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

try:
    ifs = oemolistream()
    ifs.open(sys.argv[1])
    ofs_1 = oemolostream()
    ofs_1.open('b5'+sys.argv[1][string.find(sys.argv[1], '_'):string.find(sys.argv[1], '_out')]+'_ln_out.ism')
    ofs_2 = oemolostream()
    ofs_2.open('b5'+sys.argv[1][string.find(sys.argv[1], '_'):string.find(sys.argv[1], '_out')]+'_lp_out.ism')
except IndexError:
    print '\nUsage: b5_rxn_amidine_aromatic.py molfile\n'
    raise SystemExit()


mol_hyd = OEGraphMol()
OEParseSmiles(mol_hyd, "[OH]")
# Reaction 6: OH-H nucleophilic attack at X:-C(Y)=N endocyclic or chain member) (Imine, Amidine, Guanidine)
# Nothing protonated
libgen1 = OELibraryGen("[A,H:4][C:1]([*:2])=[N:3].[O:100][H:99]>>[*:4][C:1]([*:2])([O-:100])[N:3][H:99]")
libgen1.SetExplicitHydrogens(True)
libgen1.SetValenceCorrection(False)

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('b5_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()


ifs.open('b5'+sys.argv[1][string.find(sys.argv[1], '_'):string.find(sys.argv[1], '_out')]+'_ln_out.ism')

mol_prot = OEGraphMol()
OEParseSmiles(mol_prot, "[H]")
# Leaving group X,Y: protonated
libgen2 = OELibraryGen("[C:1]([!#6;!#1:2])([O-:5])[N:3].[H:98]>>[C:1]([*+:2][H:98])([O-:5])[N:3]")
# Leaving group N protonated
libgen3 = OELibraryGen("[*:4][C:1]([*:2])([O-:5])[N:3].[H:98]>>[*:4][C:1]([*:2])([O-:5])[N+:3][H:98]")

libgen2.SetExplicitHydrogens(True)
libgen2.SetValenceCorrection(False)
libgen3.SetExplicitHydrogens(True)
libgen3.SetValenceCorrection(False)

for mol in ifs.GetOEMols():
    libgen2.AddStartingMaterial(mol, 0)
    libgen2.AddStartingMaterial(mol_prot, 1)
    libgen3.AddStartingMaterial(mol, 0)
    libgen3.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')

for products in libgen3.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')

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