polymerist.mdtools.openfftools.partialcharge.rescharge
======================================================

.. py:module:: polymerist.mdtools.openfftools.partialcharge.rescharge

.. autoapi-nested-parse::

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



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/polymerist/mdtools/openfftools/partialcharge/rescharge/calculation/index
   /autoapi/polymerist/mdtools/openfftools/partialcharge/rescharge/interface/index
   /autoapi/polymerist/mdtools/openfftools/partialcharge/rescharge/rctypes/index
   /autoapi/polymerist/mdtools/openfftools/partialcharge/rescharge/redistribution/index


Classes
-------

.. autoapisummary::

   polymerist.mdtools.openfftools.partialcharge.rescharge.LibraryCharger
   polymerist.mdtools.openfftools.partialcharge.rescharge.ChargesByResidue
   polymerist.mdtools.openfftools.partialcharge.rescharge.ChargedResidue
   polymerist.mdtools.openfftools.partialcharge.rescharge.ChargeRedistributionStrategy
   polymerist.mdtools.openfftools.partialcharge.rescharge.UniformDistributionStrategy


Functions
---------

.. autoapisummary::

   polymerist.mdtools.openfftools.partialcharge.rescharge.find_repr_residues
   polymerist.mdtools.openfftools.partialcharge.rescharge.compute_residue_charges
   polymerist.mdtools.openfftools.partialcharge.rescharge.apply_residue_charges


Package Contents
----------------

.. py:function:: find_repr_residues(offmol: openff.toolkit.topology.molecule.Molecule) -> dict[str, int]

   Determine names and smallest residue numbers of all unique residues in charged molecule
   Used as representatives for generating labelled SMARTS strings


.. py:function:: compute_residue_charges(cmol: openff.toolkit.topology.molecule.Molecule, monomer_group: polymerist.polymers.monomers.repr.MonomerGroup, cds: Optional[polymerist.mdtools.openfftools.partialcharge.rescharge.redistribution.ChargeRedistributionStrategy] = UniformDistributionStrategy(desired_net_charge=0.0)) -> polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargesByResidue

   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


.. py:function:: apply_residue_charges(offmol: openff.toolkit.topology.molecule.Molecule, chgs_by_res: polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargesByResidue) -> None

   Takes an OpenFF Molecule and a residue-wise map of averaged partial charges and applies the mapped charges to the Molecule


.. py:class:: LibraryCharger

   Bases: :py:obj:`polymerist.mdtools.openfftools.partialcharge.molchargers.MolCharger`


   Charger class for applying library charges onto residue-mapped Molecules


   .. py:attribute:: charges_by_residue
      :type:  polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargesByResidue


.. py:class:: ChargesByResidue

   Class for storing substructure charge maps by residue


   .. py:attribute:: charges
      :type:  dict[str, ChargeMap]


.. py:class:: ChargedResidue

   Dataclass for more conveniently storing averaged charges for a residue group


   .. py:attribute:: charges
      :type:  ChargeMap


   .. py:attribute:: residue_name
      :type:  str


   .. py:attribute:: SMARTS
      :type:  str


   .. py:attribute:: mol_fragment
      :type:  rdkit.Chem.rdchem.Mol


.. py:class:: ChargeRedistributionStrategy

   Bases: :py:obj:`abc.ABC`


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


   .. py:attribute:: desired_net_charge
      :type:  float
      :value: 0.0



   .. py:method:: redistributed_charges(base_charges: polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargeMap, fragment: rdkit.Chem.Mol) -> polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargeMap

      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



.. py:class:: UniformDistributionStrategy

   Bases: :py:obj:`ChargeRedistributionStrategy`


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