Conformers

Conformers#

class autode.conformers.conformers.Conformers(iterable=(), /)#
copy() → Conformers#

Return a shallow copy of the list.

property lowest_energy: Conformer | None#

Return the lowest energy conformer state from this set. If no conformers have an energy then return None

optimise(method: Method, keywords: Keywords | None = None) → None#

Optimise a set of conformers in parallel

Parameters:

keywords (autode.wrappers.keywords.Keywords)

prune(e_tol: ~autode.values.Energy | float = Energy(1.0 kJ mol-1), rmsd_tol: ~autode.values.Distance | float | None = None, n_sigma: float = 5, remove_no_energy: bool = False) → None#

Prune conformers based on both energy and root mean squared deviation (RMSD) values. Will discard any conformers that are within e_tol in energy (Ha) and rmsd in RMSD (Å) to any other

Parameters:

  • rmsd_tol (Distance | None) – RMSD tolerance. Defaults to autode.Config.rmsd_threshold

  • n_sigma (float | int)

  • remove_no_energy (bool)

prune_diff_graph(graph: MolecularGraph) → None#

Remove conformers with a different molecular graph to a defined reference. Although all conformers should have the same molecular graph there are situations where not pruning these is useful

Parameters:

graph – Reference graph

prune_on_energy(e_tol: ~autode.values.Energy | float = Energy(1.0 kJ mol-1), n_sigma: float = 5) → None#

Prune the conformers based on an energy threshold, discarding those that have energies that are similar to within e_tol. Also discards conformers with very high energies (indicating a problem with the calculation) if the are more than n_sigma standard deviations away from the mean

Parameters:

n_sigma (int) – Number of standard deviations a conformer energy must be from the average for it not to be added

prune_on_rmsd(rmsd_tol: Distance | float | None = None) → None#

Given a list of conformers add those that are unique based on an RMSD tolerance. If rmsd=None then use autode.Config.rmsd_threshold

remove_no_energy() → None#

Remove all conformers from this list that do not have an energy

single_point(method: Method, keywords: Keywords | None = None) → None#

Evaluate single point energies for a set of conformers in parallel

Parameters:

keywords (autode.wrappers.keywords.Keywords)

autode.conformers.conformers.atoms_from_rdkit_mol(rdkit_mol_obj: Mol, conf_id: int = 0) → Atoms#

Generate atoms for a conformer contained within an RDKit molecule object

Parameters:

conf_id (int) – Conformer id to convert to atoms

Returns:

Atoms

Return type:

(list(autode.atoms.Atom))

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