geomm.grouping module

geomm.grouping.group_complex(coords, complexes_idxs)

TODO

geomm.grouping.group_pair(coords, unitcell_side_lengths, member_a_idxs, member_b_idxs)

For a pair of group of coordinates (e.g. atoms) this moves member_b coordinates to the image of the periodic unitcell that minimizes the difference between the centers of geometry between the two members (e.g. a protein and ligand).

Parameters

• coords (arraylike) – The coordinate array of the particles you will be transforming.

• unitcell_side_lengths (arraylike of shape (3)) – The lengths of the sides of a rectangular unitcell.

• member_a_idxs (arraylike of int of rank 1) – Collection of the indices that define that member of the pair.

• member_b_idxs (arraylike of int of rank 1) – Collection of the indices that define that member of the pair.

Returns

grouped_coords – Transformed coordinates.

Return type

arraylike