gflownet.utils.molecule.conformer_base

Attributes

`get_torsion_angles_atoms_list`(mol)
`get_torsion_angles_values`(conf, torsion_angles_atoms_list)
`get_all_torsion_angles`(mol, conf)
`get_dummy_ad_atom_positions`()
`get_dummy_ad_conf_base`()

gflownet.utils.molecule.conformer_base.get_torsion_angles_atoms_list(mol)[source]

gflownet.utils.molecule.conformer_base.get_torsion_angles_values(conf, torsion_angles_atoms_list)[source]

gflownet.utils.molecule.conformer_base.get_all_torsion_angles(mol, conf)[source]

gflownet.utils.molecule.conformer_base.get_dummy_ad_atom_positions()[source]

class gflownet.utils.molecule.conformer_base.ConformerBase(atom_positions, smiles, freely_rotatable_tas=None)[source]

Parameters:: atom_positions – numpy.ndarray of shape [num_atoms, 3] of dtype float64

get_mol_from_smiles(smiles)[source]: Create RDKit molecule from SMILES string :param smiles: python string :returns: rdkit.Chem.rdchem.Mol object

embed_mol_and_get_conformer(mol, extra_opt=False)[source]: Embed RDkit mol with a conformer and return the RDKit conformer object (which is synchronized with the RDKit molecule object) :param mol: rdkit.Chem.rdchem.Mol object defining the molecule :param extre_opt: bool, if True, an additional optimisation of the conformer will be performed

set_atom_positions(atom_positions)[source]: Set atom positions of the self.rdk_conf to the input atom_positions values :param atom_positions: 2d numpy array of shape [num atoms, 3] with new atom positions

get_atom_positions()[source]

get_atomic_numbers()[source]: Get atomic numbers of the atoms as 1d numpy array :returns: numpy array of atomic numbers of shape [num_atoms,]

get_all_torsion_angles()[source]

get_freely_rotatable_tas_values()[source]

randomize_freely_rotatable_tas()[source]: Uniformly randomize torsion angles defined by self.freely_rotatable_tas

increment_torsion_angle(torsion_angle, increment)[source]

Parameters: