polymerist.polymers.building.mbconvert
======================================

.. py:module:: polymerist.polymers.building.mbconvert

.. autoapi-nested-parse::

   Enhanced conversions to and from mbuild Compound objects which
   preserve more molecular information than the utilities provided by



Functions
---------

.. autoapisummary::

   polymerist.polymers.building.mbconvert.mbmol_from_mono_rdmol
   polymerist.polymers.building.mbconvert.mbmol_to_rdmol
   polymerist.polymers.building.mbconvert.mbmol_to_rdkit_pdb
   polymerist.polymers.building.mbconvert.mbmol_to_openmm_pdb


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

.. py:function:: mbmol_from_mono_rdmol(rdmol: rdkit.Chem.Mol, resname: Optional[str] = None, kekulize: bool = True) -> tuple[mbuild.Compound, list[int]]

   Accepts a monomer-spec-compliant SMARTS string and returns an mbuild Compound and a list of the indices of atom ports
   If "resname" is provided, will assign that name to the mBuild Compound returned


.. py:function:: mbmol_to_rdmol(mbmol: mbuild.Compound, atom_labeller: Optional[polymerist.molfiles.pdb.SerialAtomLabeller] = None, resname_map: Optional[dict[str, str]] = None) -> rdkit.Chem.Mol

   Convert an mBuild Compound into an RDKit Mol, with correct atom coordinates and PDB residue info


.. py:function:: mbmol_to_rdkit_pdb(pdb_path: str, mbmol: mbuild.Compound, atom_labeller: Optional[polymerist.molfiles.pdb.SerialAtomLabeller] = None, resname_map: Optional[dict[str, str]] = None) -> None

.. py:function:: mbmol_to_openmm_pdb(pdb_path: pathlib.Path, mbmol: mbuild.Compound, atom_labeller: Optional[polymerist.molfiles.pdb.SerialAtomLabeller] = None, resname_map: Optional[dict[str, str]] = None) -> None