iphasimulator.trajectory_gromacs_trjconv
========================================

.. py:module:: iphasimulator.trajectory_gromacs_trjconv

.. autoapi-nested-parse::

   Small, testable wrappers around ``gmx trjconv`` preprocessing commands.



Attributes
----------

.. autoapisummary::

   iphasimulator.trajectory_gromacs_trjconv.Runner


Classes
-------

.. autoapisummary::

   iphasimulator.trajectory_gromacs_trjconv.TrjconvResult


Functions
---------

.. autoapisummary::

   iphasimulator.trajectory_gromacs_trjconv.run_trjconv
   iphasimulator.trajectory_gromacs_trjconv.center_and_compact_wrap
   iphasimulator.trajectory_gromacs_trjconv.reconstruct_molecules
   iphasimulator.trajectory_gromacs_trjconv.compact_wrap
   iphasimulator.trajectory_gromacs_trjconv.fit_trajectory


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

.. py:data:: Runner

.. py:class:: TrjconvResult

   Captured command result for a ``gmx trjconv`` operation.


   .. py:attribute:: command
      :type:  tuple[str, ...]


   .. py:attribute:: selections
      :type:  tuple[str, ...]


   .. py:attribute:: output_path
      :type:  pathlib.Path


   .. py:attribute:: returncode
      :type:  int


   .. py:attribute:: stdout
      :type:  str


   .. py:attribute:: stderr
      :type:  str


   .. py:property:: ok
      :type: bool



.. py:function:: 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.


.. py:function:: 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.


.. py:function:: 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.


.. py:function:: 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.


.. py:function:: 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.