iphasimulator.trajectory_gromacs_merge

Merge restarted GROMACS trajectory and energy outputs for one simulation.

Attributes

`Runner`
`OutputKind`
`INITIAL_PREFIX`
`CONTINUATION_PREFIX`
`TRAJECTORY_OUTPUT_PREFIX`

Classes

`DiscoveredGromacsOutputs`	Raw XTC and EDR files discovered independently.
`GromacsCheckResult`	Result of one checked `gmx check` command.
`GromacsMergeCommandResult`	Result of one checked `gmx trjcat` or `gmx eneconv` command.
`GromacsMergeOutputsResult`	Structured discovery, command, and validation results.

Functions

`discover_gromacs_outputs`(→ DiscoveredGromacsOutputs)	Discover ordered raw XTC and EDR files without inferring their times.
`maximum_trajectory_part`(→ int)	Return the highest continuation number represented by XTC files.
`maximum_energy_part`(→ int)	Return the highest continuation number represented by EDR files.
`trajectory_output_filename`(→ str)	Build `production_combined_00X.xtc` from the highest XTC part.
`energy_output_filename`(→ str)	Build `production_combined_00X.edr` from the highest EDR part.
`run_gmx_check`(→ GromacsCheckResult)	Run `gmx check` with `-f` for XTC or `-e` for EDR.
`merge_simulation_outputs`(→ GromacsMergeOutputsResult)	Discover, check, merge, and validate one simulation directory.
`build_argument_parser`(→ argparse.ArgumentParser)	Build the command-line parser for the executable module.
`main`(→ int)	Command-line entry point.

Module Contents

iphasimulator.trajectory_gromacs_merge.Runner

iphasimulator.trajectory_gromacs_merge.OutputKind

iphasimulator.trajectory_gromacs_merge.INITIAL_PREFIX = 'step7_production'

iphasimulator.trajectory_gromacs_merge.CONTINUATION_PREFIX = 'step8_production_2us'

iphasimulator.trajectory_gromacs_merge.TRAJECTORY_OUTPUT_PREFIX = 'production_combined'

class iphasimulator.trajectory_gromacs_merge.DiscoveredGromacsOutputs

Raw XTC and EDR files discovered independently.

simulation_dir: pathlib.Path

xtc_files: tuple[pathlib.Path, ...]

edr_files: tuple[pathlib.Path, ...]

class iphasimulator.trajectory_gromacs_merge.GromacsCheckResult

Result of one checked gmx check command.

kind: OutputKind

path: pathlib.Path

command: tuple[str, ...]

start_time_ps: float | None

end_time_ps: float | None

stdout: str

stderr: str

class iphasimulator.trajectory_gromacs_merge.GromacsMergeCommandResult

Result of one checked gmx trjcat or gmx eneconv command.

kind: OutputKind

command: tuple[str, ...]

input_files: tuple[pathlib.Path, ...]

output_path: pathlib.Path

stdout: str

stderr: str

class iphasimulator.trajectory_gromacs_merge.GromacsMergeOutputsResult

Structured discovery, command, and validation results.

discovered: DiscoveredGromacsOutputs

trajectory_output: pathlib.Path

energy_output: pathlib.Path

input_checks: tuple[GromacsCheckResult, ...]

trajectory_merge: GromacsMergeCommandResult | None

energy_merge: GromacsMergeCommandResult | None

output_checks: tuple[GromacsCheckResult, ...]

energy_skipped_reason: str | None

dry_run: bool

iphasimulator.trajectory_gromacs_merge.discover_gromacs_outputs(simulation_dir: str | pathlib.Path) → DiscoveredGromacsOutputs: Discover ordered raw XTC and EDR files without inferring their times.

iphasimulator.trajectory_gromacs_merge.maximum_trajectory_part(xtc_files: Sequence[pathlib.Path]) → int: Return the highest continuation number represented by XTC files.

iphasimulator.trajectory_gromacs_merge.maximum_energy_part(edr_files: Sequence[pathlib.Path]) → int: Return the highest continuation number represented by EDR files.

iphasimulator.trajectory_gromacs_merge.trajectory_output_filename(xtc_files: Sequence[pathlib.Path]) → str: Build production_combined_00X.xtc from the highest XTC part.

iphasimulator.trajectory_gromacs_merge.energy_output_filename(edr_files: Sequence[pathlib.Path]) → str: Build production_combined_00X.edr from the highest EDR part.

iphasimulator.trajectory_gromacs_merge.run_gmx_check(path: str | pathlib.Path, *, kind: OutputKind, gmx_command: str = 'gmx', runner: Runner = subprocess.run) → GromacsCheckResult: Run gmx check with -f for XTC or -e for EDR.

iphasimulator.trajectory_gromacs_merge.merge_simulation_outputs(simulation_dir: str | pathlib.Path, *, dry_run: bool = False, trajectory_only: bool = False, energy_only: bool = False, skip_check: bool = False, overwrite: bool = False, gmx_command: str = 'gmx', runner: Runner = subprocess.run, stream: TextIO = sys.stdout) → GromacsMergeOutputsResult: Discover, check, merge, and validate one simulation directory.

iphasimulator.trajectory_gromacs_merge.build_argument_parser() → argparse.ArgumentParser: Build the command-line parser for the executable module.

iphasimulator.trajectory_gromacs_merge.main(argv: Sequence[str] | None = None) → int: Command-line entry point.