iphasimulator.trajectory_gromacs_trjconv

Small, testable wrappers around gmx trjconv preprocessing commands.

Attributes

Runner

Classes

TrjconvResult

Captured command result for a gmx trjconv operation.

Functions

run_trjconv(, trjconv_args, gmx_command, cwd, runner)	Run gmx trjconv with explicit stdin group selections.
center_and_compact_wrap(→ TrjconvResult)	Center on center_group and write the full compact solvated system.
reconstruct_molecules(→ TrjconvResult)	Repair molecules split across periodic boundaries without centering.
compact_wrap(→ TrjconvResult)	Wrap the full system into a compact unit-cell representation.
fit_trajectory(→ TrjconvResult)	Fit/alignment wrapper using the centering group as the reference group.

Module Contents

iphasimulator.trajectory_gromacs_trjconv.Runner

class iphasimulator.trajectory_gromacs_trjconv.TrjconvResult

Captured command result for a gmx trjconv operation.

command: tuple[str, ...]

selections: tuple[str, ...]

output_path: pathlib.Path

returncode: int

stdout: str

stderr: str

property ok: bool

iphasimulator.trajectory_gromacs_trjconv.run_trjconv(*, trajectory: str | pathlib.Path, structure: str | pathlib.Path, output: str | pathlib.Path, index: str | pathlib.Path | None = None, selections: Sequence[str] = ('System',), trjconv_args: Sequence[str] = (), gmx_command: str = 'gmx', cwd: str | pathlib.Path | None = None, runner: Runner = subprocess.run) → TrjconvResult

Run gmx trjconv with explicit stdin group selections.

iphasimulator.trajectory_gromacs_trjconv.center_and_compact_wrap(*, trajectory: str | pathlib.Path, structure: str | pathlib.Path, index: str | pathlib.Path, output: str | pathlib.Path, center_group: str = 'center', output_group: str = 'System', gmx_command: str = 'gmx', cwd: str | pathlib.Path | None = None, runner: Runner = subprocess.run) → TrjconvResult

Center on center_group and write the full compact solvated system.

iphasimulator.trajectory_gromacs_trjconv.reconstruct_molecules(*, trajectory: str | pathlib.Path, structure: str | pathlib.Path, index: str | pathlib.Path, output: str | pathlib.Path, output_group: str = 'System', gmx_command: str = 'gmx', cwd: str | pathlib.Path | None = None, runner: Runner = subprocess.run) → TrjconvResult

Repair molecules split across periodic boundaries without centering.

iphasimulator.trajectory_gromacs_trjconv.compact_wrap(*, trajectory: str | pathlib.Path, structure: str | pathlib.Path, index: str | pathlib.Path, output: str | pathlib.Path, output_group: str = 'System', gmx_command: str = 'gmx', cwd: str | pathlib.Path | None = None, runner: Runner = subprocess.run) → TrjconvResult

Wrap the full system into a compact unit-cell representation.

iphasimulator.trajectory_gromacs_trjconv.fit_trajectory(*, trajectory: str | pathlib.Path, structure: str | pathlib.Path, index: str | pathlib.Path, output: str | pathlib.Path, fit_group: str = 'center', output_group: str = 'System', fit: str = 'rot+trans', gmx_command: str = 'gmx', cwd: str | pathlib.Path | None = None, runner: Runner = subprocess.run) → TrjconvResult

Fit/alignment wrapper using the centering group as the reference group.