# Copyright (c) 2012, GlaxoSmithKline Research & Development Ltd.
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# Created by Jameed Hussain, September 2012

import sys
import re
from rdkit import Chem
from indexing import cansmirk

if __name__ == '__main__':

  if (len(sys.argv) >= 2):
    print(
      "Program that canonicalises an input SMIRKS so its in same format as MMP identification program.\n")
    print("USAGE: ./cansmirks.py <file_of_smirks\n")
    sys.exit(1)

  #read the STDIN
  for line in sys.stdin:

    line = line.rstrip()

    line_fields = re.split('\s|,', line)
    smirks = line_fields[0]

    if (len(line_fields) == 1):
      id = ""
    else:
      id = line_fields[1]

    lhs, rhs = smirks.split(">>")

    l = Chem.MolFromSmiles(lhs)
    if (l == None):
      sys.stderr.write("Can't generate mol for: %s\n" % (lhs))
      continue

    r = Chem.MolFromSmiles(rhs)
    if (r == None):
      sys.stderr.write("Can't generate mol for: %s\n" % (rhs))
      continue

    clhs = Chem.MolToSmiles(l, isomericSmiles=True)
    crhs = Chem.MolToSmiles(r, isomericSmiles=True)

    #just need to take care of [*H:1]
    if (clhs == '[*H:1]'):
      clhs = '[*:1][H]'

    if (crhs == '[*H:1]'):
      crhs = '[*:1][H]'

    #print clhs
    #print crhs

    csmirk, context = cansmirk(clhs, crhs, "")

    print("%s %s" % (csmirk, id))
