Wrapper for SYMMOL to convert and XYZ file to a symmetrized XYZ

xyz2symxyz

#!/usr/bin/env python2

# MIT License
# 
# Copyright (c) 2017 Anders Steen Christensen
# 
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# 
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
# 
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.

import sys
import os

def read_xyz(xyz_file):

    f = open(xyz_file)
    lines = f.readlines()
    f.close()

    atoms = []
    coordinates = []

    for line in lines[2:]:
        tokens = line.split()

        if len(tokens) < 4:
            break

        atom = tokens[0]
        x = float(tokens[1])
        y = float(tokens[2])
        z = float(tokens[3])

        atoms.append(atom)
        coordinates.append([x,y,z])

    return atoms, coordinates

def write_symmol_input(atoms, coordinates):

    output = """ 1 1 1 90 90 90
    1   1   0.50000   0.50000"""
    for atom, coord in zip(atoms, coordinates):

        output += "\n%-2s     1%9.5f%9.5f%9.5f" %(atom, coord[0], coord[1], coord[2])

    f = open("temp.symmol", "w")
    f.write(output)
    f.close()

def run_symmol():

    os.system("/home/andersx/bin/symmol < temp.symmol > /dev/null")

def read_symmol():

    f = open("symmol.out")
    lines = f.readlines()
    f.close()

    read = False

    atoms = []
    coordinates = []

    for line in lines:

        if read == True:

            tokens = line.split()
            if len(tokens) < 8:
                break

            atom = tokens[0]
            x = line[8:17]
            y = line[17:26]
            z = line[26:35]

            atoms.append(atom)
            coordinates.append([x,y,z])


        if "SYMMETRIZED ORTHOGONAL COORDINATES" in line:
            read = True

    return atoms, coordinates

if __name__ == "__main__":

    xyz_file = sys.argv[1]

    atoms, coordinates = read_xyz(xyz_file)

    write_symmol_input(atoms, coordinates)
    run_symmol()
    atoms, coordinates = read_symmol()

    print len(atoms)
    print
    for atom, c in zip(atoms, coordinates):
        print "%-2s   %s  %s  %s" % (atom, c[0], c[1], c[2])