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|
==============================
gmxapi Python module reference
==============================
.. contents:: :local:
:depth: 2
.. Concise reference documentation extracted directly from code.
.. For new and non-backwards-compatible features, API versions must be given.
The Gromacs Python package includes a high-level scripting interface implemented
in pure Python and a lower-level API implemented as a C++ extension module.
The pure Python implementation provides the basic ``gmxapi`` module and
classes with a very stable syntax that can be maintained with maximal compatibility
while mapping to lower level interfaces that may take a while to sort out. The
separation also serves as a reminder that different execution contexts may be
implemented quite diffently, though Python scripts using only the high-level
interface should execute on all.
Package documentation is extracted from the ``gmxapi`` Python module and is also available
directly, using either ``pydoc`` from the command line or :py:func:`help` from within Python, such
as during an interactive session.
Refer to the Python source code itself for additional clarification.
.. seealso:: :ref:`gmxapi_package_documentation`
.. Configuration for doctest: automated syntax checking in documentation code snippets
.. testsetup::
import gmxapi as gmx
from gmxapi.data import tpr_filename
gmxapi basic package
=====================
::
import gmxapi as gmx
.. automodule:: gmxapi
:members:
:member-order: groupwise
Status messages and Logging
===========================
.. automodule:: gmxapi._logging
:members:
Exceptions module
=================
.. automodule:: gmxapi.exceptions
:members:
gmx.version module
==================
.. automodule:: gmxapi.version
:members:
Core API
========
.. automodule:: gmxapi._gmxapi
Exceptions
----------
.. autoexception:: gmxapi._gmxapi.Exception
Root exception for the C++ extension module. Derives from `gmxapi.exceptions.Error`.
.. autoexception:: gmxapi._gmxapi.NotImplementedError
.. autoexception:: gmxapi._gmxapi.ProtocolError
.. autoexception:: gmxapi._gmxapi.UnknownException
.. autoexception:: gmxapi._gmxapi.UsageError
Functions
---------
Tools for launching simulations
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. autofunction:: gmxapi._gmxapi.from_tpr
Tools to manipulate TPR input files
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. autofunction:: gmxapi._gmxapi.copy_tprfile
.. autofunction:: gmxapi._gmxapi.read_tprfile
.. autofunction:: gmxapi._gmxapi.write_tprfile
.. autofunction:: gmxapi._gmxapi.rewrite_tprfile
Classes
-------
.. autoclass:: gmxapi._gmxapi.Context
:members:
.. autoclass:: gmxapi._gmxapi.MDArgs
:members:
.. autoclass:: gmxapi._gmxapi.MDSession
:members:
.. autoclass:: gmxapi._gmxapi.MDSystem
:members:
.. autoclass:: gmxapi._gmxapi.SimulationParameters
:members:
.. autoclass:: gmxapi._gmxapi.TprFile
:members:
|
