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Revision 1228 - Directory Listing
Modified Tue Sep 7 15:41:50 2010 UTC (11 years, 3 months ago) by jmduarteg
Now PISA interfaces using same classes as our own calculated interfaces. Removed all Pisa specific classes (except for connector and parser). Introduce new class ChainInterfaceList which also simplifies some things.
PdbAsymUnitTest passes.
Revision 1226 - Directory Listing
Modified Mon Sep 6 10:15:25 2010 UTC (11 years, 3 months ago) by hstehr
Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb
Revision 1225 - Directory Listing
Modified Wed Sep 1 15:57:23 2010 UTC (11 years, 3 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 (11 years, 3 months ago) by hstehr
added some javadoc
Revision 1218 - Directory Listing
Modified Wed Sep 1 13:02:18 2010 UTC (11 years, 3 months ago) by jmduarteg
Fixed bug: was null pointing in parsing NMR cif files because they don't have crystal parameter fields. Now skipping that properly. Added NMR test entry to test cases.
Revision 1217 - Directory Listing
Modified Tue Aug 31 17:11:30 2010 UTC (11 years, 3 months ago) by jmduarteg
First fully working version (this time hopefully for real...) of interface enumeration. Works for many examples, still there are problems in many others due to area discrepancies with pisa, but those are minor things. The elimination of duplicates is based on chain codes and number of contacting atoms, it is of course possible that 2 different interfaces happen to have the same chain codes and same number of contacting atoms (but unlikely). Would need a more fine grained comparison.
New test class to compare automatically to PISA output.
Revision 1216 - Directory Listing
Modified Tue Aug 31 15:02:53 2010 UTC (11 years, 3 months ago) by jmduarteg
Committing a version that 1st) properly places the symoped generated units of the first unit cell in the first unit cell (and not elsewhere like before) 2nd) does not miss any interfaces because of just doing half of the neighbours (e.g. in 7odc it wouldn't work). Now no interfaces are missing but lots of duplicates are found. So not a fully working version yet.
Revision 1215 - Directory Listing
Modified Fri Aug 27 17:03:45 2010 UTC (11 years, 3 months ago) by jmduarteg
Fixed bug: using the negative side of the 26 translations was causing an incorrect number of interfaces reported for 1pmm and 1pmo. Not sure why but for the moment reverting to doing the positive side.
Changed cutoff to 5.9, then both 1pmm and 1pmo match pisa.
Better reporting of symops (now based on matrices converted to algebraic notation), before was not totally correct.
Still problems with the code as it does not match pisa for some examples (probably many), e.g. for 7odc reports 4 instead of 6 interfaces.
Revision 1214 - Directory Listing
Modified Fri Aug 27 09:43:03 2010 UTC (11 years, 3 months ago) by jmduarteg
Faster BSA calculation by avoiding redundant runs of NACCESS.
Revision 1213 - Directory Listing
Modified Fri Aug 27 09:07:13 2010 UTC (11 years, 3 months ago) by jmduarteg
Changed default cutoff to coincide with PISA, entry 1pmm was a good clue (one interface has a 1 atom contact with 6 cutoff). 
Now going to the negative side (instead of positive) when translating the unit cell to coincide with PISA operators.
Revision 1212 - Directory Listing
Modified Thu Aug 26 15:52:49 2010 UTC (11 years, 3 months ago) by jmduarteg
First fully working implementation of interface enumeration!! WAn exact copy of PISA's interface enumeration! (only tested with very few examples so far)
Revision 1211 - Directory Listing
Modified Thu Aug 26 08:21:24 2010 UTC (11 years, 3 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 1209 - Directory Listing
Modified Mon Aug 23 12:25:36 2010 UTC (11 years, 3 months ago) by jmduarteg
Fixed bug: was missing one operator in getTransformations
Revision 1208 - Directory Listing
Modified Mon Aug 23 12:09:34 2010 UTC (11 years, 3 months ago) by cvehlow
Scoring:KendallsTau-method added to  Statistics
Revision 1206 - Directory Listing
Modified Fri Aug 20 13:29:09 2010 UTC (11 years, 3 months ago) by jmduarteg
Moved getTransformations method to Pdb and PdbAsymUnit where it really belongs.
Revision 1205 - Directory Listing
Modified Fri Aug 20 10:49:13 2010 UTC (11 years, 3 months ago) by jmduarteg
Now all crystal transformations work properly: doing the crystal to orthonormal basis conversion properly.
Revision 1204 - Directory Listing
Modified Thu Aug 19 15:06:01 2010 UTC (11 years, 3 months ago) by jmduarteg
Implemented some methods to do translations properly along crystal axes.
Revision 1191 - Directory Listing
Modified Thu Aug 12 15:18:44 2010 UTC (11 years, 3 months ago) by jmduarteg
Considerable clean up of Pdb. Now the algorithm for calculating atom contacts is all under new class Grid (also refactored Box to GridCell). Tests for graph calculations passed.
Revision 1190 - Directory Listing
Modified Thu Aug 12 12:45:24 2010 UTC (11 years, 3 months ago) by jmduarteg
Fixed bug: now properly also including OXTs in inter-chain atom interaction graph calculation.
