polymerist.rdutils.bonding.portlib
==================================

.. py:module:: polymerist.rdutils.bonding.portlib

.. autoapi-nested-parse::

   Specification for representing, defining, and characterizing selective intermolecular bond placeholders ("ports")



Attributes
----------

.. autoapisummary::

   polymerist.rdutils.bonding.portlib.PORT_SCHEMA
   polymerist.rdutils.bonding.portlib.PORT_QUERY


Exceptions
----------

.. autoapisummary::

   polymerist.rdutils.bonding.portlib.MolPortError


Classes
-------

.. autoapisummary::

   polymerist.rdutils.bonding.portlib.Port


Functions
---------

.. autoapisummary::

   polymerist.rdutils.bonding.portlib.is_linker
   polymerist.rdutils.bonding.portlib.get_num_linkers
   polymerist.rdutils.bonding.portlib.get_port_ids
   polymerist.rdutils.bonding.portlib.get_linker_ids
   polymerist.rdutils.bonding.portlib.get_ports
   polymerist.rdutils.bonding.portlib.get_num_ports
   polymerist.rdutils.bonding.portlib.get_single_port


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

.. py:data:: PORT_SCHEMA
   :value: '[#0D1]~[!#0]'


.. py:data:: PORT_QUERY

.. py:exception:: MolPortError

   Bases: :py:obj:`Exception`


   Raised when port-related errors as encountered


.. py:function:: is_linker(rdatom: rdkit.Chem.rdchem.Atom) -> bool

   Indicate whether an atom is a linker (intermonomer "*" type atom)


.. py:function:: get_num_linkers(rdmol: rdkit.Chem.rdchem.Mol) -> int

   Count how many wild-type inter-molecule linker atoms are in a Mol


.. py:class:: Port

   Class for encapsulating the components of a "port" bonding site (linker-bond-bridgehead)


   .. py:attribute:: linker
      :type:  rdkit.Chem.rdchem.Atom


   .. py:attribute:: bond
      :type:  rdkit.Chem.rdchem.Bond


   .. py:attribute:: bridgehead
      :type:  rdkit.Chem.rdchem.Atom


   .. py:attribute:: bondable_flavors
      :type:  ClassVar[polymerist.genutils.containers.UnorderedRegistry]


   .. py:property:: flavor
      :type: int


      Return the flavor of the port


   .. py:method:: are_bondable(port_1: Port, port_2: Port) -> bool
      :staticmethod:


      Determine if two port atoms can be combined into a new bond



   .. py:method:: matches_flavor(target_flavor: Optional[int]) -> bool

      Returns whether a port has a particular flavor



.. py:function:: get_port_ids(rdmol: rdkit.Chem.rdchem.Mol) -> Generator[tuple[int, int], None, None]

   Get the linker and bridgehead indices of all ports found in an RDKit Mol


.. py:function:: get_linker_ids(rdmol: rdkit.Chem.rdchem.Mol) -> Generator[int, None, None]

   Get indices of all atoms which are ports


.. py:function:: get_ports(rdmol: rdkit.Chem.rdchem.Mol, target_atom_id: Optional[int] = None, target_flavor: Optional[int] = None) -> Generator[Port, None, None]

   Find and generate all ports in a molecule. Can optioanlly narrow scope to port whose bridegehead is a particular atom and/or whose linker has a particular flavor


.. py:function:: get_num_ports(rdmol: rdkit.Chem.rdchem.Mol, target_atom_id: Optional[int] = None, target_flavor: Optional[int] = None) -> int

   Counts the number of port atoms present in a Mol


.. py:function:: get_single_port(rdmol: rdkit.Chem.rdchem.Mol) -> Port

   Get the singular port of a Mol which contains only 1 port