iphasimulator.trajectory_centering
==================================

.. py:module:: iphasimulator.trajectory_centering

.. autoapi-nested-parse::

   Index-file helpers for reusable GROMACS centering groups.



Attributes
----------

.. autoapisummary::

   iphasimulator.trajectory_centering.GROUP_HEADER_PATTERN
   iphasimulator.trajectory_centering.DEFAULT_CENTER_GROUP
   iphasimulator.trajectory_centering.WORKFLOW_CENTER_SOURCES


Classes
-------

.. autoapisummary::

   iphasimulator.trajectory_centering.GromacsIndex
   iphasimulator.trajectory_centering.CenterIndexResult


Functions
---------

.. autoapisummary::

   iphasimulator.trajectory_centering.read_index
   iphasimulator.trajectory_centering.write_index
   iphasimulator.trajectory_centering.resolve_center_source_groups
   iphasimulator.trajectory_centering.merged_group_atoms
   iphasimulator.trajectory_centering.ensure_center_index


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

.. py:data:: GROUP_HEADER_PATTERN

.. py:data:: DEFAULT_CENTER_GROUP
   :value: 'center'


.. py:data:: WORKFLOW_CENTER_SOURCES
   :type:  dict[str, tuple[str, ...]]

.. py:class:: GromacsIndex

   Parsed GROMACS index groups, preserving group order.


   .. py:attribute:: groups
      :type:  dict[str, tuple[int, ...]]


   .. py:property:: names
      :type: tuple[str, ...]



   .. py:method:: has_group(name: str) -> bool


   .. py:method:: group(name: str) -> tuple[int, ...]


.. py:class:: CenterIndexResult

   Result from creating or reusing a dedicated centering index.


   .. py:attribute:: index_path
      :type:  pathlib.Path


   .. py:attribute:: center_group
      :type:  str


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


   .. py:attribute:: created
      :type:  bool


   .. py:attribute:: reused_existing_center
      :type:  bool


.. py:function:: read_index(index_path: str | pathlib.Path) -> GromacsIndex

   Read a GROMACS ``.ndx`` file into named atom groups.


.. py:function:: write_index(index: GromacsIndex, index_path: str | pathlib.Path) -> pathlib.Path

   Write a GROMACS index file with stable 15-atom line wrapping.


.. py:function:: resolve_center_source_groups(index: GromacsIndex, *, workflow_type: str = 'polymer', source_groups: tuple[str, ...] | list[str] | None = None) -> tuple[str, ...]

   Return source groups for a workflow, filtering to groups present in the index.


.. py:function:: merged_group_atoms(index: GromacsIndex, group_names: tuple[str, ...]) -> tuple[int, ...]

   Merge one or more index groups into a sorted unique atom list.


.. py:function:: ensure_center_index(source_index: str | pathlib.Path, output_index: str | pathlib.Path | None = None, *, workflow_type: str = 'polymer', source_groups: tuple[str, ...] | list[str] | None = None, center_group: str = DEFAULT_CENTER_GROUP) -> CenterIndexResult

   Create or reuse a GROMACS index file containing a dedicated ``center`` group.

   Existing ``[ center ]`` groups are reused. Otherwise the group is generated from
   the workflow source groups, currently ``PHA`` for polymer-only systems.