Convert TINKER xyz to regular xyz format.

tinkerxyz2xyz.py

#!/usr/bin/env python

from __future__ import print_function
import sys

def tinker2xyz(filename):

    f = open(filename, "r")
    lines = f.readlines()
    f.close()
    
    natoms = len(lines) - 1
    print(natoms)
    print()
    
    for line in lines[1:]:
    
        tokens = line.split()
        print(" %-s  %12s  %12s  %12s" % (tokens[1][0], tokens[2], tokens[3], tokens[4]))

    return

if __name__ == "__main__":

    filename = sys.argv[1]
    tinker2xyz(filename)