schrodinger.livedesign.check_reaction module

class schrodinger.livedesign.check_reaction.RxnCheckResult(num_reactants: int = - 1, num_products: int = - 1, rxn_validated: bool = False, valid_rgroups: bool = False, valid_mapping: bool = False)

Bases: object

num_reactants: int = -1

num_products: int = -1

rxn_validated: bool = False

valid_rgroups: bool = False

valid_mapping: bool = False

__init__(num_reactants: int = - 1, num_products: int = - 1, rxn_validated: bool = False, valid_rgroups: bool = False, valid_mapping: bool = False) → None

schrodinger.livedesign.check_reaction.setup_rgroup_rxn_map_nums(mol: rdkit.Chem.rdchem.Mol) → bool

Turn indexed R groups into dummy atoms with atom map numbers > 100

Reactions are commonly drawn with mapped R groups, and nothing else mapped. The R groups should be turned into star (wildcard) atoms with the correct atom mapping.

to be tested: - collisions if some existing atoms are mapped

schrodinger.livedesign.check_reaction.initialize_map_numbers(reactants: list[rdkit.Chem.rdchem.Mol], products: list[rdkit.Chem.rdchem.Mol]) → bool

A reaction isn’t fully mapped if: * There are no atoms mapped * There are are unmapped dummy atoms in the product.

It’s OK to have some unmapped atoms, that means that they are annhilated or created in the reaction. If _all_ atoms are unmapped, though, that’s a problem because we don’t know how to specific reactants interact with the reaction.

schrodinger.livedesign.check_reaction.check_rxn(rxn: rdkit.Chem.rdChemReactions.ChemicalReaction) → schrodinger.livedesign.check_reaction.RxnCheckResult