schrodinger.application.matsci.boltzmann_avg_props module¶

Utilities for Boltzmann averaging properties.

schrodinger.application.matsci.boltzmann_avg_props.get_conformer_dict(sts)¶

Return a dictionary of conformers binned from the given structures.

Parameters: sts (list[schrodinger.structure.Structure]) – the structures from which to bin conformers
Return type: dict
Returns: binned conformers, keys are str that are conformer hashes, values are list[schrodinger.structure.Structure]

schrodinger.application.matsci.boltzmann_avg_props.get_rxnwf_structures(conformer_dict, allow_sibling_groups=False)¶

Return structures prepared for a reaction workflow.

Parameters

conformer_dict (dict) – binned conformers, keys are str that are conformer hashes, values are list[schrodinger.structure.Structure]
allow_sibling_groups (bool) – whether to allow sibling groups

Return type

list[schrodinger.structure.Structure]

Returns

structures prepared for a reaction workflow

schrodinger.application.matsci.boltzmann_avg_props.get_averaged_properties(sts, energy_property_names, temps=None, allow_sibling_groups=False, atomic=False, only_lowest_energy=False, dedup_geom_eps=0.25)¶

Return averaged properties.

Parameters

sts (list[schrodinger.structure.Structure]) – the structures whose properties will be averaged
energy_property_names (list) – the energy property names to use for averaging
temps (list) – temperatures in K, only used for temperature independent property keys
allow_sibling_groups (bool) – whether to average over sibling groups
atomic (bool) – whether to also average atomic properties
only_lowest_energy (bool) – Use only the lowest energy conformer rather than averaging over conformers
dedup_geom_eps (float) – reduce the number of calculations by deduplicating the input structures based on geometry, using this threshold in Ang., and only calculating the representatives, a value of zero means no deduplicating

Raises

ValueError – if there is an issue

Return type

list[reaction_workflow_utils.EnergyAnalysisProperty]

Returns

the averaged properties

schrodinger.application.matsci.boltzmann_avg_props.get_representatives(sts, energy_property_name, temps=None, atomic=False, only_lowest_energy=False, dedup_geom_eps=0.25)¶

Return representative structures marked with average properties.

Parameters

sts (list[schrodinger.structure.Structure]) – the structures whose properties will be averaged
energy_property_name (str) – the energy property name to use for averaging
temps (list) – temperatures in K, only used for temperature independent property keys
atomic (bool) – whether to also average atomic properties
only_lowest_energy (bool) – Use only the lowest energy conformer rather than averaging over conformers
dedup_geom_eps (float) – reduce the number of calculations by deduplicating the input structures based on geometry, using this threshold in Ang., and only calculating the representatives, a value of zero means no deduplicating

Raises

ValueError – if there is an issue

Return type

list[schrodinger.structure.Structure]

Returns

the representatives