Source code for pymatgen.io.xyz

# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

from __future__ import division, unicode_literals
import re

from pymatgen.core.structure import Molecule
from monty.io import zopen

"""
Module implementing an XYZ file object class.
"""

__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Apr 17, 2012"


class XYZ(object):
    """
    Basic class for importing and exporting Molecules or Structures in XYZ
    format.

    Args:
        mol: Input molecule or list of molecules

    .. note::
        Exporting periodic structures in the XYZ format will lose information
        about the periodicity. Essentially, only cartesian coordinates are
        written in this format and no information is retained about the
        lattice.
    """
    def __init__(self, mol, coord_precision=6):
        if isinstance(mol, Molecule) or not isinstance(mol, list):
            self._mols = [mol]
        else:
            self._mols = mol
        self.precision = coord_precision

    @property
    def molecule(self):
        """
        Returns molecule associated with this XYZ. In case multiple frame
        XYZ, returns the last frame.
        """
        return self._mols[-1]

    @property
    def all_molecules(self):
        """
        Returns all the frames of molecule associated with this XYZ.
        """
        return self._mols

    @staticmethod
    def _from_frame_string(contents):
        """
        Convert a single frame XYZ string to a molecule
        """
        lines = contents.split("\n")
        num_sites = int(lines[0])
        coords = []
        sp = []
        coord_patt = re.compile(
            r"(\w+)\s+([0-9\-\.e]+)\s+([0-9\-\.e]+)\s+([0-9\-\.e]+)"
        )
        for i in range(2, 2 + num_sites):
            m = coord_patt.search(lines[i])
            if m:
                sp.append(m.group(1))  # this is 1-indexed
                # this is 0-indexed
                coords.append([float(j) for j in m.groups()[1:4]])
        return Molecule(sp, coords)

    @staticmethod
    def from_string(contents):
        """
        Creates XYZ object from a string.

        Args:
            contents: String representing an XYZ file.

        Returns:
            XYZ object
        """
        if contents[-1] != "\n":
            contents += "\n"
        white_space = r"[ \t\r\f\v]"
        natoms_line = white_space + r"*\d+" + white_space + r"*\n"
        comment_line = r"[^\n]*\n"
        coord_lines = r"(\s*\w+\s+[0-9\-\.e]+\s+[0-9\-\.e]+\s+[0-9\-\.e]+\s*\n)+"
        frame_pattern_text = natoms_line + comment_line + coord_lines
        pat = re.compile(frame_pattern_text, re.MULTILINE)
        mols = []
        for xyz_match in pat.finditer(contents):
            xyz_text = xyz_match.group(0)
            mols.append(XYZ._from_frame_string(xyz_text))
        return XYZ(mols)

    @staticmethod
    def from_file(filename):
        """
        Creates XYZ object from a file.

        Args:
            filename: XYZ filename

        Returns:
            XYZ object
        """
        with zopen(filename) as f:
            return XYZ.from_string(f.read())

    def _frame_str(self, frame_mol):
        output = [str(len(frame_mol)), frame_mol.composition.formula]
        fmtstr = "{{}} {{:.{0}f}} {{:.{0}f}} {{:.{0}f}}".format(self.precision)
        for site in frame_mol:
            output.append(fmtstr.format(site.specie, site.x, site.y, site.z))
        return "\n".join(output)

    def __str__(self):
        return "\n".join([self._frame_str(mol) for mol in self._mols])

    def write_file(self, filename):
        """
        Writes XYZ to file.

        Args:
            filename: File name of output file.
        """
        with zopen(filename, "wt") as f:
            f.write(self.__str__())