Revision
1244 -
Directory Listing
Modified
Thu Sep 30 09:09:36 2010 UTC
(11 years, 9 months 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
(11 years, 9 months 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
(11 years, 9 months 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
(11 years, 10 months 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
(11 years, 10 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, 10 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
1030 -
Directory Listing
Modified
Mon Apr 19 09:39:07 2010 UTC
(12 years, 2 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
987 -
Directory Listing
Modified
Thu Mar 18 11:08:58 2010 UTC
(12 years, 3 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, 5 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
(12 years, 10 months 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
