Source code for MDAnalysis.topology.XYZParser

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"""
XYZ Topology Parser
===================

.. versionadded:: 0.9.1

Reads an xyz file and pulls the atom information from it.  Because
xyz only has atom name information, all information about residues
and segments won't be populated.

Classes
-------

.. autoclass:: XYZParser
   :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 XYZParser(TopologyReaderBase):
    """Parse a list of atoms from an XYZ file.

    Creates the following attributes:
     - Atomnames

    Guesses the following attributes:
     - Atomtypes
     - Masses

    .. versionadded:: 0.9.1

    .. versionchanged: 1.0.0
       Store elements attribute, based on XYZ atom names
    """
    format = 'XYZ'

    def parse(self, **kwargs):
        """Read the file and return the structure.

        Returns
        -------
        MDAnalysis Topology object
        """
        with openany(self.filename) as inf:
            natoms = int(inf.readline().strip())
            inf.readline()

            names = np.zeros(natoms, dtype=object)

            # Can't infinitely read as XYZ files can be multiframe
            for i in range(natoms):
                name = inf.readline().split()[0]
                names[i] = name

        # 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