Revision 1218 - Directory Listing
Modified Wed Sep 1 13:02:18 2010 UTC (11 years, 8 months 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 (11 years, 8 months 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 1208 - Directory Listing
Modified Mon Aug 23 12:09:34 2010 UTC (11 years, 8 months ago) by cvehlow

Scoring:KendallsTau-method added to  Statistics

Revision 1195 - Directory Listing
Modified Thu Aug 19 09:56:51 2010 UTC (11 years, 9 months ago) by cvehlow

classes moved

Revision 1181 - Directory Listing
Modified Tue Aug 10 15:51:11 2010 UTC (11 years, 9 months ago) by jmduarteg

Now parsing the unit cell and crystal space group info when reading PDB sources. New simple script for unit cell volume.

Revision 1176 - Directory Listing
Modified Fri Aug 6 10:03:26 2010 UTC (11 years, 9 months ago) by jmduarteg

Now parsing the occupancy and bfactors from pdbfile, ciffile or pdbase. Tests passed (improved tests so that they can run straight from an pdb ftp mirror with gz files).

Revision 1042 - Directory Listing
Modified Wed Apr 21 16:11:08 2010 UTC (12 years ago) by jmduarteg

New SiftsConnection and SiftsFeature classes for SIFTS pdb to uniprot mapping. Implemented the HasFeatures interface in Pdb. In the future we can hopefully use that mechanism for all features (sec. strucuture, scop and so on)

Revision 1030 - Directory Listing
Modified Mon Apr 19 09:39:07 2010 UTC (12 years, 1 month 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 1029 - Directory Listing
Modified Mon Apr 19 09:01:51 2010 UTC (12 years, 1 month ago) by jmduarteg

Fixed hard-coded resources paths broken since major restructuring of project.

Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (12 years, 1 month ago) by hstehr

refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features

Revision 1008 - Directory Listing
Added Wed Mar 31 14:03:27 2010 UTC (12 years, 1 month ago) by hstehr

refactoring: adapting test packages to match new package structure