polymerist.mdtools.openmmtools.serialization

For reading OpenMM components from files and writing OpenMM components to files

Submodules

• polymerist.mdtools.openmmtools.serialization.paths
• polymerist.mdtools.openmmtools.serialization.state
• polymerist.mdtools.openmmtools.serialization.system
• polymerist.mdtools.openmmtools.serialization.topology

Attributes

StateLike
DEFAULT_STATE_PROPS

Classes

SimulationPaths

Encapsulates Paths to various files associated with an OpenMM Simulation

Functions

load_state_flexible(→ Optional[openmm.State])	Allows one to flexibly load an OpenMM state, either from a State object or file-like object
serialize_state_from_context(→ None)	For saving State data within an existing OpenMM Context to file
apply_state_to_context(→ None)	For applying saved State data to an existing OpenMM Context
serialize_system(→ None)	For saving an existing OpenMM System to file
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

Package Contents

class polymerist.mdtools.openmmtools.serialization.SimulationPaths

Encapsulates Paths to various files associated with an OpenMM Simulation

parameters_path: pathlib.Path | None = None

paths_path: pathlib.Path | None = None

system_path: pathlib.Path | None = None

topology_path: pathlib.Path | None = None

state_path: pathlib.Path | None = None

checkpoint_path: pathlib.Path | None = None

trajectory_path: pathlib.Path | None = None

state_data_path: pathlib.Path | None = None

time_data_path: pathlib.Path | None = None

spatial_data_path: pathlib.Path | None = None

init_top_and_sys_paths(out_dir: pathlib.Path, prefix: str, record: bool = True) → tuple[pathlib.Path, pathlib.Path]

Initialize Topology and System output paths for a given directory

classmethod from_dir_and_parameters(out_dir: pathlib.Path, prefix: str, sim_params: polymerist.mdtools.openmmtools.parameters.SimulationParameters, touch: bool = True) → SimulationPaths

Create file directory and initialize simulationPaths object from a set of SimulationParameters

polymerist.mdtools.openmmtools.serialization.StateLike

polymerist.mdtools.openmmtools.serialization.DEFAULT_STATE_PROPS: dict[str, bool]

polymerist.mdtools.openmmtools.serialization.load_state_flexible(state: StateLike | None = None) → openmm.State | None

Allows one to flexibly load an OpenMM state, either from a State object or file-like object

polymerist.mdtools.openmmtools.serialization.serialize_state_from_context(state_path: pathlib.Path, context: openmm.Context, state_params: dict[str, bool] = None) → None

For saving State data within an existing OpenMM Context to file

polymerist.mdtools.openmmtools.serialization.apply_state_to_context(context: openmm.Context, state: openmm.State) → None

For applying saved State data to an existing OpenMM Context

polymerist.mdtools.openmmtools.serialization.serialize_system(sys_path: pathlib.Path, system: openmm.System) → None

For saving an existing OpenMM System to file

polymerist.mdtools.openmmtools.serialization.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.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