iphasimulator.trajectory_preprocessing
End-to-end GROMACS trajectory preprocessing for polymer analysis.
Classes
Files created by the standard preprocessing workflow. |
Functions
Run the standard GROMACS preprocessing pipeline. |
Module Contents
- class iphasimulator.trajectory_preprocessing.TrajectoryPreprocessingOutputs
Files created by the standard preprocessing workflow.
- system_dir: pathlib.Path
- center_index: iphasimulator.trajectory_centering.CenterIndexResult
- raw_trajectory_path: pathlib.Path
- structure_path: pathlib.Path
- centered_trajectory_path: pathlib.Path
- fitted_trajectory_path: pathlib.Path | None
- representative_frame_path: pathlib.Path | None
- center_result: iphasimulator.trajectory_gromacs_trjconv.TrjconvResult | None
- fit_result: iphasimulator.trajectory_gromacs_trjconv.TrjconvResult | None
- frame_result: iphasimulator.trajectory_gromacs_trjconv.TrjconvResult | None
- property analysis_trajectory_path: pathlib.Path
- iphasimulator.trajectory_preprocessing.preprocess_gromacs_trajectory(system_dir: str | pathlib.Path, *, trajectory: str | pathlib.Path = 'step7_production.xtc', structure: str | pathlib.Path = 'step7_production.tpr', index: str | pathlib.Path = 'index.ndx', workflow_type: str = 'polymer', source_groups: tuple[str, ...] | list[str] | None = None, fit: bool = False, extract_representative_frame: bool = True, gmx_command: str = 'gmx', runner: iphasimulator.trajectory_gromacs_trjconv.Runner = subprocess.run, dry_run: bool = False) TrajectoryPreprocessingOutputs
Run the standard GROMACS preprocessing pipeline.
The output trajectory keeps
Systemso water and ions remain available for downstream analyses, while centering/fitting use the reusablecentergroup.