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Revision 1520 - Directory Listing
Modified Mon Feb 6 16:21:48 2012 UTC (7 years, 8 months ago) by jmduarteg
More improvements and another exclude list
Revision 1519 - Directory Listing
Modified Mon Feb 6 11:54:21 2012 UTC (7 years, 8 months ago) by jmduarteg
Improved the symmetry redundancy elimination test and added exclude list for a special case
Revision 1517 - Directory Listing
Modified Fri Jan 27 16:32:26 2012 UTC (7 years, 8 months ago) by jmduarteg
A couple of fixes to the new test 
Revision 1516 - Directory Listing
Modified Thu Jan 26 17:12:57 2012 UTC (7 years, 8 months ago) by jmduarteg
New test for interface finder with/without redundancy elimination
Revision 1513 - Directory Listing
Modified Wed Jan 25 11:37:32 2012 UTC (7 years, 8 months ago) by jmduarteg
Implemented some basic symmetry redundancy elimination in interfaces search. Moved interfaces-search to a separate class.
New pymol output file in enumerateInterfaces with all interfaces in a single session
Revision 1491 - Directory Listing
Modified Thu Nov 17 14:56:11 2011 UTC (7 years, 11 months ago) by jmduarteg
Now can pass option -v to blast (max number of hits reported)
Revision 1479 - Directory Listing
Modified Fri Oct 14 09:26:13 2011 UTC (8 years ago) by jmduarteg
Improved pisa assembly parsing and implemented a oligomeric predictor to automatically call the oligomeric assembly type from the PISA output
Revision 1472 - Directory Listing
Modified Wed Sep 28 15:06:19 2011 UTC (8 years ago) by jmduarteg
Fixed a couple of problems with ScopConnection. Added another atom type.
Revision 1455 - Directory Listing
Modified Mon Aug 22 14:51:20 2011 UTC (8 years, 1 month ago) by jmduarteg
Committing test case file that was missing since a few revisions
Revision 1448 - Directory Listing
Modified Thu Aug 18 15:23:57 2011 UTC (8 years, 1 month ago) by jmduarteg
Fixed bug in PDB file parsing: wasn't parsing correctly PDB files with no TER records and non-poly HETATMs. They were both merged together into one chain.
Revision 1447 - Directory Listing
Modified Thu Aug 18 11:51:33 2011 UTC (8 years, 2 months ago) by jmduarteg
Removing duplicate entry
Revision 1446 - Directory Listing
Modified Thu Aug 18 10:55:24 2011 UTC (8 years, 2 months 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 (8 years, 2 months 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 (8 years, 2 months ago) by jmduarteg
Removed a strange entry (after july 2011 remediation) from test list
Revision 1431 - Directory Listing
Modified Mon Aug 1 15:04:21 2011 UTC (8 years, 2 months ago) by jmduarteg
Changed behaviour of getId() in ChainInterfaceList, now uses the same ids as the interfaces, i.e. starts counting from 1 and not from 0.
New graph classes for storing interface topology
Revision 1428 - Directory Listing
Modified Fri Jul 8 13:42:10 2011 UTC (8 years, 3 months ago) by jmduarteg
Fixed bug: was calculating ASAs/BSAs with Hydrogen atoms when they were present. Calculating without them is more common practice and most importantly makes more comparable prots with/without hydrogens. Now removing Hydrogens before interfaces calculation
Revision 1419 - Directory Listing
Modified Thu Jun 16 13:34:25 2011 UTC (8 years, 4 months ago) by jmduarteg
Improvements mainly to ChainInterface and associated classes: now can detect a lot more specific interactions in interface: disulfides, hydrogen bonds, any other kind of close interactions
Revision 1417 - Directory Listing
Modified Fri Jun 10 08:31:42 2011 UTC (8 years, 4 months ago) by jmduarteg
Some improvements and fixes to enumerateInterfaces
Revision 1405 - Directory Listing
Modified Thu May 26 15:56:12 2011 UTC (8 years, 4 months ago) by jmduarteg
Now can calculate interfaces also for non-polymer chains, introduced new parameter to do only polymer chains or both poly/non-poly.
Revision 1404 - Directory Listing
Modified Thu May 26 10:24:55 2011 UTC (8 years, 4 months ago) by jmduarteg
Introduced some more checks in PDB file parser, now should be even more robust with badly formatted files.
Added some more atom types.
Revision 1400 - Directory Listing
Modified Tue May 24 12:24:01 2011 UTC (8 years, 4 months ago) by jmduarteg
Fixed some issues with writing of pdb files and wrote a test for write/read pdb files.
