polymerist.mdtools.openfftools.partition

For refining a residue cover of an OpenFF Molecule into a partition, recording partition assignments to atom metadata.

Must be called after successful call to openff.toolkit.topology.topology.from_pdb()

Code derived from original implementation and conceptualization by Connor Davel (https://github.com/openforcefield/polymer_examples/blob/main/monomer_generation/partition.py)

Attributes

BondInfoDict

Functions

partition(→ bool)

Module Contents

type polymerist.mdtools.openfftools.partition.BondInfoDict = dict[tuple[int, int], int]
polymerist.mdtools.openfftools.partition.partition(offtop: openff.toolkit.topology.Topology) → bool[source]
Parameters:

offtop (Openforcefield toolkit topology with complete metadata following successful call) – to openff.toolkit.topology.topology.from_pdb().

Returns:

  • True if partition was successful

  • False otherwise. This does not mean that the resulting assignment is invalid. It only means – that clean partitioning cannot be achieved and some matches necessarily overlap. Try choosing other substructures if partitioning is necessary.