ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/trunk/src/owl/decoyScoring
Sticky Revision:
Sort logs by:
Revision 1392 - Directory Listing
Modified Thu May 19 14:27:50 2011 UTC (8 years, 4 months ago) by jmduarteg
MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
Revision 1372 - Directory Listing
Modified Wed Mar 30 09:55:49 2011 UTC (8 years, 6 months ago) by jmduarteg
MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (8 years, 7 months ago) by jmduarteg
Renamed xxxxError classes to xxxxException as they should be.
Revision 1316 - Directory Listing
Modified Wed Feb 9 15:55:49 2011 UTC (8 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 (8 years, 8 months ago) by jmduarteg
Finally got rid of all duplicated amino acid methods in AAinfo. Now everything unified in AminoAcid enum.
Revision 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (8 years, 8 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 1208 - Directory Listing
Modified Mon Aug 23 12:09:34 2010 UTC (9 years, 1 month ago) by cvehlow
Scoring:KendallsTau-method added to  Statistics
Revision 1201 - Directory Listing
Modified Thu Aug 19 10:18:59 2010 UTC (9 years, 1 month ago) by hstehr
deleting KendallsTau class (even if it already deleted on the server)
Revision 1182 - Directory Listing
Modified Wed Aug 11 10:17:32 2010 UTC (9 years, 2 months ago) by cvehlow
Implementation of class for KendallsTau Correlation Calculation
Implementation of class for Check for Correctness of Casp server model files
Implementation of class for Calculation of geometric scoring
Revision 1059 - Directory Listing
Modified Wed May 5 14:28:19 2010 UTC (9 years, 5 months ago) by jmduarteg
Fixed java doc
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (9 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 1006 - Directory Listing
Modified Wed Mar 31 13:00:35 2010 UTC (9 years, 6 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, 6 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, 8 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, 8 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, 8 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, 8 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, 8 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 (9 years, 8 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 (9 years, 8 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 (10 years 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, 1 month 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, 1 month 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.