ai2_kit.algorithm.aos_analysis module#

ai2_kit.algorithm.aos_analysis.count_shared_polyhedra(input_traj: str, out_dir: str, center: str, ligand: str, cell: list[float], cutoff: float, coord_num: int = -1)[source]#

Count the number of shared polyhedra in each frame of the trajectory.

Parameters:

input_traj – path of input trajectory file
out_dir – path of output directory
center – central atoms, in the format of MDA atom selection string, e.g. ‘name In’
ligand – atoms that surround the central atoms, in the format of MDA atom selection string, e.g. ‘name O’
cell – cell dimensions
cutoff – cutoff distance
coord_num – coordination number

ai2_kit.algorithm.aos_analysis.ecn_analysis(input_traj: str, out_dir: str, center: str, ligand: str, cell: list[float])[source]#

Calculate ECN (effective coordination number) and l_av (average bond length).

Parameters:

input_traj – path of input trajectory file
out_dir – path of output directory
center – central atoms, in the format of MDA atom selection string, e.g. ‘name In’
ligand – atoms that surround the central atoms, in the format of MDA atom selection string, e.g. ‘name O’
cell – cell dimensions