Source code for MDAnalysis.topology.MinimalParser

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"""
Minimal topology parser
=======================

Parses only the number of atoms from a coordinate/trajectory file.
This minimal topology can be used to access coordinate data without the need
for a full-fledged topology file.



Classes
-------

.. autoclass:: MinimalParser
   :members:
   :inherited-members:

"""

from ..core._get_readers import get_reader_for
from ..core.topology import Topology
from .base import TopologyReaderBase



[docs]
class MinimalParser(TopologyReaderBase):
    """Produces a minimal topology from only the number of atoms.

    This requires that the number of atoms be given in one of two ways:
     - The number of atoms can be given as the 'n_atoms' keyword argument.
     - If this is not given, then a Reader object for the filename will be
       created and the `parse_n_atoms` method on this Reader will be called,
       (requiring that the Reader has this capability).

    This requires that the coordinate format has
    """
    format = 'MINIMAL'


[docs]
    def parse(self, **kwargs):
        """Return the minimal *Topology* object"""
        try:
            n_atoms = kwargs['n_atoms']
        except KeyError:
            reader = get_reader_for(self.filename)
            n_atoms = reader.parse_n_atoms(self.filename, **kwargs)

        return Topology(n_atoms, 1, 1)