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

rxn = 2
ifs = oemolistream()
ifs.open('ORIGINAL_MOLS/a4_kegg_012506.ism')
ofs_1 = oemolostream()
ofs_2 = oemolostream()
ofs_1.open('b'+str(rxn)+'.1_ln.ism')
ofs_2.open('b'+str(rxn)+'.1_lp.ism')

mol_hyd = OEGraphMol()
OEParseSmiles(mol_hyd, "[OH]")
# Reaction 1 aromatic: OH- nucleophilic attack at a-C(=O)-X (amide etc., O exocyclic)
# Former Carbonyl-oxygen becomes OH-group, attacking OH- becomes O-
# (AROMATIC -> partly wrong annotations in KEGG)
#leaving group NOT protonated [*:4] included, because leaving group needs to be recognized only once (if there are 2!)
libgen1 = OELibraryGen("[a&!-:4][c:1]=([O,S:3])[!#6:2].[OH:100]>>[A:4][C:1]([A-:3])([OH:100])[*:2]")

for mol in ifs.GetOEMols():
    libgen1.AddStartingMaterial(mol, 0)
    libgen1.AddStartingMaterial(mol_hyd, 1)
    mol.Clear()
    mol_hyd.Clear()

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

for products in libgen1.GetProducts():
    num = 1
    prot = 0
    title = products.GetTitle()+str(num)+'p'+str(prot)
    while title in title_list:
        num+=1
        title = products.GetTitle()+str(num)+'p'+str(prot)
    title_list.append(title)
    products.SetTitle(title)
    OEWriteMolecule(ofs_1, products)


ofs_1.close()
ifs.close()
#raise SystemExit()
ifs.open('b'+str(rxn)+'.1_ln.ism')

mol_prot = OEGraphMol()
OEParseSmiles(mol_prot, "[H+]")
#leaving group protonated - will create attacked carboxylates!(can't avoid otherwise not all pot. leaving groups recognized)
libgen2 = OELibraryGen("[#6R:1]([O,S-:3])([OH:5])[R&!#6&!-:2].[H:102]>>[C:1]([A:3])([OH:5])[*+:2][H:102]")

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

for products in libgen2.GetProducts():
    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_2, products)

ofs_2.close()
ifs.close()