Revision 1132 - Directory Listing
Modified Fri Jun 25 13:01:53 2010 UTC (12 years 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 (12 years ago) by matt4077

New Residuescoringfunctionimplementation

Revision 1106 - Directory Listing
Modified Thu Jun 10 09:24:30 2010 UTC (12 years ago) by jmduarteg

Implemented caching of blast in UniprotHomologList

Revision 1097 - Directory Listing
Modified Mon Jun 7 10:17:58 2010 UTC (12 years, 1 month 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 (12 years, 1 month ago) by jmduarteg

Implemented profile counting and entropy calculation for alignment.

Revision 1070 - Directory Listing
Modified Wed May 19 16:20:42 2010 UTC (12 years, 1 month 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 (12 years, 2 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 (12 years, 2 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 (12 years, 2 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 (12 years, 2 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 (12 years, 2 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 (12 years, 2 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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.