Source code for MDAnalysis.topology.base
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# MDAnalysis --- http://www.MDAnalysis.org
# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
# and contributors (see AUTHORS for the full list)
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# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""
Base topology reader classes --- :mod:`MDAnalysis.topology.base`
================================================================
Derive topology reader classes from the base class in this module. All
topology readers raise :exc:`IOError` upon failing to read a topology
file and :exc:`ValueError` upon failing to make sense of the read data.
Classes
-------
.. autoclass:: TopologyReader
:members:
:inherited-members:
"""
import six
from . import _PARSERS
from ..coordinates.base import IObase
from ..lib import util
class _Topologymeta(type):
def __init__(cls, name, bases, classdict):
type.__init__(type, name, bases, classdict)
try:
fmt = util.asiterable(classdict['format'])
except KeyError:
pass
else:
for f in fmt:
_PARSERS[f] = cls
[docs]class TopologyReader(six.with_metaclass(_Topologymeta, IObase)):
"""Base class for topology readers
Parameters
----------
filename : str
name of the topology file
universe : Universe, optional
Supply a Universe to the Parser. This then passes it to the
atom instances that are created within parsers.
kwargs : optional
Other keyword arguments that can vary with the specific format.
These are stored as self.kwargs
All topology readers must define a `parse` method which
returns a topology dict.
Raises
------
* :exc:`IOError` upon failing to read a topology file
* :exc:`ValueError` upon failing to make sense of the read data
.. versionadded:: 0.9.0
.. versionchanged:: 0.9.2
Added keyword 'universe' to pass to Atom creation.
"""
def __init__(self, filename, universe=None, **kwargs):
self.filename = filename
self._u = universe
self.kwargs = kwargs
def parse(self):
raise NotImplementedError("Override this in each subclass")