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Revision 1704 - (view) (annotate) - [select for diffs]
Modified Mon Jan 27 14:32:31 2014 UTC (7 years, 8 months ago) by jmduarteg
File length: 10889 byte(s)
Diff to previous 1695
Fixed bug in cif file parsing: was not tokenising correctly loop elements that had more multi-line quoting mixed with normal quoted fields and several records. Added one more test case for that.
Revision 1695 - (view) (annotate) - [select for diffs]
Modified Mon Jan 20 14:41:23 2014 UTC (7 years, 9 months ago) by jmduarteg
File length: 10716 byte(s)
Diff to previous 1669
Complete rewrite of the cif file parser: 
- not using anymore random access file but storing strings in memory: much faster
- using new helper class CifFieldInfo instead of maps: much more readable
- now correctly treats # as comments
- now will parse mmCIF where field definitions don't start at beginning of line but have some spaces in between
Revision 1669 - (view) (annotate) - [select for diffs]
Modified Fri Sep 20 10:42:28 2013 UTC (8 years, 1 month ago) by nikhilbiyani
File length: 10730 byte(s)
Diff to previous 1641
Implemented bio-unit assembly parsing in the pdb and cif file parsers. 
Revision 1641 - (view) (annotate) - [select for diffs]
Modified Thu Jun 13 09:21:02 2013 UTC (8 years, 4 months ago) by jmduarteg
File length: 10695 byte(s)
Diff to previous 1612
Fixed bug: was null pointing on pdb files with a TER record positioned just before a HETATM record in the middle of a poly chain, now added more checks for duplicated PDB chain codes assignments which will catch that problem plus possibly others
Revision 1612 - (view) (annotate) - [select for diffs]
Modified Mon Jan 28 16:51:13 2013 UTC (8 years, 8 months ago) by jmduarteg
File length: 10614 byte(s)
Diff to previous 1567
Fixed bug: was null pointing in parsing 2bi6 mmCIF file. It had a multi-line quoted value in a _struct_conf non-loop element. We weren't handling that correctly. 
Also added a new peptide-linked 3-letter code het residue
Revision 1567 - (view) (annotate) - [select for diffs]
Modified Tue Jul 31 13:31:31 2012 UTC (9 years, 2 months ago) by jmduarteg
File length: 10488 byte(s)
Diff to previous 1447
Now checking the SCALE1,2,3 PDB records when loading PDB data, in order to detect PDB entries that are not in the standard crystal frame (after remediation of 2011 only 148 non-virus entries are in nonstandard frame, marked with REMARK 285)
Revision 1447 - (view) (annotate) - [select for diffs]
Modified Thu Aug 18 11:51:33 2011 UTC (10 years, 2 months ago) by jmduarteg
File length: 10156 byte(s)
Diff to previous 1446
Removing duplicate entry
Revision 1446 - (view) (annotate) - [select for diffs]
Modified Thu Aug 18 10:55:24 2011 UTC (10 years, 2 months ago) by jmduarteg
File length: 10163 byte(s)
Diff to previous 1445
Another removed entry, this time  a mismatch of titles PDB vs CIF
Revision 1445 - (view) (annotate) - [select for diffs]
Modified Thu Aug 18 10:29:42 2011 UTC (10 years, 2 months ago) by jmduarteg
File length: 10105 byte(s)
Diff to previous 1444
Removed another strange entry (after july 2011 remediation) from test list
Revision 1444 - (view) (annotate) - [select for diffs]
Modified Thu Aug 18 09:56:40 2011 UTC (10 years, 2 months ago) by jmduarteg
File length: 9972 byte(s)
Diff to previous 1392
Removed a strange entry (after july 2011 remediation) from test list
Revision 1392 - (view) (annotate) - [select for diffs]
Modified Thu May 19 14:27:50 2011 UTC (10 years, 5 months ago) by jmduarteg
File length: 9839 byte(s)
Diff to previous 1293
MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
Revision 1293 - (view) (annotate) - [select for diffs]
Modified Mon Dec 20 09:35:49 2010 UTC (10 years, 10 months ago) by jmduarteg
File length: 9596 byte(s)
Diff to previous 1218
Now parsing experimental method, resolution, R free and R sym.
Revision 1218 - (view) (annotate) - [select for diffs]
Modified Wed Sep 1 13:02:18 2010 UTC (11 years, 1 month ago) by jmduarteg
File length: 9051 byte(s)
Diff to previous 1008
Fixed bug: was null pointing in parsing NMR cif files because they don't have crystal parameter fields. Now skipping that properly. Added NMR test entry to test cases.
Revision 1008 - (view) (annotate) - [select for diffs]
Modified Wed Mar 31 14:03:27 2010 UTC (11 years, 6 months ago) by hstehr
File length: 8925 byte(s)
Diff to previous 951
refactoring: adapting test packages to match new package structure
Revision 951 - (view) (annotate) - [select for diffs]
Modified Fri Jan 29 16:12:34 2010 UTC (11 years, 8 months ago) by duarte
Original Path: trunk/src/tests/proteinstructure/data/cullpdb_20
File length: 8925 byte(s)
Diff to previous 884
Reorganised the project with a src folder for java source files.
Added a jars dir with all jars needed for the project.
Added .project and .classpath pointing to relative path of jars. 
The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
Revision 884 - (view) (annotate) - [select for diffs]
Added Tue Aug 11 16:01:00 2009 UTC (12 years, 2 months ago) by duarte
Original Path: trunk/tests/proteinstructure/data/cullpdb_20
File length: 8925 byte(s)
Major commit: 
- change of the implementation of Pdb (interface remains backwards compatible). Now data stored in a proper object-oriented way. Pdb not abstract anymore, a protein model can be created by using one of the constructors
- added many tests and test files for Pdb (and merged some already existing tests from the default package)
- removed obsolete classes related to msd
- bug fix: PdbfilePdb now properly reads files with alt codes
- all tests passed

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