#!/usr/local2/bin/python2.3
import os, string
from openeye.oechem import *

rxn = 4

ifs = oemolistream()
ifs.open('b_react_ti_3_ln.sdf')
ofs_3 = oemolostream()
ofs_3.open('b_react_ti_4_lp.ism')
ofs_4 = oemolostream()
ofs_4.open('b_react_ti_4_lp.sdf')

mol_hyd = OEGraphMol()
OEParseSmiles(mol_hyd, "[H]")
# Reaction 3b: Protonation of all possible leaving groups (amines) of reaction 3 - not doable in one step, 
# because in case of 2 Ns each needs to be protonated one time
# protonation of leaving amine - will generate identical molecules if similar N:2 twice bonded to C:4
libgen2 = OELibraryGen("[CX4v4:1]([N:2])[O-:100].[H:99]>>[C:1]([N+:2][H:99])[O-:100]")

libgen2.SetExplicitHydrogens(True)
libgen2.SetValenceCorrection(False)

for mol in ifs.GetOEMols():
    libgen2.AddStartingMaterial(mol, 0)
    libgen2.AddStartingMaterial(mol_hyd, 1)
    mol.Clear()
    mol_hyd.Clear()

title_list = []
rxn_n = 1
while rxn_n < rxn:
  try:
    old_title_file = open('b_react_ti_'+str(rxn_n)+'_ln.ism','r')
    for title in old_title_file.readlines():
        title_list.append(string.split(title)[1])
    old_title_file.close()
  except IOError:
    pass
  try:
    old_title_file = open('b_react_ti_'+str(rxn_n)+'_lp.ism','r')
    for title in old_title_file.readlines():
        title_list.append(string.split(title)[1])
    old_title_file.close()
  except IOError:
    pass
  rxn_n+=1

for products in libgen2.GetProducts():
    if products.NumAtoms() < 76:
        num = 1
        title = products.GetTitle()[:6]+'_'+str(num)
        while title in title_list:
            num+=1
            title = products.GetTitle()[:6]+'_'+str(num)
        title_list.append(title)
        products.SetTitle(title)
        OEWriteMolecule(ofs_3, products)
        OEWriteMolecule(ofs_4, products)


ofs_3.close()
ofs_4.close()
ifs.close()