Module utilities

source code

:mod:`gromacs.utilities` -- Helper functions and classes
========================================================

The module defines some convenience functions and classes that are
used in other modules; they do *not* make use of :mod:`gromacs.tools`
or :mod:`gromacs.cbook` and can be safely imported at any time.


Classes
-------

:class:`FileUtils` provides functions related to filename handling. It
can be used as a base or mixin class. The :class:`gromacs.analysis.Simulation`
class is derived from it.

.. autoclass:: FileUtils
   :members:
.. autoclass:: AttributeDict
.. autoclass:: Timedelta

Functions
---------

Some additional convenience functions that deal with files and
directories:

.. function:: openany(directory[,mode='r'])

   Context manager to open a compressed (bzip2, gzip) or plain file
   (uses :func:`anyopen`).

.. autofunction:: anyopen
.. autofunction:: realpath
.. function:: in_dir(directory[,create=True])

   Context manager to execute a code block in a directory.

   * The *directory* is created if it does not exist (unless
     *create* = ``False`` is set)   
   * At the end or after an exception code always returns to
     the directory that was the current directory before entering
     the block.

.. autofunction:: find_first
.. autofunction:: withextsep

Functions that improve list processing and which do *not* treat
strings as lists:

.. autofunction:: iterable
.. autofunction:: asiterable


Functions that help handling Gromacs files:

.. autofunction:: unlink_f
.. autofunction:: unlink_gmx
.. autofunction:: unlink_gmx_backups
.. autofunction:: number_pdbs

Functions that make working with matplotlib_ easier:

.. _matplotlib: http://matplotlib.sourceforge.net/

.. autofunction:: activate_subplot
.. autofunction:: remove_legend


Miscellaneous functions:

.. autofunction:: convert_aa_code


Data
----

.. autodata:: amino_acid_codes

Find first *filename* with a suffix from *suffices*.

:Arguments:
  *filename*
     base filename; this file name is checked first
  *suffices*
     list of suffices that are tried in turn on the root of *filename*; can contain the 
     ext separator (:data:`os.path.extsep`) or not

:Returns: The first match or ``None``.