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

rxn = 6
ifs = oemolistream()
ifs.open('ORG_BRENDA_MOL_FILES_PREP/a4_brenda_031306.ism')
ofs_1 = oemolostream()
ofs_1.open('bb'+str(rxn)+'_ln.ism')
ofs_2 = oemolostream()
ofs_2.open('bb'+str(rxn)+'_lp.ism')

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 = []
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

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()


ifs.open('bb'+str(rxn)+'_ln.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)

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)

ifs.close()