iphasimulator.trajectory_preprocessing
======================================

.. py:module:: iphasimulator.trajectory_preprocessing

.. autoapi-nested-parse::

   End-to-end GROMACS trajectory preprocessing for polymer analysis.



Classes
-------

.. autoapisummary::

   iphasimulator.trajectory_preprocessing.TrajectoryPreprocessingOutputs


Functions
---------

.. autoapisummary::

   iphasimulator.trajectory_preprocessing.preprocess_gromacs_trajectory


Module Contents
---------------

.. py:class:: TrajectoryPreprocessingOutputs

   Files created by the standard preprocessing workflow.


   .. py:attribute:: system_dir
      :type:  pathlib.Path


   .. py:attribute:: center_index
      :type:  iphasimulator.trajectory_centering.CenterIndexResult


   .. py:attribute:: raw_trajectory_path
      :type:  pathlib.Path


   .. py:attribute:: structure_path
      :type:  pathlib.Path


   .. py:attribute:: centered_trajectory_path
      :type:  pathlib.Path


   .. py:attribute:: fitted_trajectory_path
      :type:  pathlib.Path | None


   .. py:attribute:: representative_frame_path
      :type:  pathlib.Path | None


   .. py:attribute:: center_result
      :type:  iphasimulator.trajectory_gromacs_trjconv.TrjconvResult | None


   .. py:attribute:: fit_result
      :type:  iphasimulator.trajectory_gromacs_trjconv.TrjconvResult | None


   .. py:attribute:: frame_result
      :type:  iphasimulator.trajectory_gromacs_trjconv.TrjconvResult | None


   .. py:property:: analysis_trajectory_path
      :type: pathlib.Path



.. py:function:: 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 ``System`` so water and ions remain available for
   downstream analyses, while centering/fitting use the reusable ``center`` group.