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