polymerist.rdutils.bonding.substitution
=======================================

.. py:module:: polymerist.rdutils.bonding.substitution

.. autoapi-nested-parse::

   Tools for replacing Ports and functional groups



Functions
---------

.. autoapisummary::

   polymerist.rdutils.bonding.substitution.splice_atoms
   polymerist.rdutils.bonding.substitution.saturate_ports
   polymerist.rdutils.bonding.substitution.hydrogenate_rdmol_ports


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

.. py:function:: splice_atoms(rwmol: rdkit.Chem.RWMol, atom_id_1: Optional[int] = None, atom_id_2: Optional[int] = None, flavor_pair: tuple[Optional[int], Optional[int]] = (None, None)) -> None

   Completely combine a single pair of ports on two target atoms to create a bond of desired order


.. py:function:: saturate_ports(rdmol: rdkit.Chem.Mol, cap: rdkit.Chem.Mol = Chem.MolFromSmiles('[*]-[H]'), flavor_to_saturate: int = 0) -> None

   Takes an RDKit Mol and another "cap" molecule (by default just hydrogen) and caps all valid ports (with the specified flavor) on the target Mol with the cap group


.. py:function:: hydrogenate_rdmol_ports(rdmol: rdkit.Chem.Mol) -> None

   Replace all port atoms with hydrogens