# 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:

    """
    import numpy as np

    from ..lib.util import openany
    from .base import TopologyReaderBase
    from ..core.topology import Topology
    from ..core.topologyattrs import (
        Atomnames,
        Atomids,
        Resids,
        Resnums,
        Segids,
        Elements,
    )

    class FHIAIMSParser(TopologyReaderBase):
        """Parse a list of atoms from an FHI-AIMS file

        Creates the following attributes:
         - Atomnames

        .. note::

            By default, atomtypes and masses will be guessed on Universe creation.
            This may change in release 3.0.
            See :ref:`Guessers` for more information.

        .. versionchanged:: 2.8.0
            Removed type and mass guessing (attributes guessing takes place now
            through universe.guess_TopologyAttrs() API).
        """

        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)

            attrs = [
                Atomnames(names),
                Atomids(np.arange(natoms) + 1),
                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