17.1.1.15. pysisyphus.stocastic package

17.1.1.15.1. Submodules

17.1.1.15.2. pysisyphus.stocastic.FragmentKick module

class pysisyphus.stocastic.FragmentKick.FragmentKick(geom, fragments, fix_fragments=None, displace_from=None, random_displacement=False, **kwargs)

Bases: Kick

get_fragments(fragments)

get_input_geom(geom)

get_origin()

kick_fragment(frag_coords)

print_fragments()

17.1.1.15.3. pysisyphus.stocastic.Kick module

class pysisyphus.stocastic.Kick.Kick(geom, radius=0.5, **kwargs)

Bases: Pipeline

get_input_geom(geom)

get_kick()

run_cycle(geom)

17.1.1.15.4. pysisyphus.stocastic.Pipeline module

class pysisyphus.stocastic.Pipeline.Pipeline(geom, calc_getter=None, seed=None, max_cycles=5, cycle_size=15, rmsd_thresh=0.1, energy_thresh=0.001, energy_range=0.125, compare_num=25, break_after=2, calc_kwargs=None)

Bases: object

atoms_are_too_close(geom, factor=0.7)

Determine if atoms are too close.

geom_is_close_in_energy(geom)

geom_is_new(geom)

Determine if geometry is not already known.

geom_is_valid(geom)

Filter out geometries that are None, or were the atoms are too close or when they are already known.

get_input_geom(geom)

get_unique_geometries(geoms)

get_valid_index_set(to_intersect)

log(message)

Write a log message.

Wraps the logger variable.

Parameters:

message (str) -- Message to be logged.

run()

run_geom_opt(geom)

write_geoms_to_trj(geoms, fn, comments=None)

17.1.1.15.5. pysisyphus.stocastic.align module

pysisyphus.stocastic.align.apply_transform(coords3d, swap, reflection)

Apply axis swaps and reflections to a coordinate array.

pysisyphus.stocastic.align.match_geom_atoms(ref_geom, geom_to_match, hydrogen=True)

Apply the hungarian method to geom_to_match.

Uses the scipy implementation of the Hungarian method/ Kuhn-Munkres algorithm in scipy.optimize.linear_sum_assignment.

See

[1] 10.1021/ci400534h [2] 10.1021/acs.jcim.6b00516

pysisyphus.stocastic.align.matched_rmsd(geom1, geom2, thresh=0.05)

RMSD for optimally aligned and matched geometries.

Returns:

• matched_rmsd (float) -- RMSD of optimally aligned and matched geometries.

• matched_geoms (tuple(Geometry, Geometry)) -- Tuple of the optimally aligned and matched geometries.

17.1.1.15.6. Module contents

class pysisyphus.stocastic.FragmentKick(geom, fragments, fix_fragments=None, displace_from=None, random_displacement=False, **kwargs)

Bases: Kick

get_fragments(fragments)

get_input_geom(geom)

get_origin()

kick_fragment(frag_coords)

print_fragments()

class pysisyphus.stocastic.Kick(geom, radius=0.5, **kwargs)

Bases: Pipeline

get_input_geom(geom)

get_kick()

run_cycle(geom)