porereax.molecule_structure

Module for sampling molecular structure statistics.

The module provides MoleculeStructureSampler to sample bonding environments of all atomtypes and reveal the atom structures.

Classes

MoleculeStructureSampler

Sampler class for molecule structure analysis.

Module Contents

class porereax.molecule_structure.MoleculeStructureSampler(name_out: str, dimension: str, region, process_id: int, atom_lib: dict, masses: dict, num_frames: int, box: numpy.ndarray, system_properties: dict)

Bases: porereax.meta_sampler.Sampler

Sampler class for molecule structure analysis.

sample(frame_id: int, mol_index: dict, mol_bonds: dict, bond_mask: dict, frame: object, bond_enum: object, positions_transformed: numpy.ndarray)

Sample data for the current frame. Must be implemented by subclasses.

join_samplers(num_cores)

Join sampler data from multiple processes.

Parameters:

num_cores (int) – Number of parallel processes used for sampling.