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.


.. autoclass:: XYZParser

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 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'
[docs] 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