rdtools.resonance.rdkit_backend#

This module contains the function generating resonance structures.

rdtools.resonance.rdkit_backend.generate_charged_resonance_structures(mol: RWMol, keep_isomorphic: bool = False, copy: bool = True, kekulize: bool = True, **kwargs: Any) → list[Mol]#

Generate resonance structures for a charged molecule.

Parameters:

  • mol (Chem.RWMol) – A charged molecule in RDKit RWMol.

  • keep_isomorphic (bool, optional) – If keep isomorphic resonance structures. Defaults to False.

  • copy (bool, optional) – If copy the input molecule. Defaults to True.

  • kekulize (bool, optional) – If kekulize the molecule in generating resonance structures. Defaults to True.

  • **kwargs (Any) – Additional arguments for the resonance algorithms.

Returns:

list[Chem.Mol] – a list of molecules with resonance structures.

rdtools.resonance.rdkit_backend.generate_radical_resonance_structures(mol: RWMol, keep_isomorphic: bool = False, copy: bool = True, kekulize: bool = True, **kwargs: Any) → list[Mol]#

Generate resonance structures for a radical molecule.

RDKit by design doesn’t work for radical resonance. The approach is a temporary workaround by replacing radical electrons by positive charges and generating resonance structures by RDKit ResonanceMolSupplier. Currently, this function only works for neutral radicals.

Known issues:

  • Phenyl radical only generate one resonance structure when kekulize=True, expecting 2.

Parameters:

  • mol (Chem.RWMol) – A radical molecule in RDKit RWMol.

  • keep_isomorphic (bool, optional) – If keep isomorphic resonance structures. Defaults to False.

  • copy (bool, optional) – If copy the input molecule. Defaults to True.

  • kekulize (bool, optional) – If kekulize the molecule in generating resonance structures. Defaults to True.

  • **kwargs (Any) – Additional arguments for the resonance algorithms.

Returns:

list[Chem.Mol] – a list of molecules with resonance structures.

rdtools.resonance.rdkit_backend.generate_resonance_structures(mol: RWMol, keep_isomorphic: bool = False, copy: bool = True, kekulize: bool = True, **kwargs: Any) → list[Mol]#

Generate resonance structures with RDKit algorithm.

Parameters:

  • mol (Chem.RWMol) – A charged molecule in RDKit RWMol.

  • keep_isomorphic (bool, optional) – If keep isomorphic resonance structures. Defaults to False.

  • copy (bool, optional) – If copy the input molecule. Defaults to True.

  • kekulize (bool, optional) – If kekulize the molecule in generating resonance structures. Defaults to True.

  • **kwargs (Any) – Additional arguments for the resonance algorithms.

Returns:

list[Chem.Mol] – a list of molecules with resonance structures.