Source code for MDAnalysis.topology.FHIAIMSParser

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FHI-AIMS Topology Parser --- :mod:`MDAnalysis.topolgy.FHIAIMSParser`

Reads an `FHI-AIMS`_ ``.in`` file and pulls the atom information from it.
Because an FHI-AIMS input file only has atom name information, any
information about residues and segments will not be populated.

.. _`FHI-AIMS`:

See Also


.. autoclass:: FHIAIMSParser

from __future__ import absolute_import

from six.moves import range
import numpy as np

from . import guessers
from ..lib.util import openany
from .base import TopologyReaderBase
from ..core.topology import Topology
from ..core.topologyattrs import (

[docs]class FHIAIMSParser(TopologyReaderBase): """Parse a list of atoms from an FHI-AIMS file Creates the following attributes: - Atomnames Guesses the following attributes: - Atomtypes - Masses """ format = ['IN', 'FHIAIMS']
[docs] def parse(self, **kwargs): """Read the file and return the structure. Returns ------- MDAnalysis Topology object """ # FHIAIMS geometry files are only single frames names = [] skip_tags = ["#", "lattice_vector", "initial_moment", "velocity"] with openany(self.filename) as inf: for line in inf: line = line.strip() if line.startswith("atom"): names.append(line.split()[-1]) continue if any([line.startswith(tag) for tag in skip_tags]): continue # we are now seeing something that's neither atom nor lattice raise ValueError( 'Non-conforming line: ({0})in FHI-AIMS input file {0}'.format(line, self.filename)) names = np.asarray(names) natoms = len(names) # Guessing time atomtypes = guessers.guess_types(names) masses = guessers.guess_masses(names) attrs = [Atomnames(names), Atomids(np.arange(natoms) + 1), Atomtypes(atomtypes, guessed=True), Masses(masses, guessed=True), Resids(np.array([1])), Resnums(np.array([1])), Segids(np.array(['SYSTEM'], dtype=object)), Elements(names)] top = Topology(natoms, 1, 1, attrs=attrs) return top