schrodinger.application.matsci.polymer module¶

Module containing functionalities related to polymers

schrodinger.application.matsci.polymer.create_polymer_name(mol)¶

Create a polymer name for the passed molecule by finding its monomers. Returns None if the molecule is not a polymer or has unexpected composition, e.g. more than one initiator. The format is “a-{initiator}-w-{terminator}-poly({list of other monomers})” Example: a-chloro-w-fluoro-poly(caprolactam-chloroprene)

Parameters: mol (structure._Molecule) – The molecule to get the name for
Return type: str or None
Returns: The polymer name, or None if the molecule is not a polymer

schrodinger.application.matsci.polymer.find_polymer_species(structs)¶

Convenience function to find polymer species in the passed structures. Molecules that are not polymers are grouped by SMILES. See clusterstruct.find_species for more information

Parameters: structs (iterable) – The structures to get species for
Return type: dict
Returns: Keys are unique SMILES strings or group names for species, values are SpeciesData objects for that species

schrodinger.application.matsci.polymer.get_carb_atom_identifier_map(struct, atom_ids=None)¶

Get a mapping of carbohydrate atom identifiers to atom IDs for the passed structure

Parameters

struct (structure._Structure) – The structure to get the mapping for
atom_ids (iterable) – The atom IDs to get the mapping for. If None, all atoms are used

Return type

dict

Returns

A mapping of carbohydrate atom identifiers to atom IDs