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Revision 1355 - Directory Listing
Modified Fri Mar 25 11:30:15 2011 UTC (9 years, 7 months ago) by hstehr
Fixed some conflicts when running multiple instances of this on the same machine
Revision 1347 - Directory Listing
Modified Mon Mar 21 10:38:06 2011 UTC (9 years, 7 months ago) by hstehr
moving project CCCP to this repository
Revision 1345 - Directory Listing
Modified Thu Mar 17 13:58:32 2011 UTC (9 years, 7 months ago) by jmduarteg
Now the colors of chains of pymol generated images are consistent with the letter codes (given a chain letter code the color will always be the same for it for all images generated)
Revision 1341 - Directory Listing
Modified Tue Mar 15 08:40:43 2011 UTC (9 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 1338 - Directory Listing
Modified Fri Mar 11 16:53:33 2011 UTC (9 years, 7 months ago) by jmduarteg
Fixed bug. Pymol was blocking
Revision 1336 - Directory Listing
Modified Wed Mar 9 11:05:05 2011 UTC (9 years, 7 months ago) by jmduarteg
New runner for pymol
Revision 1335 - Directory Listing
Modified Wed Mar 9 08:38:35 2011 UTC (9 years, 7 months ago) by jmduarteg
Now throwing InterruptedException. Refactor BlastErro to BlastException
Revision 1334 - Directory Listing
Modified Wed Mar 9 08:13:04 2011 UTC (9 years, 7 months ago) by jmduarteg
Refactoring xxxError to xxxException
Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (9 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 (9 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 (9 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 (9 years, 8 months ago) by jmduarteg
Finally got rid of all duplicated amino acid methods in AAinfo. Now everything unified in AminoAcid enum.
Revision 1306 - Directory Listing
Modified Tue Jan 25 14:15:20 2011 UTC (9 years, 9 months ago) by jmduarteg
Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
Revision 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (9 years, 9 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 (9 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 1242 - Directory Listing
Modified Wed Sep 29 15:22:49 2010 UTC (10 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 1230 - Directory Listing
Modified Wed Sep 8 16:30:40 2010 UTC (10 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 1211 - Directory Listing
Modified Thu Aug 26 08:21:24 2010 UTC (10 years, 2 months ago) by jmduarteg
First implementation of enumeration of interfaces (based on crystal transformations), equivalent to PISA's. This is still a very rough implementation (far too slow) and not totally correct: some of the interfaces are duplicated. Needs more work but still good as a starting point. 
Revision 1199 - Directory Listing
Modified Thu Aug 19 10:14:54 2010 UTC (10 years, 2 months ago) by hstehr
added some debug output (commented out)
Revision 1132 - Directory Listing
Modified Fri Jun 25 13:01:53 2010 UTC (10 years, 4 months ago) by jmduarteg
New SelectonRunner class. More taxonomy information retrieved from uniprot.
Revision 1127 - Directory Listing
Modified Wed Jun 23 09:44:17 2010 UTC (10 years, 4 months ago) by matt4077
New Residuescoringfunctionimplementation
Revision 1106 - Directory Listing
Modified Thu Jun 10 09:24:30 2010 UTC (10 years, 4 months ago) by jmduarteg
Implemented caching of blast in UniprotHomologList
Revision 1097 - Directory Listing
Modified Mon Jun 7 10:17:58 2010 UTC (10 years, 4 months ago) by jmduarteg
Now explicitely specifying output dnd file in tcoffee so it can be removed by the calling program.
Revision 1074 - Directory Listing
Modified Fri May 21 10:02:24 2010 UTC (10 years, 5 months ago) by jmduarteg
Implemented profile counting and entropy calculation for alignment.
Revision 1070 - Directory Listing
Modified Wed May 19 16:20:42 2010 UTC (10 years, 5 months ago) by jmduarteg
Fixed bug in TcoffeeRunner. The t_coffee process was hanging after spawning. This didn't happen before, it can be related to the version of t_coffee (I'm using 8.14). Basically t_coffee seems to be doing something weird with stderr and stdout, java doesn't like it and makes the process hang (as usual java has a lot of problems in this area, see StreamGobbler class). The way to solve it is use the -quiet switch of t_coffee that can be used to redirect output to a file or have a complete quiet terminal.
Revision 1057 - Directory Listing
Modified Mon May 3 15:51:54 2010 UTC (10 years, 5 months ago) by matt4077
add psi/phi constraints from secondary structure to tinker reconstructions
Revision 1046 - Directory Listing
Modified Mon Apr 26 15:26:59 2010 UTC (10 years, 6 months ago) by hstehr
JPredConnection now returns a SecondaryStructure object; some updated javadocs
Revision 1045 - Directory Listing
Modified Mon Apr 26 12:55:28 2010 UTC (10 years, 6 months ago) by jmduarteg
Uniprot and embl ws dbfetch connections can now do multiple entries per request. Update to parse also the hit_def tag in blast parser.
Revision 1043 - Directory Listing
Modified Thu Apr 22 12:21:37 2010 UTC (10 years, 6 months ago) by jmduarteg
Fixed blast parsing bug: was parsing the Hit_def tag instead of the Hit_id tag for the subject id. When formatdb is run with option "-o T" then indices are properly generated and Hit_id contains the correct tag.
Revision 1041 - Directory Listing
Modified Wed Apr 21 13:24:18 2010 UTC (10 years, 6 months ago) by hstehr
New class JPredConnection for querying the Barton group's JPred server for secondary structure-, burial- and coiled coil prediction. Minor updates of javadocs.
Revision 1032 - Directory Listing
Modified Mon Apr 19 10:13:10 2010 UTC (10 years, 6 months ago) by jmduarteg
Extracted the calc-vol and calc-surf runner code to its own Runner class.
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (10 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 1007 - Directory Listing
Modified Wed Mar 31 13:27:18 2010 UTC (10 years, 6 months ago) by hstehr
refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
Revision 1006 - Directory Listing
Modified Wed Mar 31 13:00:35 2010 UTC (10 years, 6 months ago) by hstehr
refactoring: created packages runners.blast, runners.gromacs, structure.graphs, moved actionTools to util, structure.decoyScoring to owl.decoyScoring, tinker to runners.tinker
Revision 1005 - Directory Listing
Modified Wed Mar 31 12:29:26 2010 UTC (10 years, 6 months ago) by hstehr
Copied from: trunk/src/runners revision 1002
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Revision 1000 - Directory Listing
Modified Mon Mar 29 10:20:38 2010 UTC (10 years, 7 months ago) by jmduarteg
Original Path: trunk/src/runners
Now DsspRunner is purely static (makes more sense)
Revision 996 - Directory Listing
Modified Thu Mar 25 12:07:41 2010 UTC (10 years, 7 months ago) by matt4077
Original Path: trunk/src/runners
reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.  
Revision 988 - Directory Listing
Modified Thu Mar 18 12:02:13 2010 UTC (10 years, 7 months ago) by jmduarteg
Original Path: trunk/src/runners
Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.

Revision 987 - Directory Listing
Added Thu Mar 18 11:08:58 2010 UTC (10 years, 7 months ago) by jmduarteg
Original Path: trunk/src/runners
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.