Source code for MDAnalysis.topology.TXYZParser

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# Please cite your use of MDAnalysis in published work:
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# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
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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.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""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
onwards.

.. _Tinker: https://dasher.wustl.edu/tinker/

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


Classes
-------

.. autoclass:: TXYZParser
   :members:
   :inherited-members:

"""

import itertools
import numpy as np
import warnings

from ..guesser.tables import SYMB2Z
from ..lib.util import openany
from .base import TopologyReaderBase
from ..core.topology import Topology
from ..guesser.tables import SYMB2Z
from ..core.topologyattrs import (
    Atomnames,
    Atomids,
    Atomtypes,
    Bonds,
    Resids,
    Resnums,
    Segids,
    Elements,
)




class TXYZParser(TopologyReaderBase):
    """Parse a list of atoms from a Tinker XYZ file.

    Creates the following attributes:

    - Atomnames
    - Atomtypes
    - Elements (if all atom names are element symbols)

    .. note::

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

    .. versionadded:: 0.17.0
    .. versionchanged:: 2.4.0
       Adding the `Element` attribute if all names are valid element symbols.
    .. versionchanged:: 2.8.0
       Removed mass guessing (attributes guessing takes place now
       through universe.guess_TopologyAttrs() API).

    """
    format = ['TXYZ', 'ARC']



    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))

        attrs = [Atomnames(names),
                 Atomids(atomids),
                 Atomtypes(types),
                 Bonds(tuple(bonds)),
                 Resids(np.array([1])),
                 Resnums(np.array([1])),
                 Segids(np.array(['SYSTEM'], dtype=object)),
                 ]
        if all(n.capitalize() in SYMB2Z for n in names):
            attrs.append(Elements(np.array(names, dtype=object)))

        else:
            warnings.warn("Element information is missing, elements attribute "
                          "will not be populated. If needed these can be "
                          "guessed using universe.guess_TopologyAttrs("
                          "to_guess=['elements']).")

        top = Topology(natoms, 1, 1,
                       attrs=attrs)

        return top