Revision 1397 - Directory Listing
Modified Mon May 23 15:55:38 2011 UTC (8 years, 4 months ago) by jmduarteg
Now using hetatoms for testing interfaces against pisa
Revision 1392 - Directory Listing
Modified Thu May 19 14:27:50 2011 UTC (8 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 1376 - Directory Listing
Modified Thu Mar 31 07:59:09 2011 UTC (8 years, 6 months ago) by jmduarteg
Another test
Revision 1372 - Directory Listing
Modified Wed Mar 30 09:55:49 2011 UTC (8 years, 6 months ago) by jmduarteg
MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
Revision 1358 - Directory Listing
Modified Mon Mar 28 09:32:42 2011 UTC (8 years, 6 months ago) by jmduarteg
More optimisation on geometric hashing algorithm.
Revision 1341 - Directory Listing
Modified Tue Mar 15 08:40:43 2011 UTC (8 years, 7 months ago) by jmduarteg
Now parsing pdb titles in PDB, CIF and pdbase. Tests pass.
Moved some constants from Pdb to PdbAsymUnit
Revision 1337 - Directory Listing
Modified Fri Mar 11 08:47:52 2011 UTC (8 years, 7 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 (8 years, 7 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 1330 - Directory Listing
Modified Tue Mar 8 09:11:34 2011 UTC (8 years, 7 months ago) by jmduarteg
Now the re-numbering of residue serials in PDB files has been improved. Instead of aligning the sequences whenever the serials don't match SEQRES, we first try to see if there is a shift in the serials with respect to SEQRES (happens in many cases). Only if we can't find a shift that fully matches SEQRES we proceed to re-aligning. We also treat properly now the ins codes. Mapping is as close to CIF as possible. The parsers test passes for the whole cullpdb20. For some entries like 2ofz the mapping does not coincide 100% with CIF as there are ambiguities in the alignment.
Revision 1329 - Directory Listing
Modified Sat Mar 5 15:38:12 2011 UTC (8 years, 7 months ago) by jmduarteg
Important change: now the PDB file reader will try to read and fix the numbering of PDB files. Whenever the alignment is wrong it will realign and renumber using the jaligner package. The result of reading original PDB files now will be the same as that of reading CIF files, including proper mapping of classical PDB numbers to SEQRES residue serials (as in CIF). 
There is one change of behaviour in comparison to before: when no SEQRES present the sequence is taken to be that of ATOM lines instead of padding it with Xs.
Still in this version the re-alignment is not perfect as there are some times when ambiguities occur and they are not solved (e.g. in 2nwr where alignment in an unobserved loop can be at two possible places for a GLY). That is anyway a rather minor problem (coordinates are still fine, just the chain is not ordered correctly at 1 or 2 points) and rare (~1% of files)
Revision 1328 - Directory Listing
Modified Thu Mar 3 15:45:42 2011 UTC (8 years, 7 months ago) by jmduarteg
Removed two exception classes that were only used privately, didn't make much sense. Now using PdbLoadException
Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (8 years, 7 months ago) by jmduarteg
Renamed xxxxError classes to xxxxException as they should be.
Revision 1324 - Directory Listing
Modified Thu Mar 3 10:55:54 2011 UTC (8 years, 7 months ago) by jmduarteg
A few bug fixes and improvements in pdb data parsing.
- bug fix: in some cases exptl method field has more than 1 value (e.g. 2krl). In cif files this was causing a null pointer. We now parse it properly (taking first one as the exptl method) in both cif and pdb files
- improved very slightly the cif file parser moving out of loops the index getters
- drop fullLength as a field in Pdb, now we have only getFullLength()
- pdb file atom parsing is now column based and not regex based (hopefully will make it slightly faster)
- now parsing the element column of pdb files: now the atom type detection comes from the appropriate field in pdb/cif/pdbase. If in pdb file and not present we still try to guess it as before

Revision 1316 - Directory Listing
Modified Wed Feb 9 15:55:49 2011 UTC (8 years, 8 months ago) by jmduarteg
Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
Revision 1314 - Directory Listing
Modified Wed Feb 9 11:36:04 2011 UTC (8 years, 8 months ago) by jmduarteg
Finally got rid of all duplicated amino acid methods in AAinfo. Now everything unified in AminoAcid enum.
Revision 1313 - Directory Listing
Modified Wed Feb 9 10:28:56 2011 UTC (8 years, 8 months ago) by jmduarteg
Now taking paths from owl_test_paths.dat file
Revision 1308 - Directory Listing
Modified Fri Jan 28 18:44:21 2011 UTC (8 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 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (8 years, 8 months ago) by jmduarteg
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
Revision 1304 - Directory Listing
Modified Sun Jan 16 16:06:09 2011 UTC (8 years, 9 months ago) by jmduarteg
Fixed important bug: we didn't model the blast data properly. A hit is composed of several hsps. Now our classes following that data model properly (before we treated a hit as an hsp).
Revision 1296 - Directory Listing
Modified Fri Jan 7 11:16:43 2011 UTC (8 years, 9 months ago) by jmduarteg
Bringing back the PISA classes for interface, molecule and residues. We store things first into them and only then convert to our own ChainInterface if needed. This is a much better approach less prone to errors. Tests pass.
