mmtbx.ions.geometry module

This module provides tools for examining a set of vectors and find the geometry that best fits from a set of built in shapes.

mmtbx.ions.geometry.find_coordination_geometry(nearby_atoms, minimizer_method=False, cutoff=2.9)

Searches through a list of geometries to find those that fit nearby_atom.

Geometries are recognized by generating a list of all combinations of angles between the vectors and comparing them against the angles among the vectors of the ideal geometry.

Parameters:

  • nearby_atoms (list of mmtbx.ions.environment.atom_contact) – A list of atom contacts, indicating the vertices of the shape to be recognized.

  • minimizer_method (bool, optional) – Optional parameter to use the new, more efficient version of geometry recognition. The old method will be depreciated in later versions of cctbx.

  • cutoff (float, optional) – A cutoff distance, past which vectors are not included in geometry calculations.

Returns:

A list of found geometries. Each tuple contains the name of the geometry in string form followed by the deviation from ideal angles.

Return type:

list of tuples of str, float

See also

mmtbx.ions.geometry.SUPPORTED_GEOMETRY_NAMES, mmtbx.ions.geometry.SUPPORTED_GEOMETRIES_OLD