schrodinger.livedesign.reaction module

class schrodinger.livedesign.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.reaction.setup_rgroup_rxn_map_nums(mol: 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.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.reaction.check_rxn(rxn: ChemicalReaction) → RxnCheckResult

schrodinger.livedesign.reaction.check_reaction(rxn_input: str) → dict[str, int]

Validate reaction structure and return JSON-serializable result data.

Parameters:

rxn_input – reaction definition in any supported format, such as RXN or reaction SMARTS.

Returns:

dictionary describing the reaction’s reactant/product counts and validation results.

schrodinger.livedesign.reaction.enumerate_reactions(rxn_input: str, reactant_lists: list[list[str]], reactant_id_lists: list[list[str]] = None, max_products: int = None, property_filters: dict[str, str] = None) → dict[str, list[str]]

Execute a reaction on one or more sets of reagents

Basically, each “reaction” can have one or more than reagents, and could be run on one or more sets of reagents.

Parameters:

• rxn_input – reaction definition in any supported format, such as RXN or reaction SMARTS.

• reactant_lists – lists of reactants in any supported format, such as MOL or SMILES. Each list has to have the correct length, matching the number of reactant templates used by the reaction.

• reactant_lists – lists of IDs of the reactants. Each list should have exactly the same size as the corresponding list in reactant_lists. For reactants with no ID, an empty string should be used.

• max_products – yield at most this many unique products. If not provided, all products are returned without limit or deduplication. (The canonical SMILES is used as the key.)

• property_filters – dictionary with JSON data describing the property filters, with the schema expected by schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter.

Returns:

dictionary with product SDF blocks and source reactant ID lists.