polymerist.mdtools.openmmtools.serialization.topology

For handling serialization of molecular topologies and positions in OpenMM format

Attributes

LOGGER

Functions

serialize_openmm_pdb(→ None)	Configure and write an Protein DataBank File from an OpenMM Topology and array of positions
serialize_topology_from_simulation(→ None)	Saves a PDB of the current state of a simulation's Topology

Module Contents

polymerist.mdtools.openmmtools.serialization.topology.LOGGER

polymerist.mdtools.openmmtools.serialization.topology.serialize_openmm_pdb(pdb_path: pathlib.Path, topology: openmm.app.Topology, positions: numpy.typing.NDArray | list[openmm.Vec3], keep_chain_and_res_ids: bool = True, atom_labeller: polymerist.molfiles.pdb.SerialAtomLabeller | None = None, resname_map: dict[str, str] | None = 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

polymerist.mdtools.openmmtools.serialization.topology.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