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

# wie 1, aber =S dort vergessen!

rxn = 13
ifs = oemolistream()
ifs.open('a_kegg_filter_1.sdf')
ofs_1 = oemolostream()
ofs_1.open('b_react_ti_'+str(rxn)+'_ln.ism')
ofs_2 = oemolostream()
ofs_2.open('b_react_ti_'+str(rxn)+'_ln.sdf')
ofs_3 = oemolostream()
ofs_3.open('b_react_ti_'+str(rxn)+'_lp.ism')
ofs_4 = oemolostream()
ofs_4.open('b_react_ti_'+str(rxn)+'_lp.sdf')

mol_hyd = OEGraphMol()
OEParseSmiles(mol_hyd, "[OH]")
mol_wat = OEGraphMol()
OEParseSmiles(mol_wat, "O(H)H")
# Reaction 1: OH- nucleophilic attack at A-C(=O)-X (amide, ester etc., O exocyclic) (Non-aromatic)
# Former Carbonyl-oxygen becomes OH-group, attacking OH- becomes O-
# leaving group NOT protonated  [*:4] included, because leaving group needs to be recognized only once (if there are 2!)
libgen1 = OELibraryGen("[*&!-:4][C:1]=([S:3])[!#6&!-&!#1:2].[O:100][H:102]>>[*:4][C:1]([S:3][H:102])([O-:100])[*:2]")
# leaving group protonated - will create attacked carboxylates! -> removing
libgen2 = OELibraryGen("[C:1]=([S:3])[!#6&!-&!#1:2].[O:100]([H:102])[H:101]>>[C:1]([S:3][H:102])([O-:100])[*+:2][H:101]")

libgen1.SetExplicitHydrogens(True)
libgen1.SetValenceCorrection(False)
libgen2.SetExplicitHydrogens(True)
libgen2.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)
    mol.Clear()
    mol_wat.Clear()
    mol_hyd.Clear()

title_list = []   
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)
        OEWriteMolecule(ofs_2, products)

hydcooh = OESubSearch()
hydcooh.Init('[O-][C&X4]([OH])[O-]')

for products in libgen2.GetProducts():
    if products.NumAtoms() < 76:
        if hydcooh.SingleMatch(products) != 1:
            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)
            OEWriteMolecule(ofs_4, products)

ofs_1.close()
ofs_2.close()
ofs_3.close()
ofs_4.close()
ifs.close()