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Revision 926 - Directory Listing
Modified Tue Nov 17 13:38:29 2009 UTC (9 years, 11 months ago) by gmueller
helper class
Revision 884 - Directory Listing
Modified Tue Aug 11 16:01:00 2009 UTC (10 years, 2 months ago) by duarte
Major commit: 
- change of the implementation of Pdb (interface remains backwards compatible). Now data stored in a proper object-oriented way. Pdb not abstract anymore, a protein model can be created by using one of the constructors
- added many tests and test files for Pdb (and merged some already existing tests from the default package)
- removed obsolete classes related to msd
- bug fix: PdbfilePdb now properly reads files with alt codes
- all tests passed
Revision 861 - Directory Listing
Modified Fri Jun 5 09:13:01 2009 UTC (10 years, 4 months ago) by duarte
Fixed +1 issues
Revision 860 - Directory Listing
Modified Fri May 29 15:55:47 2009 UTC (10 years, 4 months ago) by gmueller
class to estimate the correlation function to a given error function, deals onlz with Population arrays
Revision 858 - Directory Listing
Modified Fri May 29 15:44:06 2009 UTC (10 years, 4 months ago) by gmueller
new class to deal with arrays of Individuals class, provides methods to generate new arrays of Individuals
Revision 857 - Directory Listing
Modified Fri May 29 15:41:56 2009 UTC (10 years, 4 months ago) by gmueller
major bugs removed and documentation added, couple of method removed to new classes, i.g. Population class and CorrelationFunction class
Revision 856 - Directory Listing
Modified Thu Apr 30 15:21:32 2009 UTC (10 years, 5 months ago) by gmueller
fixed randomSets method
Revision 855 - Directory Listing
Modified Thu Apr 30 14:21:59 2009 UTC (10 years, 5 months ago) by gmueller
new class for some evolution
Revision 853 - Directory Listing
Modified Tue Apr 7 12:47:24 2009 UTC (10 years, 6 months ago) by gmueller
distance map and contact map error function
Revision 845 - Directory Listing
Modified Mon Mar 16 13:26:35 2009 UTC (10 years, 7 months ago) by duarte
Move the scoring methods to their own class as statics. Did a bit of refactoring.
Revision 843 - Directory Listing
Modified Fri Mar 6 16:31:07 2009 UTC (10 years, 7 months ago) by duarte
One more command line argument: contact percent sampling
Revision 835 - Directory Listing
Modified Mon Jan 26 13:38:34 2009 UTC (10 years, 8 months ago) by duarte
Changed scoring: from sum(upi-ui)2 to sum of max(0,upi-ui).
New methods to write subsets to files in table (tab delimited) format.
Now main() writes out all scores/subsets to two files instead of only outputting best, worse and ensemble of bests.
Moved ScoreSet to its own file, new static methods to read subsets from db.
Revision 833 - Directory Listing
Modified Wed Jan 21 10:24:20 2009 UTC (10 years, 8 months ago) by duarte
New method to get an ensemble RIG from a group of best scoring sets.
Revision 832 - Directory Listing
Modified Tue Jan 20 12:01:34 2009 UTC (10 years, 8 months ago) by duarte
Changed the scoring so that is an error function: now it is the average sum square upper bounds deviation from the contact map. A perfect fit to the contact maps is err=0.
Cleaned up, refactored and documented.
Revision 831 - Directory Listing
Modified Mon Jan 19 17:09:04 2009 UTC (10 years, 9 months ago) by duarte
New experimental class Distiller
Revision 826 - Directory Listing
Modified Fri Jan 16 18:26:07 2009 UTC (10 years, 9 months ago) by duarte
Now printing statistics for both lower and upper violations.
Revision 825 - Directory Listing
Modified Fri Jan 16 12:03:14 2009 UTC (10 years, 9 months ago) by duarte
Fixed bug: this time really fixed bug from last revision. Now references of the bounds arrays are properly handled (hopefully!). Tests seem correct: now the output models when metrizing seem not to be correlated anymore
Revision 824 - Directory Listing
Modified Thu Jan 15 18:19:27 2009 UTC (10 years, 9 months ago) by duarte
Fixed bug: was reusing the same bounds after every metrization in reconstruct(), now restarting from the initial bounds for each metrization.