Revision 1189 - Directory Listing
Modified Thu Aug 12 12:24:04 2010 UTC (11 years, 3 months ago) by jmduarteg
Implemented inter-chain contact calculation (using same hashing algorithm as in intra-chain).
Revision 1188 - Directory Listing
Modified Wed Aug 11 15:33:22 2010 UTC (11 years, 3 months ago) by jmduarteg
New class PdbAsymUnit (which should be called Pdb, but we can't for obvious reasons). 
Fixed bug in Pdb.copy(), wasn't copying the new fields crystalCell and spaceGroup
Revision 1182 - Directory Listing
Modified Wed Aug 11 10:17:32 2010 UTC (11 years, 3 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 1181 - Directory Listing
Modified Tue Aug 10 15:51:11 2010 UTC (11 years, 3 months ago) by jmduarteg
Now parsing the unit cell and crystal space group info when reading PDB sources. New simple script for unit cell volume.
Revision 1180 - Directory Listing
Modified Tue Aug 10 10:48:23 2010 UTC (11 years, 3 months ago) by jmduarteg
Now correctly parsing the right short name field
Revision 1179 - Directory Listing
Modified Tue Aug 10 09:26:16 2010 UTC (11 years, 3 months ago) by jmduarteg
New classes to parse and store crystallographic space groups info.
Revision 1177 - Directory Listing
Modified Mon Aug 9 07:44:15 2010 UTC (11 years, 3 months ago) by cvehlow
actual version
Revision 1176 - Directory Listing
Modified Fri Aug 6 10:03:26 2010 UTC (11 years, 4 months ago) by jmduarteg
Now parsing the occupancy and bfactors from pdbfile, ciffile or pdbase. Tests passed (improved tests so that they can run straight from an pdb ftp mirror with gz files).
Revision 1175 - Directory Listing
Modified Fri Aug 6 09:21:33 2010 UTC (11 years, 4 months ago) by cvehlow
Method to get translated and rotated coordinates.
Revision 1174 - Directory Listing
Modified Thu Aug 5 14:47:11 2010 UTC (11 years, 4 months ago) by jmduarteg
New method setChainCode
Revision 1170 - Directory Listing
Modified Wed Aug 4 10:43:52 2010 UTC (11 years, 4 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 (11 years, 4 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 (11 years, 4 months ago) by cvehlow
print function
Revision 1150 - Directory Listing
Modified Tue Jul 6 10:46:50 2010 UTC (11 years, 5 months ago) by cvehlow
PrintOut method ion RIGGeometry
Revision 1138 - Directory Listing
Modified Mon Jun 28 14:51:24 2010 UTC (11 years, 5 months ago) by cvehlow
Getter for Atoms-TreeMap.
Revision 1135 - Directory Listing
Modified Fri Jun 25 13:40:27 2010 UTC (11 years, 5 months ago) by cvehlow
Check for consistency in translation rotation framework.
Revision 1129 - Directory Listing
Modified Wed Jun 23 10:24:30 2010 UTC (11 years, 5 months ago) by cvehlow
Additional method for coordinate transversion.
Revision 1127 - Directory Listing
Modified Wed Jun 23 09:44:17 2010 UTC (11 years, 5 months ago) by matt4077
New Residuescoringfunctionimplementation
Revision 1125 - Directory Listing
Modified Mon Jun 21 15:39:04 2010 UTC (11 years, 5 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 (11 years, 5 months ago) by cvehlow
RIGGeometry: class that computes and stores geometry information for graph based on rotation and translation invariant framework.
Revision 1111 - Directory Listing
Modified Mon Jun 14 15:50:46 2010 UTC (11 years, 5 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 (11 years, 5 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 (11 years, 6 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 (11 years, 6 months ago) by matt4077
renamed  conflicting ContactMap class.
Revision 1067 - Directory Listing
Modified Wed May 12 16:36:24 2010 UTC (11 years, 6 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 (11 years, 6 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 (11 years, 6 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 (11 years, 7 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 (11 years, 7 months ago) by stehr
New example implementation of ResidueContactScoringFunction
Revision 1052 - Directory Listing
Modified Tue Apr 27 16:07:48 2010 UTC (11 years, 7 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 (11 years, 7 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 (11 years, 7 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 (11 years, 7 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 (11 years, 7 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 (11 years, 7 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 (11 years, 7 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 (11 years, 7 months ago) by matt4077
revert. wasn't the best idea.
Revision 1037 - Directory Listing
Modified Tue Apr 20 09:53:00 2010 UTC (11 years, 7 months ago) by matt4077
adding phi/psi constraints to edges
Revision 1035 - Directory Listing
Modified Mon Apr 19 13:10:39 2010 UTC (11 years, 7 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 (11 years, 7 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 (11 years, 7 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 (11 years, 7 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 (11 years, 7 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 (11 years, 7 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, 7 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, 7 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 (11 years, 8 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 (11 years, 8 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 (11 years, 8 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 (11 years, 8 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 (11 years, 8 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 (11 years, 8 months ago) by hstehr
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core