polymerist.mdtools.openfftools.partialcharge.rescharge

Tools for handling library charges, both for computing from and applying to Molecules

Submodules

Classes

`LibraryCharger`	Charger class for applying library charges onto residue-mapped Molecules
`ChargesByResidue`	Class for storing substructure charge maps by residue
`ChargedResidue`	Dataclass for more conveniently storing averaged charges for a residue group
`ChargeRedistributionStrategy`	Interface for defining how any excess charge should be distributed within residues to ensure a given overall net charge
`UniformDistributionStrategy`	Simplest possible strategy, distribute any excess charge in a residue according to a uniform distribution (spread evenly)

Functions

`find_repr_residues`(→ dict[str, int])	Determine names and smallest residue numbers of all unique residues in charged molecule
`compute_residue_charges`(...)	Takes a charged molecule and a collection of monomer-spec SMARTS and generates monomer-averages library charges for each repeating residue
`apply_residue_charges`(→ None)	Takes an OpenFF Molecule and a residue-wise map of averaged partial charges and applies the mapped charges to the Molecule

Package Contents

polymerist.mdtools.openfftools.partialcharge.rescharge.find_repr_residues(offmol: openff.toolkit.topology.molecule.Molecule) → dict[str, int][source]: Determine names and smallest residue numbers of all unique residues in charged molecule Used as representatives for generating labelled SMARTS strings

polymerist.mdtools.openfftools.partialcharge.rescharge.compute_residue_charges(cmol: openff.toolkit.topology.molecule.Molecule, monomer_group: polymerist.polymers.monomers.repr.MonomerGroup, cds: polymerist.mdtools.openfftools.partialcharge.rescharge.redistribution.ChargeRedistributionStrategy | None = UniformDistributionStrategy(desired_net_charge=0.0)) → polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargesByResidue[source]

Takes a charged molecule and a collection of monomer-spec SMARTS and generates monomer-averages library charges for each repeating residue Can optionally specify a strategy for redistributing any excess charge (by default, will ensure charges are neutral)

Returns a ChargesByRresidue object containing a dict of mapped residue charges keyed by residue name

polymerist.mdtools.openfftools.partialcharge.rescharge.apply_residue_charges(offmol: openff.toolkit.topology.molecule.Molecule, chgs_by_res: polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargesByResidue) → None[source]: Takes an OpenFF Molecule and a residue-wise map of averaged partial charges and applies the mapped charges to the Molecule

class polymerist.mdtools.openfftools.partialcharge.rescharge.LibraryCharger[source]

Bases: polymerist.mdtools.openfftools.partialcharge.molchargers.MolCharger

Charger class for applying library charges onto residue-mapped Molecules

charges_by_residue: polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargesByResidue

class polymerist.mdtools.openfftools.partialcharge.rescharge.ChargesByResidue[source]

Class for storing substructure charge maps by residue

charges: dict[str, ChargeMap]

class polymerist.mdtools.openfftools.partialcharge.rescharge.ChargedResidue[source]

Dataclass for more conveniently storing averaged charges for a residue group

charges: ChargeMap

residue_name: str

SMARTS: str

mol_fragment: rdkit.Chem.rdchem.Mol

class polymerist.mdtools.openfftools.partialcharge.rescharge.ChargeRedistributionStrategy[source]

Bases: abc.ABC

Interface for defining how any excess charge should be distributed within residues to ensure a given overall net charge

desired_net_charge: float = 0.0

redistributed_charges(base_charges: polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargeMap, fragment: rdkit.Chem.Mol) → polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargeMap[source]: Take a map of base charges and a structural fragment for a residue and a desired net charge (typically neutral, i.e. 0) and return a new charge map with the excess/deficit charge distributed in such a way as to make the residue have the desired net charge

class polymerist.mdtools.openfftools.partialcharge.rescharge.UniformDistributionStrategy[source]

Bases: ChargeRedistributionStrategy

Simplest possible strategy, distribute any excess charge in a residue according to a uniform distribution (spread evenly)