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

rxn = 3

ifs = oemolistream()
ifs.open('a_kegg_filter_1.sdf')
ofs_1 = oemolostream()
ofs_1.open('b_react_ti_3_ln.ism')
ofs_2 = oemolostream()
ofs_2.open('b_react_ti_3_ln.sdf')

mol_wat = OEGraphMol()
mol_hyd = OEGraphMol()
OEParseSmiles(mol_hyd, "[OH-]")
# Reaction 3: OH-H nucleophilic attack at N-C=X (X(not CvO) endocyclic or chain member) (amidine, guanidine) NON_AROMATIC
# leaving amine not protonated 
libgen1 = OELibraryGen("[H,A:4][C:1]([N:2])=[!C&!O:3].[O-:100][H:99]>>[H,A:4][C:1]([N:2])([O-:100])[*: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:
    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()
    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()
    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)
        OEWriteMolecule(ofs_2, products)

ofs_1.close()
ofs_2.close()
ifs.close()