syndirella.fairy

syndirella.fairy.py

This module provides functions to find similar cheaper reactants, filter out reactants based on simple filters, fingerprint generation, and others…

Attributes

logger

Functions

`load_reactant_filters`(→ Dict[str, Dict[str, Any]])
`load_additional_rxn_options`(→ List[Dict[str, str]])
`do_i_need_alternative_route`(→ bool)	Check if the reaction names need an alternative route.
`find_similar_reactants`(→ List[str] \| None)	Find additional similar reactants that are cheaper as defined in the reactant_filters.
`get_similar_reactant`(→ Optional[str])	Make similar reactant to query reactant from the reactant_filters.
`make_similar_reactant`(→ str)	Create a similar reactant by modifying the original reactant according to matched_details.
`filter_molecules`(→ List[str])	Filter out reactants and return a dictionary with SMILES strings as keys and their associated scores as values.
`simple_filters`(→ List[syndirella.error.Chem.Mol])	Filter out molecules based on repeats, and non-abundant isotopes.
`remove_hydrogen_ions`(→ List[syndirella.error.Chem.Mol])	Remove molecules with only hydrogen ions.
`remove_repeat_mols`(→ List[syndirella.error.Chem.Mol])	Remove repeated molecules by checking for Tanimoto similarity of 1.
`remove_non_abundant_isotopes`(...)	Remove molecules with non-abundant isotopes.
`remove_chirality`(→ List[syndirella.error.Chem.Mol])	Remove chirality from all molecules in the list.
`remove_chirality_from_mol`(→ syndirella.error.Chem.Mol)	Remove chirality from a single molecule.
`print_diff`(→ None)	Print the difference between the original number of molecules and the number of valid molecules.
`calculate_tanimoto`(→ float)
`find_reaction_by_name`(→ Optional[Dict[str, Any]])	Find a reaction by name in the additional_rxn_options.
`get_morgan_fingerprint`(...)	Get the fingerprint of a molecule.
`generate_inchi_ID`(→ str \| syndirella.error.MolError)	This function is used to generate a unique id for the route just using the scaffold.
`check_mol_sanity`(→ syndirella.error.Chem.Mol \| None)	Check if the molecule can be sanitized.

Module Contents

syndirella.fairy.logger[source]

syndirella.fairy.load_reactant_filters() → Dict[str, Dict[str, Any]][source]

syndirella.fairy.load_additional_rxn_options() → List[Dict[str, str]][source]

syndirella.fairy.do_i_need_alternative_route(reaction_names: List[str], additional_rxn_options: List[Dict[str, str]]) → bool[source]: Check if the reaction names need an alternative route.

syndirella.fairy.find_similar_reactants(reactant: syndirella.error.Chem.Mol, reaction_name: str, reactant_filters: Dict[str, Dict[str, Any]]) → List[str] | None[source]: Find additional similar reactants that are cheaper as defined in the reactant_filters.

syndirella.fairy.get_similar_reactant(reactant: syndirella.error.Chem.Mol, reactant_filters: Dict[str, str]) → str | None[source]: Make similar reactant to query reactant from the reactant_filters.

syndirella.fairy.make_similar_reactant(reactant: syndirella.error.Chem.Mol, to_replace: str, matched_details: Dict[str, Any]) → str[source]: Create a similar reactant by modifying the original reactant according to matched_details.

syndirella.fairy.filter_molecules(hits: List[Tuple[str, float]]) → List[str][source]: Filter out reactants and return a dictionary with SMILES strings as keys and their associated scores as values.

syndirella.fairy.simple_filters(mols: List[syndirella.error.Chem.Mol]) → List[syndirella.error.Chem.Mol][source]: Filter out molecules based on repeats, and non-abundant isotopes.

syndirella.fairy.remove_hydrogen_ions(mols: List[syndirella.error.Chem.Mol]) → List[syndirella.error.Chem.Mol][source]: Remove molecules with only hydrogen ions.

syndirella.fairy.remove_repeat_mols(mols: List[syndirella.error.Chem.Mol]) → List[syndirella.error.Chem.Mol][source]: Remove repeated molecules by checking for Tanimoto similarity of 1.

syndirella.fairy.remove_non_abundant_isotopes(mols: List[syndirella.error.Chem.Mol]) → List[syndirella.error.Chem.Mol][source]: Remove molecules with non-abundant isotopes.

syndirella.fairy.remove_chirality(mols: List[syndirella.error.Chem.Mol]) → List[syndirella.error.Chem.Mol][source]: Remove chirality from all molecules in the list.

syndirella.fairy.remove_chirality_from_mol(mol: syndirella.error.Chem.Mol) → syndirella.error.Chem.Mol[source]: Remove chirality from a single molecule.

syndirella.fairy.print_diff(hits: List[Tuple[str, float]], valid_mols: List[syndirella.error.Chem.Mol], desc: str) → None[source]: Print the difference between the original number of molecules and the number of valid molecules.

syndirella.fairy.calculate_tanimoto(mol1: syndirella.error.Chem.Mol, mol2: syndirella.error.Chem.Mol) → float[source]

syndirella.fairy.find_reaction_by_name(reaction_name: str, additional_rxn_options: List[Dict[str, str]]) → Dict[str, Any] | None[source]: Find a reaction by name in the additional_rxn_options.

syndirella.fairy.get_morgan_fingerprint(mol: syndirella.error.Chem.Mol) → rdkit.Chem.rdFingerprintGenerator.MorganFP[source]: Get the fingerprint of a molecule.

syndirella.fairy.generate_inchi_ID(smiles: str | None = None, mol: syndirella.error.Chem.Mol | None = None, isomeric: bool = False) → str | syndirella.error.MolError[source]: This function is used to generate a unique id for the route just using the scaffold.

syndirella.fairy.check_mol_sanity(mol: syndirella.error.Chem.Mol) → syndirella.error.Chem.Mol | None[source]: Check if the molecule can be sanitized.