Source code for MDAnalysis.topology.XYZParser

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# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
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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:
   :inherited-members:

"""
from __future__ import absolute_import

from ..core.AtomGroup import Atom
from ..lib.util import openany
from .core import get_atom_mass, guess_atom_charge, guess_atom_element
from .base import TopologyReader


[docs]class XYZParser(TopologyReader): """Parse a list of atoms from an XYZ file. .. versionadded:: 0.9.1 """
[docs] def parse(self): """Read the file and return the structure. :Returns: MDAnalysis internal *structure* dict. """ with openany(self.filename, 'r') as inf: natoms = int(inf.readline().strip()) inf.readline() segid = "SYSTEM" resid = 1 resname = "SYSTEM" atoms = [] # Can't infinitely read as XYZ files can be multiframe for i in range(natoms): name = inf.readline().split()[0] elem = guess_atom_element(name) mass = get_atom_mass(elem) charge = guess_atom_charge(name) at = Atom(i, name, elem, resname, resid, segid, mass, charge, universe=self._u) atoms.append(at) struc = {"atoms": atoms} return struc