Source code for MDAnalysis.topology.TXYZParser

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"""TXYZ topology parser

Tinker_ topology parser: reads information from .txyz and .arc files.
Atom types are read from column 6, while bond connectivity is read from column 7

.. _Tinker:

See Also
MDAnalysis.coordinates.TXYZ : further documentation on the Tinker format


.. autoclass:: TXYZParser


import itertools
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 TXYZParser(TopologyReaderBase): """Parse a list of atoms from a Tinker XYZ file. Creates the following attributes: - Atomnames - Atomtypes .. versionadded:: 0.17.0 """ format = ['TXYZ', 'ARC']
[docs] def parse(self, **kwargs): """Read the file and return the structure. Returns ------- MDAnalysis Topology object """ with openany(self.filename) as inf: #header natoms = int(inf.readline().split()[0]) atomids = np.zeros(natoms, dtype=int) names = np.zeros(natoms, dtype=object) types = np.zeros(natoms, dtype=object) bonds = [] # Find first atom line, maybe there's box information fline = inf.readline() try: # If a box second value will be a float # If an atom, second value will be a string float(fline.split()[1]) except ValueError: # If float conversion failed, we have first atom line pass else: # If previous try succeeded it was a box # so read another line to find the first atom line fline = inf.readline() # Can't infinitely read as XYZ files can be multiframe for i, line in zip(range(natoms), itertools.chain([fline], inf)): line = line.split() atomids[i]= line[0] names[i] = line[1] types[i] = line[5] bonded_atoms = line[6:] for other_atom in bonded_atoms: other_atom = int(other_atom) - 1 if i < other_atom: bonds.append((i, other_atom)) # Guessing time masses = guessers.guess_masses(names) attrs = [Atomnames(names), Atomids(atomids), Atomtypes(types), Bonds(tuple(bonds)), Masses(masses, guessed=True), Resids(np.array([1])), Resnums(np.array([1])), Segids(np.array(['SYSTEM'], dtype=object)), ] top = Topology(natoms, 1, 1, attrs=attrs) return top