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


# could produce some doubles
ifs = oemolistream()
ifs.open('b6.2'+sys.argv[1]+'_ln_out.ism')
ofs_1 = oemolostream()
ofs_1.open('b6.3'+sys.argv[1]+'_lp_out.ism')

# Leaving group X protonated
libgen2 = OELibraryGen("[R:4][#6R:1]([N:2])([R&!#6:3])[O-:100].[H:98]>>[*:4][*:1]([N:2])([O-:100])[AR+:3][H:98]")
# Leaving  amine N protonated
libgen3 = OELibraryGen("[R:4][#6R:1]([N:2])([R&!#6:3])[O-:100].[H:98]>>[*:4][C:1]([N+:2][H:98])([O-:100])[AR:3]")
# Leaving group A:4 protonated (if 3 heteroatoms at the attacked center!)
libgen4 = OELibraryGen("[#7,#8,#15,#16:4][#6R:1]([N:2])([R&!#6:3])[O-:100].[H:98]>>[A+:4]([H:98])[C:1]([N:2])([O-:100])[AR:3]")

libgen2.SetExplicitHydrogens(True)
libgen2.SetValenceCorrection(False)
libgen3.SetExplicitHydrogens(True)
libgen3.SetValenceCorrection(False)
libgen4.SetExplicitHydrogens(True)
libgen4.SetValenceCorrection(False)

mol_prot = OEGraphMol()
OEParseSmiles(mol_prot, "[H]")
for mol in ifs.GetOEMols():
    libgen2.AddStartingMaterial(mol, 0)
    libgen2.AddStartingMaterial(mol_prot, 1)
    libgen3.AddStartingMaterial(mol, 0)
    libgen3.AddStartingMaterial(mol_prot, 1)
    libgen4.AddStartingMaterial(mol, 0)
    libgen4.AddStartingMaterial(mol_prot, 1)
    mol.Clear()
    mol_prot.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('b6_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')

for products in libgen3.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')

for products in libgen4.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()