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Revision 1111 - Directory Listing
Modified Mon Jun 14 15:50:46 2010 UTC (10 years, 2 months ago) by jmduarteg
Now getPdbResSerFromResSer and getResSerFromPdbResSer will return null/-1 whenever there's no mapping. Allows then for checking from the caller.
Revision 1109 - Directory Listing
Modified Thu Jun 10 16:29:42 2010 UTC (10 years, 2 months ago) by jmduarteg
Deep copy method for Pdb, Residue and Atom. Tested only minimally, likely to have issues now or in the future. Needs a proper test case.
Revision 1094 - Directory Listing
Modified Wed Jun 2 13:19:21 2010 UTC (10 years, 2 months ago) by jmduarteg
Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
Revision 1084 - Directory Listing
Modified Mon May 31 13:38:56 2010 UTC (10 years, 2 months ago) by matt4077
renamed  conflicting ContactMap class.
Revision 1067 - Directory Listing
Modified Wed May 12 16:36:24 2010 UTC (10 years, 3 months ago) by hstehr
fixed a bug in SecondaryStructure.print(); added SecStrucElement.toString()
Revision 1066 - Directory Listing
Modified Wed May 12 12:00:11 2010 UTC (10 years, 3 months 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 (10 years, 3 months ago) by stehr
fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public
Revision 1057 - Directory Listing
Modified Mon May 3 15:51:54 2010 UTC (10 years, 3 months ago) by matt4077
add psi/phi constraints from secondary structure to tinker reconstructions
Revision 1056 - Directory Listing
Modified Fri Apr 30 11:31:45 2010 UTC (10 years, 3 months ago) by stehr
New example implementation of ResidueContactScoringFunction
Revision 1052 - Directory Listing
Modified Tue Apr 27 16:07:48 2010 UTC (10 years, 3 months 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 1049 - Directory Listing
Modified Tue Apr 27 12:36:16 2010 UTC (10 years, 3 months ago) by hstehr
removing @Override annotations which were causing compilation errors for me
Revision 1047 - Directory Listing
Modified Mon Apr 26 16:13:36 2010 UTC (10 years, 3 months ago) by jmduarteg
SecondaryStructure now implements Iterable after refactoring of getIterator
Revision 1046 - Directory Listing
Modified Mon Apr 26 15:26:59 2010 UTC (10 years, 3 months ago) by hstehr
JPredConnection now returns a SecondaryStructure object; some updated javadocs
Revision 1044 - Directory Listing
Modified Mon Apr 26 10:37:14 2010 UTC (10 years, 3 months ago) by hstehr
New interface ResidueContactScoringFunction to be used in CMView and for decoy scoring.
Revision 1042 - Directory Listing
Modified Wed Apr 21 16:11:08 2010 UTC (10 years, 3 months ago) by jmduarteg
New SiftsConnection and SiftsFeature classes for SIFTS pdb to uniprot mapping. Implemented the HasFeatures interface in Pdb. In the future we can hopefully use that mechanism for all features (sec. strucuture, scop and so on)
Revision 1041 - Directory Listing
Modified Wed Apr 21 13:24:18 2010 UTC (10 years, 3 months ago) by hstehr
New class JPredConnection for querying the Barton group's JPred server for secondary structure-, burial- and coiled coil prediction. Minor updates of javadocs.
Revision 1038 - Directory Listing
Modified Tue Apr 20 10:08:47 2010 UTC (10 years, 3 months ago) by matt4077
revert. wasn't the best idea.
Revision 1037 - Directory Listing
Modified Tue Apr 20 09:53:00 2010 UTC (10 years, 3 months ago) by matt4077
adding phi/psi constraints to edges
Revision 1035 - Directory Listing
Modified Mon Apr 19 13:10:39 2010 UTC (10 years, 3 months ago) by jmduarteg
Extracted the EC data parsing code to its own connection class.
Revision 1034 - Directory Listing
Modified Mon Apr 19 12:42:21 2010 UTC (10 years, 3 months ago) by jmduarteg
Extracted Scop parsing code to its own connection class.
Revision 1033 - Directory Listing
Modified Mon Apr 19 12:26:22 2010 UTC (10 years, 3 months ago) by jmduarteg
Extracted the CSA parsing code to its own connection class.
Revision 1032 - Directory Listing
Modified Mon Apr 19 10:13:10 2010 UTC (10 years, 3 months ago) by jmduarteg
Extracted the calc-vol and calc-surf runner code to its own Runner class.
Revision 1031 - Directory Listing
Modified Mon Apr 19 10:00:34 2010 UTC (10 years, 3 months ago) by jmduarteg
Removed the PISA/PQS oligomeric state code because: a) was not used, b) PQS is obsolete, c) I'm going to redo the PISA stuff soon. Oligomeric state should be implemented as some kind of feature.
Revision 1022 - Directory Listing
Modified Sun Apr 11 17:37:12 2010 UTC (10 years, 4 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 (10 years, 4 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 (10 years, 4 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 1012 - Directory Listing
Modified Thu Apr 1 08:41:01 2010 UTC (10 years, 4 months ago) by hstehr
bugfix: hard-coded paths to files aapairsBounds.dat and contactTypes.dat had to be updated following the refactoring (this was already fixed by previous commit); introduced proper error messags if files are not found
Revision 1011 - Directory Listing
Modified Wed Mar 31 20:21:01 2010 UTC (10 years, 4 months ago) by jmduarteg
Fixed bug introduced in refactoring: the resource path for the contact data files is hard coded in the AAinfo class. 
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (10 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 (10 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 (10 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
Added Wed Mar 31 12:29:26 2010 UTC (10 years, 4 months ago) by hstehr
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core