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

rxn = 8
ifs = oemolistream()
ifs.open('a_kegg_filter_1.sdf')
ofs_1 = oemolostream()
ofs_1.open('b_react_ti_'+str(rxn)+'_not_filtered_ln.sdf')
ofs_3 = oemolostream()
ofs_3.open('b_react_ti_'+str(rxn)+'_not_filtered_lp.sdf')

mol_wat = OEGraphMol()
OEParseSmiles(mol_wat, "O(H)H")
mol_hyd = OEGraphMol()
OEParseSmiles(mol_hyd, "[OH]")
# Reaction 7: OH-H nucleophilic attack at X-C=N (X (not C) endocyclic or chain member) (Imine) (rxn6 - AROMATIC - wrong annot. in Kegg)
# nothing protonated
libgen1 = OELibraryGen("[a:4][c:1](=[N:2])[a&!#6:3].[O:100][H:99]>>[*:4][C:1]([N:2][H:99])([O-:100])[A:3]")
# Leaving group X protonated
libgen2 = OELibraryGen("[a:4][c:1](=[N:2])[aR&!#6:3].[O:100]([H:98])[H:99]>>[*:4][C:1]([N:2][H:99])([O-:100])[AR+:3][H:98]")
# Leaving  amine N protonated
libgen3 = OELibraryGen("[a:4][c:1](=[N:2])[aR&!#6:3].[O:100]([H:98])[H:99]>>[*:4][C:1]([N+:2]([H:99])[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][c:1](=[N:2])[aR&!#6:3].[O:100]([H:99])[H:98]>>[A+:4]([H:98])[C:1]([N:2][H:99])([O-:100])[AR:3]")

libgen1.SetExplicitHydrogens(True)
libgen1.SetValenceCorrection(False)
libgen2.SetExplicitHydrogens(True)
libgen2.SetValenceCorrection(False)
libgen3.SetExplicitHydrogens(True)
libgen3.SetValenceCorrection(False)
libgen4.SetExplicitHydrogens(True)
libgen4.SetValenceCorrection(False)

for mol in ifs.GetOEMols():
    libgen1.AddStartingMaterial(mol, 0)
    libgen1.AddStartingMaterial(mol_hyd, 1)
    libgen2.AddStartingMaterial(mol, 0)
    libgen2.AddStartingMaterial(mol_wat, 1)
    libgen3.AddStartingMaterial(mol, 0)
    libgen3.AddStartingMaterial(mol_wat, 1)
    libgen4.AddStartingMaterial(mol, 0)
    libgen4.AddStartingMaterial(mol_wat, 1)
    mol.Clear()
    mol_wat.Clear()
    mol_hyd.Clear()

title_list = []
rxn_n = 1
while rxn_n < rxn:
  try:
    old_title_file = open('b_react_ti_'+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:
    pass
  try:
    old_title_file = open('b_react_ti_'+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:
    pass
  rxn_n+=1



for products in libgen1.GetProducts():
    if products.NumAtoms() < 76:
        num = 1
        title = products.GetTitle()+str(num)
        while title in title_list:
            num+=1
            title = products.GetTitle()+str(num)
        title_list.append(title)
        products.SetTitle(title)
        OEWriteMolecule(ofs_1, products)

ofs_1.close()

for products in libgen2.GetProducts():
    if products.NumAtoms() < 76:
        num = 1
        title = products.GetTitle()+str(num)
        while title in title_list:
            num+=1
            title = products.GetTitle()+str(num)
        title_list.append(title)
        products.SetTitle(title)
        OEWriteMolecule(ofs_3, products)

for products in libgen3.GetProducts():
    if products.NumAtoms() < 76:
        num = 1
        title = products.GetTitle()+str(num)
        while title in title_list:
            num+=1
            title = products.GetTitle()+str(num)
        title_list.append(title)
        products.SetTitle(title)
        OEWriteMolecule(ofs_3, products)

for products in libgen4.GetProducts():
    if products.NumAtoms() < 76:
        num = 1
        title = products.GetTitle()+str(num)
        while title in title_list:
            num+=1
            title = products.GetTitle()+str(num)
        title_list.append(title)
        products.SetTitle(title)
        OEWriteMolecule(ofs_3, products)

ofs_3.close()
ifs.close()