Molecule_features

Helper functions for extracting features from molecules conformers to generate graph representations in conformer_rl.environments.environment_components.obs_mixins.

conformer_rl.environments.environment_components.molecule_features.bond_type(bond: rdkit.Chem.Bond) → List[bool]

Extracts features from a bond in a molecule.

Parameters

bond (rdkit Bond object) – The bond to extract features from

Returns

• List of bools of length 6

• Each element corresponds to, respectively, whether the bond is –

  • A single bond

  • A double bond

  • A triple bond

  • An aromatic bond

  • Is conjugated

  • Is in a ring structure

conformer_rl.environments.environment_components.molecule_features.get_bond_pairs(mol: rdkit.Chem.Mol) → List[List[int]]

Returns a list of all pairs of atoms that have a bond between each other.

conformer_rl.environments.environment_components.molecule_features.atom_coords(atom: rdkit.Chem.Atom, conf: rdkit.Chem.Conformer) → List[float]

Returns the x, y, and z coordinates of an atom in a molecule conformer.

conformer_rl.environments.environment_components.molecule_features.atom_type_CO(atom: rdkit.Chem.Atom) → List[bool]

Returns a one-hot list of length 2 for whether atom is a carbon or oxygen atom.