Revision 1293 - Directory Listing
Modified Mon Dec 20 09:35:49 2010 UTC (8 years, 9 months ago) by jmduarteg
Now parsing experimental method, resolution, R free and R sym.
Revision 1277 - Directory Listing
Modified Tue Nov 9 14:22:53 2010 UTC (8 years, 11 months ago) by jmduarteg
Forgot to fix 2 problems in last commit.
Revision 1270 - Directory Listing
Modified Tue Oct 26 15:28:24 2010 UTC (8 years, 11 months ago) by jmduarteg
Fixed bug: was still not converting well algebraic transformations to matrix: was failing for transformations with terms like "X-Y+1/3"
Revision 1269 - Directory Listing
Modified Tue Oct 26 13:42:40 2010 UTC (8 years, 11 months ago) by jmduarteg
Fixed bug in SpaceGroupTest. Now it works and test passes.
Introduced checking for clashes in interfaces. Added it to the PdbAsymUnitTest
Revision 1268 - Directory Listing
Modified Fri Oct 22 17:07:57 2010 UTC (8 years, 11 months ago) by jmduarteg
Fixed some bugs with parsing symop.lib and conversion of transformations. Properly testing SpaceGroups and parsing now. Still one test (transpose equal inverse) does not work for trigonal and hexagonal groups.
Revision 1258 - Directory Listing
Modified Fri Oct 8 13:15:13 2010 UTC (9 years ago) by jmduarteg
Fixed bug: now we properly parse from pisa both the orthonormal and the crystal coords operators.
Added a test for SpaceGroup to test for proper parsing of algebraic strings
Revision 1254 - Directory Listing
Modified Thu Oct 7 08:38:10 2010 UTC (9 years ago) by jmduarteg
Made conf file path a resource path so that it is readable from jar file too.
Revision 1252 - Directory Listing
Modified Wed Oct 6 14:22:03 2010 UTC (9 years ago) by jmduarteg
Implemented some parallelisation in ASA calculation. It doesn't scale very well (could measure x2 speed-up with 4 CPUs in a Core2 Quad) but at least we have it, now this is starting to be better than NACCESS!
Revision 1251 - Directory Listing
Modified Tue Oct 5 12:46:24 2010 UTC (9 years ago) by jmduarteg
Some more complete tests.
Revision 1249 - Directory Listing
Modified Mon Oct 4 14:30:40 2010 UTC (9 years ago) by jmduarteg
Some optimisation of the asa code, run time improved substantially.
Revision 1247 - Directory Listing
Modified Fri Oct 1 12:53:40 2010 UTC (9 years ago) by jmduarteg
Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!
Revision 1246 - Directory Listing
Modified Thu Sep 30 16:19:58 2010 UTC (9 years ago) by jmduarteg
Some minor improvements: now populating ids of ChainInterfaces, now interface area is half to match pisa's. 
Fixed bug in getAllInterfaces tester, wasn't comparing properly in small values. 
Revision 1244 - Directory Listing
Modified Thu Sep 30 09:09:36 2010 UTC (9 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 (9 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 (9 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 1238 - Directory Listing
Modified Tue Sep 21 09:43:32 2010 UTC (9 years ago) by jmduarteg
Fixed minor bug in test, was not comparing properly the interface count of pisa vs ours.
Revision 1230 - Directory Listing
Modified Wed Sep 8 16:30:40 2010 UTC (9 years, 1 month ago) by jmduarteg
Fixed bug: bsa values were wrongly calculated. 
Now sort of interfaces is always descending.
Some more testing for individual residues asa and bsa values. 
Still an issue: individual bsas are not matching pisa's even though total interface areas are fine.
Revision 1228 - Directory Listing
Modified Tue Sep 7 15:41:50 2010 UTC (9 years, 1 month ago) by jmduarteg
Now PISA interfaces using same classes as our own calculated interfaces. Removed all Pisa specific classes (except for connector and parser). Introduce new class ChainInterfaceList which also simplifies some things.
PdbAsymUnitTest passes.
Revision 1225 - Directory Listing
Modified Wed Sep 1 15:57:23 2010 UTC (9 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 (9 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 (9 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 1208 - Directory Listing
Modified Mon Aug 23 12:09:34 2010 UTC (9 years, 1 month ago) by cvehlow
Scoring:KendallsTau-method added to  Statistics
Revision 1195 - Directory Listing
Modified Thu Aug 19 09:56:51 2010 UTC (9 years, 1 month ago) by cvehlow
classes moved
Revision 1181 - Directory Listing
Modified Tue Aug 10 15:51:11 2010 UTC (9 years, 2 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 (9 years, 2 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 (9 years, 5 months 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 (9 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 1029 - Directory Listing
Modified Mon Apr 19 09:01:51 2010 UTC (9 years, 5 months 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 (9 years, 6 months 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 (9 years, 6 months ago) by hstehr
refactoring: adapting test packages to match new package structure