: load [file info] FILTER "[filter string]" # new feature: load [file info] FILTER "BIOMOLECULE n" # new feature: load [file info] FILTER "BIOMOLECULE n;APPLY SYMMETRY" # new feature: load [file info] FILTER "[filter string];BIOMOLECULE n" # # The first format loads only those atoms matching a specific filter or set of # filter terms -- only a crude filter here, only for PDB files: # # .XX an atom name, such as .CA # :X a chain ID # ^X an insertion code # %X an alternative location code # # multiple matches are allowed -- implied AND: # # load "1sva.pdb" FILTER "*.CA" # # the match IS CASE SENSITIVE # # also, "BIOMOLECULE 1" automatically selects for the chains listed for biomolecule 1 # in REMARK 350, and APPLY SYMMETRY applies the symmetry as described in those REMARKS # Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2008-04-28 07:19:29 UTC (rev 9330) +++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2008-04-28 07:21:07 UTC (rev 9331) @@ -28,6 +28,8 @@ import org.jmol.api.JmolAdapter; +import org.jmol.util.Logger; + import java.io.BufferedReader; import java.util.Hashtable; import java.util.Vector; @@ -221,6 +223,7 @@ chainlist = ":" + line.replace(' ', ':'); if (filter != null && filter.toUpperCase().indexOf("BIOMOLECULE " + iMolecule + ";") >= 0) { filter += chainlist; + Logger.info("filter set to \"" + filter + "\""); this.biomts = biomts; } continue; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2008-04-29 20:48:16
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Revision: 9341 http://jmol.svn.sourceforge.net/jmol/?rev=9341&view=rev Author: hansonr Date: 2008-04-29 13:48:10 -0700 (Tue, 29 Apr 2008) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2008-04-29 20:14:09 UTC (rev 9340) +++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2008-04-29 20:48:10 UTC (rev 9341) @@ -141,7 +141,7 @@ formul(); continue; } - if (line.startsWith("REMARK 350")) { + if (line.startsWith("REMARK 350 GENERATING THE BIOMOLECULE")) { remark350(); continue; } @@ -243,6 +243,8 @@ Logger.info("filter set to \"" + filter + "\""); this.biomts = biomts; } + if (info == null) + return; //bad file format info.put("chains", chainlist); continue; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |