Revision 826 - Directory Listing
Modified Fri Jan 16 18:26:07 2009 UTC (13 years, 5 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 (13 years, 5 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 (13 years, 5 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 (13 years, 5 months ago) by duarte

Now printing restrains viols and bounds viols.

Revision 822 - Directory Listing
Modified Wed Jan 14 16:08:19 2009 UTC (13 years, 5 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 (13 years, 5 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 (13 years, 7 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 (13 years, 7 months ago) by duarte

Fisrt full implementation of metrization 

Revision 802 - Directory Listing
Modified Mon Nov 17 18:27:21 2008 UTC (13 years, 7 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 (13 years, 7 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 (13 years, 7 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 (13 years, 7 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 (13 years, 7 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 (13 years, 7 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 (13 years, 7 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.