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Revision 1455 - Directory Listing
Modified Mon Aug 22 14:51:20 2011 UTC (11 years, 1 month ago) by jmduarteg
Committing test case file that was missing since a few revisions
Revision 1447 - Directory Listing
Modified Thu Aug 18 11:51:33 2011 UTC (11 years, 1 month ago) by jmduarteg
Removing duplicate entry
Revision 1446 - Directory Listing
Modified Thu Aug 18 10:55:24 2011 UTC (11 years, 1 month ago) by jmduarteg
Another removed entry, this time  a mismatch of titles PDB vs CIF
Revision 1445 - Directory Listing
Modified Thu Aug 18 10:29:42 2011 UTC (11 years, 1 month ago) by jmduarteg
Removed another strange entry (after july 2011 remediation) from test list
Revision 1444 - Directory Listing
Modified Thu Aug 18 09:56:40 2011 UTC (11 years, 1 month ago) by jmduarteg
Removed a strange entry (after july 2011 remediation) from test list
Revision 1392 - Directory Listing
Modified Thu May 19 14:27:50 2011 UTC (11 years, 4 months ago) by jmduarteg
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 1337 - Directory Listing
Modified Fri Mar 11 08:47:52 2011 UTC (11 years, 6 months ago) by jmduarteg
Changing file names of contact map test files, windows didn't like the ':' in the file names
Revision 1332 - Directory Listing
Modified Tue Mar 8 15:00:46 2011 UTC (11 years, 6 months ago) by jmduarteg
Another fix to PdbfilePdb parser. Now it is more robust with bad formatting, tested on a whole tar ball of CASP predictions. Added the CASP predictions test set to tests.
Revision 1308 - Directory Listing
Modified Fri Jan 28 18:44:21 2011 UTC (11 years, 8 months ago) by jmduarteg
Fixed important bug that broke the reconstruction programs. Tinker output files don't contain occupancy/bfactors. Thus we have to make their parsing optional. Added a test case for this.
Revision 1293 - Directory Listing
Modified Mon Dec 20 09:35:49 2010 UTC (11 years, 9 months ago) by jmduarteg
Now parsing experimental method, resolution, R free and R sym.
Revision 1244 - Directory Listing
Modified Thu Sep 30 09:09:36 2010 UTC (12 years ago) by jmduarteg
Finally ASA/BSA comparison to PISA test passes. Have to exclude one case where slight difference interface area values led to different sorting and so comparsion doesn't work. This will still be a problem whenever that happens (whenever different sorting of PISA vs ours)
Revision 1242 - Directory Listing
Modified Wed Sep 29 15:22:49 2010 UTC (12 years ago) by jmduarteg
Fixed bug: NACCESS (weirdly) calculates slightly different ASA values for same molecule in different orientation (i.e. it depends on the choice of axes)!! That produces then some strange BSA values (including some negative) and slight discrepancies. Thus now we run NACCESS always for each of the 2 isolated molecules of the interface and then the complex (and so losing efficiency).
Revision 1241 - Directory Listing
Modified Tue Sep 21 17:08:36 2010 UTC (12 years ago) by jmduarteg
Fixed bug: the bsa values of residues of the different interfaces were being updated on the same references, we have to copy before creating ChainInterface objects in getAllInterfaces.
Implemented interface pdb file outputting in enumerateInterfaces
Still interfaces tests don't pass because of 2 problems: a) order of first/second molecule not necessarily same as PISA (and in case of same chain codes can't catch it with chain codes), b) in many cases there are many minor discrepancies, usually associated to a lot of small negative bsa values.
Revision 1225 - Directory Listing
Modified Wed Sep 1 15:57:23 2010 UTC (12 years, 1 month ago) by jmduarteg
Now elimination of redundant interfaces not based only on count of edges, but also on identity of each of the contacts (atom's serials, atom codes, residue serials, residue types). Added more test cases. Seems to be working fine.
Revision 1218 - Directory Listing
Modified Wed Sep 1 13:02:18 2010 UTC (12 years, 1 month ago) by jmduarteg
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 1217 - Directory Listing
Modified Tue Aug 31 17:11:30 2010 UTC (12 years, 1 month ago) by jmduarteg
First fully working version (this time hopefully for real...) of interface enumeration. Works for many examples, still there are problems in many others due to area discrepancies with pisa, but those are minor things. The elimination of duplicates is based on chain codes and number of contacting atoms, it is of course possible that 2 different interfaces happen to have the same chain codes and same number of contacting atoms (but unlikely). Would need a more fine grained comparison.
New test class to compare automatically to PISA output.
Revision 1030 - Directory Listing
Modified Mon Apr 19 09:39:07 2010 UTC (12 years, 5 months ago) by jmduarteg
Extracted constants to owl_test_paths.dat and added CASP7 fasta files to resources dir. Now BlastParsersTest should be able to run anywhere.
Revision 1008 - Directory Listing
Modified Wed Mar 31 14:03:27 2010 UTC (12 years, 6 months ago) by hstehr
Copied from: trunk/src/tests/proteinstructure/data revision 1006
refactoring: adapting test packages to match new package structure
Revision 987 - Directory Listing
Modified Thu Mar 18 11:08:58 2010 UTC (12 years, 6 months ago) by jmduarteg
Original Path: trunk/src/tests/proteinstructure/data
New package runners for Runner classes. At the moment only contains the new class NaccessRunner (moved out of Pdb class)
Introduced a config file for tests so that one can set externally the executable paths and any other necessary data to run tests (at the moment only implemented in PdbTest.java). PdbTest now should run anywhere (if you have a local pdbase installation!)
Moved the consurf parser out of Pdb to its own class ConsurfConnection in the connection package.

Revision 951 - Directory Listing
Modified Fri Jan 29 16:12:34 2010 UTC (12 years, 8 months ago) by duarte
Original Path: trunk/src/tests/proteinstructure/data
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 - Directory Listing
Modified Tue Aug 11 16:01:00 2009 UTC (13 years, 1 month ago) by duarte
Original Path: trunk/tests/proteinstructure/data
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
Revision 813 - Directory Listing
Added Tue Dec 16 11:11:39 2008 UTC (13 years, 9 months ago) by duarte
Original Path: trunk/tests/proteinstructure/data
Fixed runNaccess to use unique file names and documented it. Wrote also a junit test case for it.