schrodinger.structutils.measure.DistanceCellIterator

Iterate through neighbors of specified atoms. This class replaces the dist_cell_iterator function.

Construct the distance cell to use for finding neighbors

Parameters:

struc (schrodinger.structure.Structure) - The structure to use for building the distance cell
dist (float) - The distance cutoff for calculating neighbors
atoms (list) - A list of atom numbers for struc. If given, the distance cell will only contain the specified subset of atoms, so all other atoms will be ignored when calculating neighbors. If not given, all atoms will be used.

Overrides: object.__init__

Iterate over neighboring atoms (atoms within dist Angstrom of each other)

Parameters:

struc (schrodinger.structure.Structure) - The query structure. Neighbors will be found for each atom of this structure. If not given, the structure passed to __init__ will be used as the query structure.
atoms (list) - A list of atom numbers for the query structure. If given, only the specified atoms will be examined. If not given, all atoms of the query structure will be used.

Returns: generator

A generator that iterates through neighbors. Each iteration will yield a tuple of:

Note: This method returns atom indices instead of atom object due to speed concerns. Profiling (using timeit) showed that:

returning atom indices instead of atom objects reduced runtime by ~25%
using coord = mm.mmct_atom_get_xyz(struc.handle, atom_num) in place of coord = struc.atom[atom_num].xyz also reduced runtime by ~25%

Class DistanceCellIterator