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

ifs = oemolistream()
ifs.open('a_aa_outofkegg.sdf')
ifs2 = oemolistream()
ofs_3 = oemolostream()
ofs_3.open('g_create_dp.smi')
ofs_3.SetFormat(OEFormat_SMI)
ofs_4 = oemolostream()
ofs_4.open('g_create_dp.sdf')
ofs_4.SetFormat(OEFormat_SDF)

# Reaction 1: Formation of a peptide bond (OE doesn't handle stereochem)
# with explicit hydrogens
#libgen = OELibraryGen("[N:1][C:2][C:3](=[O:4])[O].[N:101]([H:106])([H])[C:102][C:103](=[O:104])[O:105]>>[N:1][C:2][C:3](=[O:4])[N:101]([H:106])[C:102][C:103](=[O:104])[O:105]")
# or with Implicit hydrogens
# libgen = OELibraryGen("[N:1][C:2][C:3](=[O:4])[O].[N:101][C:102][C:103](=[O:104])[O:105]>>[N:1][C:2][C:3](=[O:4])[Nh1:101][C:102][C:103](=[O:104])[O:105]")
#libgen.SetExplicitHydrogens(False)
# or with automatic valence correction
#libgen = OELibraryGen("[N:1][C:2][C:3](=[O:4])[O].[N:101][C:102][C:103](=[O:104])[O:105]>>[N:1][C:2][C:3](=[O:4])[N:101][C:102][C:103](=[O:104])[O:105]")
libgen = OELibraryGen("[C:3](=[O:4])[O].[Nh3,Nh2,Nh1&R:101][Ch1:102]>>[C:3](=[O:4])[N:101][C:102]")
libgen.SetExplicitHydrogens(False)
libgen.SetValenceCorrection(True)

# Kein Parsing des Smiles, da sonst Verlust der Stereochemistry information
# (dafuer 5-bindiger Bug in Aromatischen Systemen->filter.py)
# mol_s = OEGraphMol()
title_list = []    
for aa in ifs.GetOEMols():
    ifs2.open('a_aa_outofkegg.sdf')
    for aa2 in ifs2.GetOEMols():
        libgen.SetStartingMaterial(aa, 0)
        libgen.SetStartingMaterial(aa2, 1)
        for products in libgen.GetProducts():
            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)

ifs.open('a_aa_outofkegg.sdf')
libgen2 = OELibraryGen("[C:3](=[O:4])[O].[Nh3,Nh2:101][Ch2&!R:102]>>[C:3](=[O:4])[N:101][C:102]")
libgen2.SetExplicitHydrogens(False)
libgen2.SetValenceCorrection(True)

# Kein Parsing des Smiles, da sonst Verlust der Stereochemistry information
# (dafuer 5-bindiger Bug in Aromatischen Systemen->filter.py)
# mol_s = OEGraphMol()
for aa in ifs.GetOEMols():
    ifs2.open('a_aa_outofkegg.sdf')
    for aa2 in ifs2.GetOEMols():
        libgen2.SetStartingMaterial(aa, 0)
        libgen2.SetStartingMaterial(aa2, 1)
        for products in libgen2.GetProducts():
            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_3.close()
ofs_4.close()
ifs.close()