polymerist.rdutils.reactions.fragment
=====================================

.. py:module:: polymerist.rdutils.reactions.fragment

.. autoapi-nested-parse::

   For fragmenting molecules by reaction and residue information



Attributes
----------

.. autoapisummary::

   polymerist.rdutils.reactions.fragment.LOGGER
   polymerist.rdutils.reactions.fragment.P
   polymerist.rdutils.reactions.fragment.HEAVY_FORMER_LINKER_QUERY_ATOM
   polymerist.rdutils.reactions.fragment.bond_adjoins_linker
   polymerist.rdutils.reactions.fragment.IBIS


Classes
-------

.. autoapisummary::

   polymerist.rdutils.reactions.fragment.IntermonomerBondIdentificationStrategy
   polymerist.rdutils.reactions.fragment.ReseparateRGroups
   polymerist.rdutils.reactions.fragment.CutMinimumCostBondsStrategy


Functions
---------

.. autoapisummary::

   polymerist.rdutils.reactions.fragment.bridgehead_atom_ids
   polymerist.rdutils.reactions.fragment.get_shortest_path_bonds
   polymerist.rdutils.reactions.fragment.bond_is_newly_formed


Module Contents
---------------

.. py:data:: LOGGER

.. py:data:: P

.. py:data:: HEAVY_FORMER_LINKER_QUERY_ATOM
   :type:  rdkit.Chem.QueryAtom

.. py:function:: bridgehead_atom_ids(product: rdkit.Chem.Mol) -> Generator[int, None, None]

   Generates the indices of all atoms in a reaction product which were tagged
   as R-group bridgehead (i.e. wild) atoms in the reaction template definition


.. py:function:: get_shortest_path_bonds(rdmol: rdkit.Chem.Mol, start_atom_idx: int, end_atom_idx: int) -> list[int]

   Returns bond indices along shortest path between two atoms in a Mol


.. py:function:: bond_is_newly_formed(bond: rdkit.Chem.Bond) -> bool

   Bond condition checking if a bond was newly formed in a reaction
   (i.e. present in the product(s) but not the reactant(s))


.. py:data:: bond_adjoins_linker
   :type:  polymerist.rdutils.selection.BondCondition

.. py:class:: IntermonomerBondIdentificationStrategy

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


   Abstract base for Intermonomer Bond Identification Strategies for fragmentation during in-silico polymerization


   .. py:method:: locate_intermonomer_bonds(product: rdkit.Chem.Mol) -> Generator[int, None, None]

      Generates the indices of all identified inter-monomer bonds by molecule, no more than once each



   .. py:method:: produce_fragments(product: rdkit.Chem.Mol, separate: bool = True) -> Union[rdkit.Chem.Mol, tuple[rdkit.Chem.Mol]]

      Apply break all bonds identified by this IBIS algorithm and return the resulting fragments



.. py:data:: IBIS

.. py:class:: ReseparateRGroups

   Bases: :py:obj:`IntermonomerBondIdentificationStrategy`


   IBIS which cleaves any new bonds formed between atoms that were formerly the start of an R-group in the reaction template


.. py:class:: CutMinimumCostBondsStrategy(base_bond_cost: Optional[float] = None, bond_discounts: Optional[dict[str, tuple[int, Callable[[rdkit.Chem.Mol], tuple[int, int]]]]] = None, bond_cost_keyword: Optional[str] = 'cost_to_cut', max_bonds_per_cut: int = 1, *args: P, **kwargs: P)

   Bases: :py:obj:`IntermonomerBondIdentificationStrategy`


   Subtype of IBIS which chooses bonds as solutions to minimum graph cut problem
   All bonds in a molecule are given some base cost to cut, then a discount is applied to some bonds by specified conditions

   Cuts are then made (no more than once) on the lowest cost bond(s) separating each pair of R-groups


   .. py:attribute:: base_bond_cost
      :value: None



   .. py:attribute:: bond_discounts
      :value: None



   .. py:attribute:: bond_cost_keyword
      :value: 'cost_to_cut'



   .. py:attribute:: max_bonds_per_cut
      :value: 1