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.


.. autoclass:: MinimalParser


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)