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Revision **802** -
Directory Listing

Modified*Mon Nov 17 18:27:21 2008 UTC*
(13 years, 10 months ago)
by *duarte*

Modified

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, 10 months ago)
by *duarte*

Modified

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, 10 months ago)
by *duarte*

Modified

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, 10 months ago)
by *duarte*

Modified

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, 10 months ago)
by *duarte*

Modified

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, 10 months ago)
by *duarte*

Modified

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, 10 months ago)
by *duarte*

Added

First implementation of the embedding part of the EMBED algorithm by Havel: from an exact complete distance matrix gives 3d coordinates for the embedding.