polymerist.mdtools.openmmtools.serialization.topology
=====================================================

.. py:module:: polymerist.mdtools.openmmtools.serialization.topology

.. autoapi-nested-parse::

   For handling serialization of molecular topologies and positions in OpenMM format



Attributes
----------

.. autoapisummary::

   polymerist.mdtools.openmmtools.serialization.topology.LOGGER


Functions
---------

.. autoapisummary::

   polymerist.mdtools.openmmtools.serialization.topology.serialize_openmm_pdb
   polymerist.mdtools.openmmtools.serialization.topology.serialize_topology_from_simulation


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

.. py:data:: LOGGER

.. py:function:: serialize_openmm_pdb(pdb_path: pathlib.Path, topology: openmm.app.Topology, positions: Union[numpy.typing.NDArray, list[openmm.Vec3]], keep_chain_and_res_ids: bool = True, atom_labeller: Optional[polymerist.molfiles.pdb.SerialAtomLabeller] = None, resname_map: Optional[dict[str, str]] = None) -> None

   Configure and write an Protein DataBank File from an OpenMM Topology and array of positions
   Provides options to configure atom ID numbering, residue numbering, and residue naming


.. py:function:: serialize_topology_from_simulation(pdb_path: pathlib.Path, sim: openmm.app.Simulation, keep_ids: bool = False) -> None

   Saves a PDB of the current state of a simulation's Topology