polymerist.rdutils.reactions.reactors
Classes for implementing reactions with respect to some set of reactant RDKit Mols
Attributes
Classes
Reactor which exhaustively generates monomers fragments according to a given a polymerization mechanism |
Module Contents
- polymerist.rdutils.reactions.reactors.LOGGER
- class polymerist.rdutils.reactions.reactors.PolymerizationReactor[source]
Reactor which exhaustively generates monomers fragments according to a given a polymerization mechanism
- fragment_strategy: polymerist.rdutils.reactions.fragment.IBIS
- propagate_pooled(monomers: Iterable[rdkit.Chem.rdchem.Mol], rxn_depth_max: int = 5, allow_resampling: bool = False, clear_map_labels: bool = True, clear_dummy_labels: bool = False, sanitize_ops: rdkit.Chem.rdmolops.SanitizeFlags = SANITIZE_ALL, aromaticity_model: rdkit.Chem.rdmolops.AromaticityModel = AROMATICITY_MDL) dict[polymerist.smileslib.cleanup.Smiles, rdkit.Chem.rdchem.Mol][source]
Discovers and enumerates all possible repeat unit fragments formable from a given polymerization step reaction mechanism
Propagation acts on a pool of fragments reactants (initially just the “monomers” passed in) and proceeds in rounds where all reactible subsets are adducted and fragmented, and any previously-unseen fragments are added to the pool Enumeration halts either when no new fragments have been found or the set maximum number of reaction step(s) is reached
“Uniqueness” of a fragment is assessed by its RDKit-canonicalized SMILES representation
- propagate(monomers: Sequence[rdkit.Chem.rdchem.Mol], clear_map_labels: bool = True, sanitize_ops: rdkit.Chem.rdmolops.SanitizeFlags = SANITIZE_ALL, aromaticity_model: rdkit.Chem.rdmolops.AromaticityModel = AROMATICITY_MDL) Generator[tuple[tuple[rdkit.Chem.rdchem.Mol, Ellipsis], tuple[rdkit.Chem.rdchem.Mol, Ellipsis]], None, None][source]
Keep reacting and fragmenting a pair of monomers until all reactive sites have been reacted Returns fragment pairs at each step of the chain propagation process