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)[source]

Bases: Kick

get_fragments(fragments)[source]
get_input_geom(geom)[source]
get_origin()[source]
kick_fragment(frag_coords)[source]
print_fragments()[source]

17.1.1.15.3. pysisyphus.stocastic.Kick module

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

Bases: Pipeline

get_input_geom(geom)[source]
get_kick()[source]
run_cycle(geom)[source]

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)[source]

Bases: object

atoms_are_too_close(geom, factor=0.7)[source]

Determine if atoms are too close.

geom_is_close_in_energy(geom)[source]
geom_is_new(geom)[source]

Determine if geometry is not already known.

geom_is_valid(geom)[source]

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

get_input_geom(geom)[source]
get_unique_geometries(geoms)[source]
get_valid_index_set(to_intersect)[source]
log(message)[source]

Write a log message.

Wraps the logger variable.

Parameters:

message (str) -- Message to be logged.

run()[source]
run_geom_opt(geom)[source]
write_geoms_to_trj(geoms, fn, comments=None)[source]

17.1.1.15.5. pysisyphus.stocastic.align module

pysisyphus.stocastic.align.apply_transform(coords3d, swap, reflection)[source]

Apply axis swaps and reflections to a coordinate array.

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

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)[source]

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)[source]

Bases: Kick

get_fragments(fragments)[source]
get_input_geom(geom)[source]
get_origin()[source]
kick_fragment(frag_coords)[source]
print_fragments()[source]
class pysisyphus.stocastic.Kick(geom, radius=0.5, **kwargs)[source]

Bases: Pipeline

get_input_geom(geom)[source]
get_kick()[source]
run_cycle(geom)[source]