#!/usr/bin/env python2
"""
convert zmatrix and input for spin multiplicity and charge from the SI of 
J. Chem. Phys. 131, 154112 (2009); https://doi.org/10.1063/1.3247288

into a zmatrix usable by the QP, and spits the correct command to execute
Usage:
    qp_create_ezfio_from_g09_zmat g09_zmat basis 

Produces the ezfio folder g09_zmat.ezfio 

"""

import sys
import os
import subprocess


try:
    import qp_path
except ImportError:
    print "source .quantum_package.rc"
    raise
try:
    QP_ROOT = os.environ["QP_ROOT"]
    QP_EZFIO = os.environ["QP_EZFIO"]
except KeyError:
    print "Error: QP_ROOT environment variable not found."
    sys.exit(1)
else:
    sys.path = [QP_EZFIO + "/Python",
                QP_ROOT + "/install/resultsFile",
                QP_ROOT + "/install",
                QP_ROOT + "/scripts"] + sys.path



def findall(sub, string):
    """
    >>> text = "Allowed Hello Hollow"
    >>> tuple(findall('ll', text))
    (1, 10, 16)
    """
    index = 0 - len(sub)
    try:
        while True:
            index = string.index(sub, index + len(sub))
            yield index
    except ValueError:
        pass

filepath = sys.argv[1]
basis = sys.argv[2]
icount = 0
zmat = []
with open(filepath, "r") as fp:
   cipsi = []
   for line in fp:
     if (icount == 0 ):
      a=line.split(',')
      charge = int(a[0])
      spin = int(a[1])
     else: 
      a=line.split()
      if(len(a)>0):
       n=a[0].count(',')
       if(n > 6):
        listfind=list(findall(',', a[0]))
        char=a[0]
        a[0]=char[0:listfind[n-1]]

       b=a[0].replace(',', ' ')
       b=b.replace('=', ' ')
       zmat.append(b)
      else:
       b=" " 
       zmat.append(b)

     icount += 1

c = filepath.split('.')
file_origin = c[0]
ezfio = file_origin+".ezfio"
zmat_file = file_origin+".zmt"
file_zmat = open(zmat_file,"w+")
for l in zmat:
  file_zmat.write(l +'\n')

command="qp_create_ezfio -m %s -c %s -b %s -o %s  %s" % (spin,charge,basis,ezfio,zmat_file)
print command
#os.system(command)