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

rxn = 5

ifs = oemolistream()
ifs.open('bb'+str(rxn-1)+'_ln.ism')
ofs_1 = oemolostream()
ofs_1.open('bb'+str(rxn)+'_lp.ism')

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('bb'+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:
        print 'bb'+str(rxn_n)+'_ln.ism not existent\n'
    try:
        old_title_file = open('bb'+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:
        print 'bb'+str(rxn_n)+'_lp.ism not existent\n'
    rxn_n+=1

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)


ofs_1.close()
ifs.close()