Module tools

source code

:mod:`gromacs.tools` -- Gromacs commands classes
================================================

A Gromacs command class can be thought of as a factory function that
produces an instance of a gromacs command
(:class:`gromacs.core.GromacsCommand`) with initial default values.

By convention, a class has the capitalized name of the corresponding Gromacs
tool; dots are replaced by underscores to make it a valid python identifier.

The list of Gromacs tools to be loaded is configured in
:data:`gromacs.config.gmx_tool_groups`.

It is also possible to extend the basic commands and patch in additional
functionality. For example, the :class:`GromacsCommandMultiIndex` class makes a
command accept multiple index files and concatenates them on the fly; the
behaviour mimics Gromacs' "multi-file" input that has not yet been enabled for
all tools.

.. autoclass:: GromacsCommandMultiIndex
   :members: run, _fake_multi_ndx, __del__

Example
-------

In this example we create two instances of the :class:`gromacs.tools.Trjconv` command (which
runs the Gromacs ``trjconv`` command)::

  import gromacs.tools as tools

  trjconv = tools.Trjconv()
  trjconv_compact = tools.Trjconv(ur='compact', center=True, boxcenter='tric', pbc='mol',
                                  input=('protein','system'),
                                  doc="Returns a compact representation of the system centered on the protein")

The first one, ``trjconv``, behaves as the standard commandline tool but the
second one, ``trjconv_compact``, will by default create a compact
representation of the input data by taking into account the shape of the unit
cell. Of course, the same effect can be obtained by providing the corresponding
arguments to ``trjconv`` but by naming the more specific command differently
one can easily build up a library of small tools that will solve a specifi,
repeatedly encountered problem reliably. This is particularly helpful when doing
interactive work.

Gromacs tools
-------------
.. The docs for the tool classes are auto generated.