rdtools.conversion.rmg#

Convert RMG Molecule to RDKit Mol and vice versa.

rdtools.conversion.rmg.mol_from_rmg_mol(rmgmol: rmgpy.molecule.molecule.Molecule, remove_hs: bool = False, sanitize: bool = True) → RWMol#

Convert a RMG Mol to an RDKit Mol object.

Uses RDKit to perform the conversion. Adopted from rmgpy/molecule/converter.py

Parameters:

  • rmgmol (mm.Molecule) – An RMG Molecule object for the conversion.

  • remove_hs (bool, optional) – Whether to remove hydrogen atoms from the molecule, True to remove.

  • sanitize (bool, optional) – Whether to sanitize the RDKit molecule, True to sanitize.

Returns:

Chem.RWMol – An RWMol molecule object corresponding to the input RMG Molecule object.

rdtools.conversion.rmg.mol_to_rmg_mol(rdkitmol: Mol, sort: bool = False, raise_atomtype_exception: bool = True) → rmgpy.molecule.molecule.Molecule#

Convert a RDKit Mol object to an RMG molecular structure.

Uses RDKit to perform the conversion. This Kekulizes everything, removing all aromatic atom types.

Parameters:

  • rdkitmol (Chem.Mol) – An RDKit Mol object for the conversion.

  • sort (bool, optional) – Whether to sort the atoms in the molecule. Defaults to False.

  • raise_atomtype_exception (bool, optional) – Whether to raise an exception if atom types cannot be assigned. Defaults to True.

Returns:

mm.Molecule – An RMG Molecule object corresponding to the input RDKit Mol object.