Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (12 years, 2 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 1006 - Directory Listing
Modified Wed Mar 31 13:00:35 2010 UTC (12 years, 2 months ago) by hstehr
Copied from: trunk/src/owl/core/structure/decoyScoring revision 1005

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, 2 months ago) by hstehr
Original Path: trunk/src/owl/core/structure/decoyScoring
Copied from: trunk/src/proteinstructure/decoyScoring revision 1002

refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core

Revision 957 - Directory Listing
Modified Fri Feb 12 15:06:04 2010 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/src/proteinstructure/decoyScoring

Added some useful tools to the default package from my workspace. More clean up.

Revision 952 - Directory Listing
Modified Fri Feb 5 16:41:47 2010 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/src/proteinstructure/decoyScoring

Added some new prediction measures for DecoyScoreSet: rank, delta rmsd, n% enrichment value
Extended the range of the distance bins.

Revision 951 - Directory Listing
Modified Fri Jan 29 16:12:34 2010 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/src/proteinstructure/decoyScoring
Copied from: trunk/proteinstructure/decoyScoring revision 950

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 950 - Directory Listing
Modified Fri Jan 29 11:57:38 2010 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/proteinstructure/decoyScoring
Copied from: trunk/proteinstructure/DecoyScoring revision 948

Major refactoring and clean-up.
Most important changes are some methods in Pdb class: get_graph->getRIGraph and dump2pdb->writeToPDBFile
Removed all specific FileFormatError exception classes, now using only the generic FileFormatError.
All tests passed.

Revision 945 - Directory Listing
Modified Wed Jan 27 16:49:49 2010 UTC (12 years, 4 months ago) by duarte
Original Path: trunk/proteinstructure/DecoyScoring

Added new scoring method: atom distance based scoring (scoring based on multiple distance bins, instead of just on contacts)

Revision 944 - Directory Listing
Modified Fri Jan 22 17:47:21 2010 UTC (12 years, 5 months ago) by duarte
Original Path: trunk/proteinstructure/DecoyScoring

Fixed bug (hopefully, didn't test!) introduced in last revision. Wasn't initialising properly the maps

Revision 942 - Directory Listing
Modified Fri Jan 22 14:03:44 2010 UTC (12 years, 5 months ago) by duarte
Original Path: trunk/proteinstructure/DecoyScoring

Moved up to Scorer initResMap and initAtomMap

Revision 906 - Directory Listing
Modified Tue Sep 22 13:25:42 2009 UTC (12 years, 9 months ago) by duarte
Original Path: trunk/proteinstructure/DecoyScoring

New classes for triplet scoring.

Revision 905 - Directory Listing
Modified Sun Sep 6 10:43:03 2009 UTC (12 years, 9 months ago) by duarte
Original Path: trunk/proteinstructure/DecoyScoring

Now printing some more rmsd stats (numbers of structs below certain rmsd cutoffs).

Revision 904 - Directory Listing
Added Thu Sep 3 15:34:21 2009 UTC (12 years, 9 months ago) by duarte
Original Path: trunk/proteinstructure/DecoyScoring

Moved all decoy scoring stuff to its own package.
Split CombinedScorer into two classes AtomCombinedScorer and ResCombinedScorer. Made combined scorer more efficient: now loading only once the graphs.