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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.