#!/usr/bin/python
import os, string, sys
from openeye.oechem import *

try:
    ifs = oemolistream()
    ifs.open('b4.3'+sys.argv[1]+'_ln_out.ism')
    ofs_1 = oemolostream()
    ofs_1.open('b4.4'+sys.argv[1][string.find(sys.argv[1], '_'):string.find(sys.argv[1], '_ln')]+'_lp_out.ism')
except IndexError:
    print '\nUsage: b4.4_rxn_amidine_aromatic.py molfile\n'
    raise SystemExit()

mol_hyd = OEGraphMol()
OEParseSmiles(mol_hyd, "[H]")
# Reaction 4: 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 = []

for title_file in os.listdir('.'):
    if title_file[-11:] == '_titles.txt':
        print 'Open & read '+title_file
        titlef = open(title_file, 'r')
        for line in titlef.readlines():
            title_list.append(line[:-1])
        titlef.close()

title_f = open('b4_titles.txt', 'a')

product_smiles = []

for products in libgen2.GetProducts():
    if OECreateIsoSmiString(products) in product_smiles:
        continue
    else:
        product_smiles.append(OECreateIsoSmiString(products))
    prot = 0
    title = products.GetTitle()[:string.find(products.GetTitle(), 'p0')]+'p'+str(prot)
    while title in title_list:
        prot+=1
        title = products.GetTitle()[:string.find(products.GetTitle(), 'p')]+'p'+str(prot)
    title_list.append(title)
    products.SetTitle(title)
    OEWriteMolecule(ofs_1, products)
    title_f.write(title+'\n')

ofs_1.close()
ifs.close()
title_f.close()