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

try:
    ifs = oemolistream()
    ifs.open(sys.argv[1])
    ofs_1 = oemolostream()
    ofs_2 = oemolostream()
    ofs_1.open('b2.1'+sys.argv[1][string.find(sys.argv[1], '_'):string.find(sys.argv[1], '_out')]+'_ln.ism')
    ofs_2.open('b2.1'+sys.argv[1][string.find(sys.argv[1], '_'):string.find(sys.argv[1], '_out')]+'_lp.ism')
    date = sys.argv[1][string.find(sys.argv[1], '_'):string.find(sys.argv[1], '_out')]
except IndexError:
    print '\nUsage:  b2.1_rxn_aromatic_cleav.py molfile\n'
    raise SystemExit()

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 = []   

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('b2_titles.txt', 'w')

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)
    title_f.write(title+'\n')

ofs_1.close()
ifs.close()

# Protonation
ifs.open('b2.1'+sys.argv[1][string.find(sys.argv[1], '_'):string.find(sys.argv[1], '_out')]+'_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)
    title_f.write(title+'\n')

ofs_2.close()
ifs.close()
title_f.close()

print '\nStart b2.2_rxn_aromatic_cleav.py\n'
os.system('b2.2_rxn_aromatic_cleav.py '+date)