Package gromacs

source code

:mod:`gromacs` -- GromacsWrapper Package Overview
=================================================

**GromacsWrapper** (package :mod:`gromacs`) is a thin shell around the `Gromacs`_
tools for light-weight integration into python scripts or interactive use in
`ipython`_.

.. _`Gromacs`: http://www.gromacs.org
.. _`ipython`: http://ipython.scipy.org


Modules
-------

:mod:`gromacs`
     The top level module contains all gromacs tools; each tool can be
     run directly or queried for its documentation. It also defines
     the root logger class (name *gromacs* by default).

:mod:`gromacs.config`
     Configuration options. Not really used much at the moment.

:mod:`gromacs.cbook`
     The Gromacs cook book contains typical applications of the tools. In many
     cases this not more than just an often-used combination of parameters for
     a tool.

:mod:`gromacs.tools`
     Contains classes that wrap the gromacs tools. They are automatically
     generated from the list of tools in :data:`gromacs.tools.gmx_tools`.

:mod:`gromacs.formats`
     Classes to represent data files in various formats such as
     xmgrace graphs. The classes allow reading and writing and for
     graphs, also plotting of the data.

:mod:`gromacs.utilities`
     Convenience functions and mixin-classes that are used as helpers
     in other modules.

:mod:`gromacs.setup`
     Functions to set up a MD simulation, containing tasks such as solvation
     and adding ions, energy minimizqtion, MD with position-restraints, and
     equilibrium MD.

:mod:`gromacs.qsub`
     Functions to handle batch submission queuing systems.

:mod:`gromacs.run`
     Classes to run :program:`mdrun` in various way, including on
     multiprocessor systems.

:mod:`gromacs.analysis`
     A package that collects whole analysis tasks. It uses the gromacs but is
     otherwise only loosely coupled with the rest. At the moment it only
     contains the infrastructure and an example application. See the package
     documentation.


Examples
--------

The following examples should simply convey the flavour of using the
package. See the individual modules for more examples.

Getting help
............

In python::

   help(gromacs.g_dist)
   gromacs.g_dist.help()
   gromacs.g_dist.help(long=True)

In ``ipython``::

   gromacs.g_dist ?


Simple usage
............

Gromacs flags are given as python keyword arguments::

   gromacs.g_dist(v=True, s='topol.tpr', f='md.xtc', o='dist.xvg', dist=1.2)

Input to stdin of the command can be supplied::

   gromacs.make_ndx(f='topol.tpr', o='md.ndx', 
                    input=('keep "SOL"', '"SOL" | r NA | r CL', 'name 2 solvent', 'q'))

Output of the command can be caught in a variable and analyzed::

   rc, output, junk = gromacs.grompp(..., stdout=False)        # collects command output
   for line in output.split('\n'):
       line = line.strip()
       if line.startswith('System has non-zero total charge:'):
             qtot = float(line[34:])
             break

(See :func:`gromacs.cbook.grompp_qtot` for a more robust implementation of this
application.)


Warnings and Exceptions
-----------------------

A number of package-specific exceptions (:exc:`GromacsError`) and
warnings (:exc:`Gromacs*Warning`, :exc:`AutoCorrectionWarning`,
:exc:`BadParameterWarning`) can be raised.

If you want to stop execution at, for instance, a :exc:`AutoCorrectionWarning` or
:exc:`BadParameterWarning` then use the python :mod:`warnings` filter::
 
  import warnings
  warnings.simplefilter('error', gromacs.AutoCorrectionWarning)
  warnings.simplefilter('error', gromacs.BadParameterWarning)

This will make python raise an exception instead of moving on. The default is
to always report, eg::

  warnings.simplefilter('always', gromacs.BadParameterWarning)

The following *exceptions* are defined:

.. autoexception:: GromacsError
.. autoexception:: MissingDataError
.. autoexception:: ParseError

The following *warnings* are defined:

.. autoexception:: GromacsFailureWarning
.. autoexception:: GromacsImportWarning
.. autoexception:: GromacsValueWarning
.. autoexception:: AutoCorrectionWarning
.. autoexception:: BadParameterWarning
.. autoexception:: MissingDataWarning
.. autoexception:: UsageWarning
.. autoexception:: LowAccuracyWarning


Logging
-------

The library uses python's logging_ module to keep a history of what it has been
doing. In particular, every wrapped Gromacs command logs its command line
(including piped input) to the log file (configured in
:data:`gromacs.config.logfilename`). This facilitates debugging or simple
re-use of command lines for very quick and dirty work. The logging facilty
appends to the log file and time-stamps every entry. See :mod:`gromacs.config`
for more details on configuration.

.. _logging: http://docs.python.org/library/logging.html

Version
-------

The package version can be queried with the :func:`gromacs.get_version` function.

.. autofunction:: get_version
.. autofunction:: get_version_tuple

Enable ("always") specified warnings from the gromacs package.

*categories* must be a list of warning classes or strings.
``None`` selects the defaults, :data:`gromacs._less_important_warnings`.

Set the :meth:`warnings.simplefilter` to *action*.

*categories* must be a list of warning classes or strings.
``None`` selects the defaults,  :data:`gromacs.less_important_warnings`.