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Revision 1059 - Directory Listing
Modified Wed May 5 14:28:19 2010 UTC (9 years, 8 months ago) by jmduarteg
Fixed java doc
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (9 years, 9 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 (9 years, 9 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 (9 years, 9 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 (9 years, 11 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 (9 years, 11 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 (9 years, 11 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 (9 years, 11 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 (9 years, 11 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 (10 years 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 (10 years 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 (10 years, 4 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 (10 years, 4 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 (10 years, 4 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.