In metrize() final sampled matrix is now always reinitialising seed.

Revision 823 - Directory Listing
Modified Thu Jan 15 16:09:59 2009 UTC (10 years, 9 months ago) by duarte
Now printing restrains viols and bounds viols.
Revision 822 - Directory Listing
Modified Wed Jan 14 16:08:19 2009 UTC (10 years, 9 months ago) by duarte
Now Reconstructer can also take RIGraphs with "unobserved" residues (i.e. with missing nodes).
Model pdb files that Reconstructer creates now contain strictly only CA atoms.
Revision 821 - Directory Listing
Modified Tue Jan 13 18:52:50 2009 UTC (10 years, 9 months ago) by duarte
New classes Reconstructer and ModelPdb. Reconstructer is a one-stop solution for reconstructing from contact maps (RIGraph) using BoundsSmoother and Embedder. At the moment doesn't support reconstruction of contact maps with non-observed residues.
Revision 804 - Directory Listing
Modified Tue Nov 18 17:49:17 2008 UTC (10 years, 11 months ago) by duarte
Made Bound[][] bounds a member, thus changing the signature of most methods. Refactored getBoundsAllPairs(bounds) to better name computeTriangleInequality: now it uses as input the bounds member variable and updates it as output.
Revision 803 - Directory Listing
Modified Tue Nov 18 13:21:34 2008 UTC (10 years, 11 months ago) by duarte
Fisrt full implementation of metrization 
Revision 802 - Directory Listing
Modified Mon Nov 17 18:27:21 2008 UTC (10 years, 11 months ago) by duarte
Some big changes: now internally we use the data structure Bound[][] for all steps. We only use graphs for when we need to calculate shortest paths.
Define some static functions for printing info.
Made the scaling method an option passed as an argument to embed()
Extracted to separate file the Bound class.
Drafted an implementation of metrize
Revision 800 - Directory Listing
Modified Fri Nov 14 17:20:56 2008 UTC (10 years, 11 months ago) by duarte
Introduced scaling of the embedded coordinates (first good embedding ever!!)
Make the random generation more consistent. Also introduced for debugging a fixed seed.
Revision 799 - Directory Listing
Modified Thu Nov 13 17:56:16 2008 UTC (10 years, 11 months ago) by duarte
Fixed in BoundsSmoother: now the lower bound will be set to the triangle inequality value only if the newly found lower bound is bigger than the hard spheres bound.
Now we also introduce contiguous CA distance constraints (3.8)
In main now checking for violations to the full bounds matrix.
New method in Pdb for getting distance matrix as Jama object
Revision 798 - Directory Listing
Modified Thu Nov 13 11:31:06 2008 UTC (10 years, 11 months ago) by duarte
New method in Pdb to set atoms for all coordinates of a given atom. Used in BoundsSmoother and Embedder mains.
Changed slightly how parameters are passed in BoundsSmoother.
Revision 797 - Directory Listing
Modified Wed Nov 12 16:13:39 2008 UTC (10 years, 11 months ago) by duarte
Lower bounds bounds-smoothing now also implemented (using Dijkstra's shortest path algorithm and offsetting to avoid negative weights).
Revision 796 - Directory Listing
Modified Tue Nov 11 10:01:20 2008 UTC (10 years, 11 months ago) by duarte
First implementation of BoundsSmoother. Does only bounds smoothing through triangle inequality for the upper bounds (for lower bounds just takes a hard-spheres distance value)
Revision 787 - Directory Listing
Added Mon Nov 3 14:17:04 2008 UTC (10 years, 11 months ago) by duarte
First implementation of the embedding part of the EMBED algorithm by Havel: from an exact complete distance matrix gives 3d coordinates for the embedding.