xyz.py

# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

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

import re
from io import StringIO

import pandas as pd
from monty.io import zopen

from pymatgen.core.structure import Molecule


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

    .. 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: Molecule, coord_precision: int = 6):
        """
        Args:
            mol: Input molecule or list of molecules
            coord_precision: Precision to be used for coordinates.
        """
        if isinstance(mol, Molecule) or not isinstance(mol, list):
            self._mols = [mol]
        else:
            self._mols = mol
        self.precision = coord_precision

    @property
    def molecule(self) -> Molecule:
        """
        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\-\+\.*^eEdD]+)\s+([0-9\-\+\.*^eEdD]+)\s+" r"([0-9\-\+\.*^eEdD]+)")
        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
                # in case of 0.0D+00 or 0.00d+01 old double precision writing
                # replace d or D by e for ten power exponent,
                # and some files use *^ convention in place of e
                xyz = [val.lower().replace("d", "e").replace("*^", "e") for val in m.groups()[1:4]]
                coords.append([float(val) for val in xyz])
        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\-\+\.*^eEdD]+\s+[0-9\-\+\.*^eEdD]+" r"\s+[0-9\-\+\.*^eEdD]+.*\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, "rt") as f:
            return XYZ.from_string(f.read())

    def as_dataframe(self):
        """
        Generates a coordinates data frame with columns: atom, x, y, and z
        In case of multiple frame XYZ, returns the last frame.

        Returns:
            pandas.DataFrame

        """
        lines = str(self)

        sio = StringIO(lines)
        df = pd.read_csv(
            sio,
            header=None,
            skiprows=[0, 1],
            comment="#",
            delim_whitespace=True,
            names=["atom", "x", "y", "z"],
        )
        df.index += 1
        return df

    def _frame_str(self, frame_mol):
        output = [str(len(frame_mol)), frame_mol.composition.formula]
        fmtstr = f"{{}} {{:.{self.precision}f}} {{:.{self.precision}f}} {{:.{self.precision}f}}"
        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: str) -> None:
        """
        Writes XYZ to file.

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