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[Jmol-commits] SF.net SVN: jmol: [4866] trunk/Jmol/src/org/jmol/adapter/smarter
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From: <eg...@us...> - 2006-04-02 11:05:58
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Revision: 4866 Author: egonw Date: 2006-04-02 04:05:14 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4866&view=rev Log Message: ----------- Step one: the _struct_asym.pdbx_blank_PDB_chainid_flag field is read Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java Added Paths: ----------- trunk/Jmol/src/org/jmol/adapter/smarter/Strand.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java 2006-04-01 09:09:39 UTC (rev 4865) +++ trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java 2006-04-02 11:05:14 UTC (rev 4866) @@ -24,6 +24,8 @@ package org.jmol.adapter.smarter; import java.io.BufferedReader; +import java.util.Hashtable; +import java.util.Map; /** * CIF file reader for CIF and mmCIF files. @@ -43,6 +45,7 @@ String line; RidiculousFileFormatTokenizer tokenizer = new RidiculousFileFormatTokenizer(); + Map strandsMap; void initialize() { notionalUnitcell = new float[6]; @@ -53,6 +56,7 @@ AtomSetCollection readAtomSetCollection(BufferedReader reader) throws Exception { this.reader = reader; atomSetCollection = new AtomSetCollection("cif"); + strandsMap = new Hashtable(); // this loop is a little tricky // the CIF format seems to generate lots of problems for parsers @@ -71,6 +75,8 @@ processCellParameter(); } else if (line.startsWith("_symmetry_space_group_name_H-M")) { processSymmetrySpaceGroupNameHM(); + } else if (line.startsWith("_struct_asym")) { + processStructAsymBlock(); } line = reader.readLine(); } @@ -144,6 +150,10 @@ processAtomSiteLoopBlock(); return; } + if (line.startsWith("_struct_asym")) { + processStructAsymBlock(); + return; + } if (line.startsWith("_geom_bond")) { processGeomBondLoopBlock(); return; @@ -408,6 +418,56 @@ return fieldCount; } + Object[] parseAndProcessStructParameters( + String[] fields, + byte[] fieldMap, + int[] fieldTypes, + boolean[] propertyReferenced) throws Exception { + int fieldCount = 0; + Strand struct = new Strand(); + outer_loop: + for (; line != null && + (line = line.trim()).length() > 0 && + line.charAt(0) == '_'; + ++fieldCount, line = reader.readLine()) { + logger.log("Processing line: ", line); + for (int i = fields.length; --i >= 0; ) { + tokenizer.setString(line); + String key = tokenizer.nextToken(); + // take this valid mmCIF into account: + // _struct_asym.id A + String value = null; + if (tokenizer.hasMoreTokens()) { + value = tokenizer.nextToken(); + logger.log("Found a value: " + value); + logger.log("Found a value: ", value); + switch (fieldTypes[i]) { + case STRUCT_ASYM_ID: + struct.chainID = value; + break; + case STRUCT_BLANK_CHAIN_ID: + struct.isBlank = "Y".equals(value) ? true : false; + break; + } + } else { + struct = null; + } + if (isMatch(key, fields[i])) { + int iproperty = fieldMap[i]; + propertyReferenced[iproperty] = true; + fieldTypes[fieldCount] = iproperty; + continue outer_loop; + } + } + } + logger.log("parseLoopParameters sees fieldCount=" + fieldCount); + logger.log("struct" + struct); + Object[] results = new Object[2]; + results[0] = new Integer(fieldCount); + results[1] = struct; + return results; + } + //////////////////////////////////////////////////////////////// // bond data //////////////////////////////////////////////////////////////// @@ -665,6 +725,97 @@ } //////////////////////////////////////////////////////////////// + // strand data + //////////////////////////////////////////////////////////////// + + final static byte STRUCT_ASYM_ID = 1; + final static byte STRUCT_BLANK_CHAIN_ID = 2; + final static byte STRUCT_PROPERTY_MAX = 18; + + final static String[] structAsymNames = + {"_struct_asym.id", "_struct_asym.pdbx_blank_PDB_chainid_flag"}; + + final static byte[] structAsymMap = { + STRUCT_ASYM_ID, STRUCT_BLANK_CHAIN_ID + }; + + static { + if (structAsymMap.length != structAsymNames.length) + structAsymNames[100] = "explode"; + } + + private void processStructAsymBlock() throws Exception { + // logger.log("processAtomSiteLoopBlock()-------------------------"); + int[] fieldTypes = new int[10]; // should be enough + boolean[] structPropertyReferenced = new boolean[STRUCT_PROPERTY_MAX]; + Object[] results = parseAndProcessStructParameters( + structAsymNames, structAsymMap, + fieldTypes, structPropertyReferenced); + int fieldCount = ((Integer)results[0]).intValue(); + Strand struct = ((Strand)results[1]); + // now that headers are parsed, check to see if we want + // cartesian or fractional coordinates; + if (struct != null) { + /* Then this syntax was found: + * _struct_asym.id A + * _struct_asym.pdbx_blank_PDB_chainid_flag Y + * _struct_asym.pdbx_modified N + * _struct_asym.entity_id 1 + * _struct_asym.details ? + * # + */ + logger.log("Found only one chain: " + struct.chainID.length()); + logger.log("Found only one chain: ", struct.chainID); + strandsMap.put(struct.chainID, struct); + } else { + /* Then the 'normal' _loop format was found. */ + logger.log("Found multiple chains... parsing them now"); + for (; line != null; line = reader.readLine()) { + int lineLength = line.length(); + if (lineLength == 0) + break; + char chFirst = line.charAt(0); + if (chFirst == '#' || + chFirst == '_' || + line.startsWith("loop_") || + line.startsWith("data_")) + break; + if (chFirst == ' ') { + int i; + for (i = lineLength; --i >= 0 && line.charAt(i) == ' '; ) { + } + if (i < 0) + break; + } + // logger.log("line:" + line); + // logger.log("of length = " + line.length()); + if (line.length() == 1) + System.out.println("char value is " + (chFirst + 0)); + tokenizer.setString(line); + // logger.log("reading an atom"); + struct = new Strand(); + for (int i = 0; i < fieldCount; ++i) { + if (! tokenizer.hasMoreTokens()) + tokenizer.setString(reader.readLine()); + String field = tokenizer.nextToken(); + if (field == null) + System.out.println("field == null!"); + switch (fieldTypes[i]) { + case STRUCT_ASYM_ID: + struct.chainID = field; + break; + case STRUCT_BLANK_CHAIN_ID: + struct.isBlank = "Y".equals(field) ? true : false; + break; + } + } + logger.log(" found chain: ", struct.chainID); + strandsMap.put(struct.chainID, struct); + } + } + } + + //////////////////////////////////////////////////////////////// // special tokenizer class //////////////////////////////////////////////////////////////// Added: trunk/Jmol/src/org/jmol/adapter/smarter/Strand.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Strand.java (rev 0) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Strand.java 2006-04-02 11:05:14 UTC (rev 4866) @@ -0,0 +1,39 @@ +/* $RCSfile$ + * $Author: egonw $ + * $Date: 2005-11-10 16:52:44 +0100 (Thu, 10 Nov 2005) $ + * $Revision: 4255 $ + * + * Copyright (C) 2006 Jmol Development, www.jmol.org + * + * Contact: mi...@jm... + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.jmol.adapter.smarter; + +class Strand { + + String chainID; + String authorID; + boolean isBlank; + + Strand() { } + + Strand(String chainID, String authorID, boolean isBlank) { + this.chainID = chainID; + this.authorID = authorID; + this.isBlank = isBlank; + } +} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |