e3fp.conformer.generator module

Conformer generation.

Author: Seth Axen E-mail: seth.axen@gmail.com

class ConformerGenerator(num_conf: int = -1, first: int = -1, rmsd_cutoff: float = 0.5, max_energy_diff: float = -1.0, forcefield: str = 'uff', pool_multiplier: int = 1, seed: int = -1, get_values: bool = False, sparse_rmsd: bool = True, store_energies: bool = True)[source]

Bases: object

Generate conformers using RDKit.

Procedure

Generate a pool of conformers.
Minimize conformers.
Filter conformers using an RMSD threshold and optional minimum energy difference.

Note that pruning is done _after_ minimization, which differs from the protocol described in the references.

References

http://rdkit.org/docs/GettingStartedInPython.html #working-with-3d-molecules
http://pubs.acs.org/doi/full/10.1021/ci2004658
https://github.com/skearnes/rdkit-utils/blob/master/rdkit_utils/ conformers.py

embed_molecule(mol)[source]

Generate conformers, possibly with pruning.

Parameters:: mol (RDKit Mol) – Molecule.

filter_conformers(mol)[source]

Filter conformers which do not meet an RMSD threshold.

Parameters:

mol (RDKit Mol) – Molecule.

Returns:

A new RDKit Mol containing the chosen conformers, sorted by
increasing energy.

generate_conformers(mol)[source]

Generate conformers for a molecule.

Parameters:: mol (RDKit Mol) – Molecule.
Returns:: RDKit Mol
Return type:: copy of the input molecule with embedded conformers

get_conformer_energies(mol)[source]

Calculate conformer energies.

Parameters:: mol (RDKit Mol) – Molecule.
Returns:: energies – Minimized conformer energies.
Return type:: array_like

get_molecule_force_field(mol, conf_id=None, **kwargs)[source]

Get a force field for a molecule.

Parameters:

mol (RDKit Mol) – Molecule.
conf_id (int, optional) – ID of the conformer to associate with the force field.
**kwargs (dict, optional) – Keyword arguments for force field constructor.

static get_num_conformers(mol)[source]

Return ideal number of conformers from rotatable bond number in model.

Parameters:: mol (Mol) – RDKit Mol object for molecule
Yields:: num_conf (int) – Target number of conformers to accept

minimize_conformers(mol)[source]

Minimize molecule conformers.

Parameters:: mol (RDKit Mol) – Molecule.

static reverse_enumerate(iterable)[source]

Enumerate, but with the last result first but still numbered last.

Parameters:: iterable (some 1-D iterable)
Returns:: Reverse of enumerate function
Return type:: iterable