Revision 1032 - Directory Listing
Modified Mon Apr 19 10:13:10 2010 UTC (12 years, 3 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 5 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, 5 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.