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.