Revision 823 - (view) (annotate) - [select for diffs]
Modified Thu Jan 15 16:09:59 2009 UTC (15 years, 8 months ago) by duarte
File length: 18736 byte(s)
Diff to previous 822

Now printing restrains viols and bounds viols.

Revision 822 - (view) (annotate) - [select for diffs]
Modified Wed Jan 14 16:08:19 2009 UTC (15 years, 8 months ago) by duarte
File length: 18606 byte(s)
Diff to previous 821

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 - (view) (annotate) - [select for diffs]
Modified Tue Jan 13 18:52:50 2009 UTC (15 years, 8 months ago) by duarte
File length: 21160 byte(s)
Diff to previous 804

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 - (view) (annotate) - [select for diffs]
Modified Tue Nov 18 17:49:17 2008 UTC (15 years, 10 months ago) by duarte
File length: 24773 byte(s)
Diff to previous 803

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 - (view) (annotate) - [select for diffs]
Modified Tue Nov 18 13:21:34 2008 UTC (15 years, 10 months ago) by duarte
File length: 23426 byte(s)
Diff to previous 802

Fisrt full implementation of metrization 

Revision 802 - (view) (annotate) - [select for diffs]
Modified Mon Nov 17 18:27:21 2008 UTC (15 years, 10 months ago) by duarte
File length: 21455 byte(s)
Diff to previous 800

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 - (view) (annotate) - [select for diffs]
Modified Fri Nov 14 17:20:56 2008 UTC (15 years, 10 months ago) by duarte
File length: 19572 byte(s)
Diff to previous 799

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 - (view) (annotate) - [select for diffs]
Modified Thu Nov 13 17:56:16 2008 UTC (15 years, 10 months ago) by duarte
File length: 19361 byte(s)
Diff to previous 798

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 - (view) (annotate) - [select for diffs]
Modified Thu Nov 13 11:31:06 2008 UTC (15 years, 10 months ago) by duarte
File length: 17813 byte(s)
Diff to previous 797

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 - (view) (annotate) - [select for diffs]
Modified Wed Nov 12 16:13:39 2008 UTC (15 years, 10 months ago) by duarte
File length: 17191 byte(s)
Diff to previous 796

Lower bounds bounds-smoothing now also implemented (using Dijkstra's shortest path algorithm and offsetting to avoid negative weights).

Revision 796 - (view) (annotate) - [select for diffs]
Added Tue Nov 11 10:01:20 2008 UTC (15 years, 10 months ago) by duarte
File length: 11130 byte(s)

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)