polymerist.mdtools.openmmtools.reporters

Utilities for handlling setup of Simulation Reporters

Attributes

LOGGER
TrajectoryReporter
Reporter
ReporterInitializer
TRAJ_REPORTERS
CHK_REPORTERS
STATE_DAT_REPORTERS
DEFAULT_STATE_DATA_PROPS

Classes

StateReporter	CheckpointReporter which is forced to report States; greatly simplifies interface, documentation, and logging
ReporterConfig	Interface for generating a Reporter and associated Path in a uniform and standardized way
ReporterParameters	Parameters for specifying Simulation reporters

Module Contents

polymerist.mdtools.openmmtools.reporters.LOGGER

class polymerist.mdtools.openmmtools.reporters.StateReporter(file, reportInterval)

Bases: openmm.app.CheckpointReporter

CheckpointReporter which is forced to report States; greatly simplifies interface, documentation, and logging

type polymerist.mdtools.openmmtools.reporters.TrajectoryReporter = PDBReporter | PDBxReporter | DCDReporter

type polymerist.mdtools.openmmtools.reporters.Reporter = CheckpointReporter | StateReporter | StateDataReporter | TrajectoryReporter

type polymerist.mdtools.openmmtools.reporters.ReporterInitializer = Callable[..., Reporter]

class polymerist.mdtools.openmmtools.reporters.ReporterConfig

Interface for generating a Reporter and associated Path in a uniform and standardized way

label: str

extension: str

reporter_dict: dict[str, ReporterInitializer]

extra_kwargs: dict[str, Any]

property initializer: ReporterInitializer

Returns the particular class or initializer

polymerist.mdtools.openmmtools.reporters.TRAJ_REPORTERS

polymerist.mdtools.openmmtools.reporters.CHK_REPORTERS

polymerist.mdtools.openmmtools.reporters.STATE_DAT_REPORTERS

polymerist.mdtools.openmmtools.reporters.DEFAULT_STATE_DATA_PROPS

class polymerist.mdtools.openmmtools.reporters.ReporterParameters

Parameters for specifying Simulation reporters

report_checkpoint: bool = True

report_state: bool = True

report_trajectory: bool = True

report_state_data: bool = True

traj_ext: str | None = 'dcd'

num_steps: int | None = None

state_data: dict[str, bool] | None

reporter_paths: dict[str, pathlib.Path] | None = None

property rep_configs: list[ReporterConfig]

Generate Reporter configurations for currently specified reporters

init_reporter_paths(out_dir: pathlib.Path, prefix: str) → None

Generate paths for all configured and enabled reporters

prepare_reporters(report_interval: int) → list[Reporter]

Prepare all reporters specified by internal parameters and return Paths linked to said reporters