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`: https://aimsclub.fhi-berlin.mpg.de/


See Also
--------
:mod:`MDAnalysis.coordinates.FHIAIMS`


Classes
-------

.. autoclass:: FHIAIMSParser
   :members:
   :inherited-members:

"""
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 (
    Atomnames,
    Atomids,
    Atomtypes,
    Masses,
    Resids,
    Resnums,
    Segids,
    Elements,
)


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']

    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