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Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (10 years, 3 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 (10 years, 4 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 (10 years, 4 months ago) by jmduarteg
Finally got rid of all duplicated amino acid methods in AAinfo. Now everything unified in AminoAcid enum.
Revision 1306 - Directory Listing
Modified Tue Jan 25 14:15:20 2011 UTC (10 years, 4 months ago) by jmduarteg
Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
Revision 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (10 years, 4 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 1292 - Directory Listing
Modified Fri Dec 17 18:21:05 2010 UTC (10 years, 5 months ago) by cvehlow
Control database access! for CGAP
Revision 1287 - Directory Listing
Modified Fri Dec 10 15:17:04 2010 UTC (10 years, 6 months ago) by matt4077

Revision 1276 - Directory Listing
Modified Tue Nov 9 13:58:05 2010 UTC (10 years, 7 months ago) by jmduarteg
More methods to report on interfaces clashes. Extracted clash distance constant.
Revision 1269 - Directory Listing
Modified Tue Oct 26 13:42:40 2010 UTC (10 years, 7 months ago) by jmduarteg
Fixed bug in SpaceGroupTest. Now it works and test passes.
Introduced checking for clashes in interfaces. Added it to the PdbAsymUnitTest
Revision 1225 - Directory Listing
Modified Wed Sep 1 15:57:23 2010 UTC (10 years, 9 months ago) by jmduarteg
Now elimination of redundant interfaces not based only on count of edges, but also on identity of each of the contacts (atom's serials, atom codes, residue serials, residue types). Added more test cases. Seems to be working fine.
Revision 1219 - Directory Listing
Modified Wed Sep 1 13:35:16 2010 UTC (10 years, 9 months ago) by hstehr
added some javadoc
Revision 1211 - Directory Listing
Modified Thu Aug 26 08:21:24 2010 UTC (10 years, 9 months ago) by jmduarteg
First implementation of enumeration of interfaces (based on crystal transformations), equivalent to PISA's. This is still a very rough implementation (far too slow) and not totally correct: some of the interfaces are duplicated. Needs more work but still good as a starting point. 
Revision 1208 - Directory Listing
Modified Mon Aug 23 12:09:34 2010 UTC (10 years, 9 months ago) by cvehlow
Scoring:KendallsTau-method added to  Statistics
Revision 1189 - Directory Listing
Modified Thu Aug 12 12:24:04 2010 UTC (10 years, 10 months ago) by jmduarteg
Implemented inter-chain contact calculation (using same hashing algorithm as in intra-chain).
Revision 1182 - Directory Listing
Modified Wed Aug 11 10:17:32 2010 UTC (10 years, 10 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 1177 - Directory Listing
Modified Mon Aug 9 07:44:15 2010 UTC (10 years, 10 months ago) by cvehlow
actual version
Revision 1175 - Directory Listing
Modified Fri Aug 6 09:21:33 2010 UTC (10 years, 10 months ago) by cvehlow
Method to get translated and rotated coordinates.
Revision 1170 - Directory Listing
Modified Wed Aug 4 10:43:52 2010 UTC (10 years, 10 months ago) by hstehr
adding secondary structure functions to RIGEnsemble and GraphAverager: GraphAverager can now use DSSP to get consensus secondary structure from underlying structures.
Revision 1165 - Directory Listing
Modified Fri Jul 30 11:03:57 2010 UTC (10 years, 10 months ago) by cvehlow
HahpMap keytype changed to Pair instead of String
Revision 1158 - Directory Listing
Modified Wed Jul 21 11:00:08 2010 UTC (10 years, 10 months ago) by cvehlow
print function
Revision 1150 - Directory Listing
Modified Tue Jul 6 10:46:50 2010 UTC (10 years, 11 months ago) by cvehlow
PrintOut method ion RIGGeometry
Revision 1135 - Directory Listing
Modified Fri Jun 25 13:40:27 2010 UTC (10 years, 11 months ago) by cvehlow
Check for consistency in translation rotation framework.
Revision 1129 - Directory Listing
Modified Wed Jun 23 10:24:30 2010 UTC (10 years, 11 months ago) by cvehlow
Additional method for coordinate transversion.
Revision 1127 - Directory Listing
Modified Wed Jun 23 09:44:17 2010 UTC (10 years, 11 months ago) by matt4077
New Residuescoringfunctionimplementation
Revision 1125 - Directory Listing
Modified Mon Jun 21 15:39:04 2010 UTC (10 years, 11 months ago) by cvehlow
Rotation and translation procedure transfered into extra class GmbpGeometry
Revision 1118 - Directory Listing
Modified Fri Jun 18 10:34:00 2010 UTC (10 years, 11 months ago) by cvehlow
RIGGeometry: class that computes and stores geometry information for graph based on rotation and translation invariant framework.
Revision 1066 - Directory Listing
Modified Wed May 12 12:00:11 2010 UTC (11 years, 1 month ago) by hstehr
new methods needed for CCCP: RIGraph.addEdgeIJ(i,j,weight), RIGEnsembl.loadFromDirectory(), GraphAverager.addZeroEdges(), SecondaryStructure.print()
Revision 1062 - Directory Listing
Modified Sun May 9 21:54:40 2010 UTC (11 years, 1 month ago) by stehr
fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public
Revision 1052 - Directory Listing
Modified Tue Apr 27 16:07:48 2010 UTC (11 years, 1 month ago) by hstehr
Fixing bad bug in JPredConnection which would always load the results from my test example instead of the real one; some minor edits in RIGraph
Revision 1038 - Directory Listing
Modified Tue Apr 20 10:08:47 2010 UTC (11 years, 1 month ago) by matt4077
revert. wasn't the best idea.
Revision 1037 - Directory Listing
Modified Tue Apr 20 09:53:00 2010 UTC (11 years, 1 month ago) by matt4077
adding phi/psi constraints to edges
Revision 1022 - Directory Listing
Modified Sun Apr 11 17:37:12 2010 UTC (11 years, 2 months ago) by stehr
new methods in RIGEnsemble: loadFromMultiModelFile(File file, String chain), getAverageGraph(), getConsensusGraph(double weightCutoff)
Revision 1021 - Directory Listing
Modified Fri Apr 9 15:30:15 2010 UTC (11 years, 2 months ago) by hstehr
adding some methods to RIGraph which are needed by CMView: discretizeByWeightCutoff(double), discretizeByNumContacts(int), getFullLength()
Revision 1017 - Directory Listing
Modified Fri Apr 9 09:42:32 2010 UTC (11 years, 2 months ago) by jmduarteg
New methods for random sampling a RIGraph and randomly adding noise. The code was already somewhere in the embed package but here seems more convenient.
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (11 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
Added Wed Mar 31 13:00:35 2010 UTC (11 years, 2 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