From: <ha...@us...> - 2011-10-28 14:31:28
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Revision: 16415 http://jmol.svn.sourceforge.net/jmol/?rev=16415&view=rev Author: hansonr Date: 2011-10-28 14:31:17 +0000 (Fri, 28 Oct 2011) Log Message: ----------- first shot at TLS parser for PDBReader. more fully tested. Adds REMARK 7 support (1zyg) Use getProperty auxiliaryInfo.models[1].tlsGroups to inspect. 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 2011-10-28 14:22:34 UTC (rev 16414) +++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2011-10-28 14:31:17 UTC (rev 16415) @@ -218,7 +218,7 @@ remark290(); return false; } - if (!tlsSeen && line.indexOf("TLS") > 0) { + if (!tlsSeen && line.indexOf("TLS DETAILS") > 0) { return remarkTls(); } checkLineForScript(); @@ -1193,6 +1193,12 @@ REMARK 3 REMARK 3 TLS GROUP : 2 ... + or (1zy8) + REMARK 7 + REMARK 7 TLS DEFINITIONS USED IN A FEW FINAL ROUNDS + REMARK 7 OF REFINEMENT: + REMARK 7 TLS DETAILS + */ private boolean remarkTls() throws Exception { int nGroups = 0; @@ -1202,7 +1208,8 @@ List<Map<String, Object>> ranges = null; Map<String, Object> range = null; tlsSeen = true; - while (readLine() != null && line.startsWith("REMARK 3")) { + String remark = line.substring(0, 11); + while (readLine() != null && line.startsWith(remark)) { try { String[] tokens = getTokens(line.substring(10).replace(':', ' ')); if (tokens.length < 2) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |