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

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

title_list = []

# N-Acetyl
nacet = OEGraphMol()
OEParseSmiles(nacet, "CC(=O)Cl")

libgen = OELibraryGen("[N:1][C:2][C:3](=[O:4])[O:5].[C:6][C:7](=[O:8])[Cl:9]>>[CH3:6][C:7](=[O:8])[N:1][C:2][C:3](=[O:4])[O:5]")
libgen.SetExplicitHydrogens(False)
libgen.SetValenceCorrection(True)
for mol in ifs.GetOEMols():
    libgen.AddStartingMaterial(mol, 0)
    libgen.AddStartingMaterial(nacet, 1)
    mol.Clear()
    nacet.Clear()
for products in libgen.GetProducts():
    title = products.GetTitle()+'nacetyl'
    products.SetTitle(title)
    title_list.append(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)
ifs.close()

ifs.open('a_aa_outofkegg.sdf')
nacet = OEGraphMol()
OEParseSmiles(nacet, "CC(=O)Cl")

libgen2 = OELibraryGen("[Nh3,Nh2:101][Ch2&!R:102][Ch2:103].[C:6][C:7](=[O:8])[Cl:9]>>[CH3:6][C:7](=[O:8])[N:101][*:102][*:103]")
libgen2.SetExplicitHydrogens(False)
libgen2.SetValenceCorrection(True)
for mol in ifs.GetOEMols():
    libgen2.AddStartingMaterial(mol, 0)
    libgen2.AddStartingMaterial(nacet, 1)
    mol.Clear()
    nacet.Clear()
for products in libgen2.GetProducts():
    num = 1
    title = products.GetTitle()+'nacetyl_'+str(num)
    while title in title_list:
        num+=1
        title = products.GetTitle()+'nacetyl_'+str(num)
    title_list.append(title)
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)
ifs.close()

# N-Succinyl
ifs.open('a_aa_outofkegg.sdf')
succ = OEGraphMol()
OEParseSmiles(succ, "[O-]C(=O)CCC(=O)Cl")
libgen3 = OELibraryGen("[N:1][C:2][C:3](=[O:4])[O:5].[O-:6][C:7](=[O:8])[C:9][C:10][C:11](=[O:12])[Cl:13]>>[O-:6][C:7](=[O:8])[C:9][C:10][C:11](=[O:12])[N:1][C:2][C:3](=[O:4])[O:5]")
libgen3.SetExplicitHydrogens(False)
libgen3.SetValenceCorrection(True)
for mol in ifs.GetOEMols():
    libgen3.AddStartingMaterial(mol, 0)
    libgen3.AddStartingMaterial(succ, 1)
    mol.Clear()
    succ.Clear()
for products in libgen3.GetProducts():
    num = 1
    title = products.GetTitle()+'nsuccinyl_'+str(num)
    while title in title_list:
        num+=1
        title = products.GetTitle()+'nsuccinyl_'+str(num)
    title_list.append(title)
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)
ifs.close()

ifs.open('a_aa_outofkegg.sdf')
succ = OEGraphMol()
OEParseSmiles(succ, "[O-]C(=O)CCC(=O)Cl")
libgen3 = OELibraryGen("[Nh3,Nh2:101][Ch2&!R:102][Ch2:103].[O-:6][C:7](=[O:8])[C:9][C:10][C:11](=[O:12])[Cl:13]>>[O-:6][C:7](=[O:8])[C:9][C:10][C:11](=[O:12])[N:101][*:102][*:103]")
libgen3.SetExplicitHydrogens(False)
libgen3.SetValenceCorrection(True)
for mol in ifs.GetOEMols():
    libgen3.AddStartingMaterial(mol, 0)
    libgen3.AddStartingMaterial(succ, 1)
    mol.Clear()
    succ.Clear()
for products in libgen3.GetProducts():
    num = 1
    title = products.GetTitle()+'nsuccinyl_'+str(num)
    while title in title_list:
        num+=1
        title = products.GetTitle()+'nsuccinyl_'+str(num)
    title_list.append(title)
    products.SetTitle(title)
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)
ifs.close()

# N-Formyl
ifs.open('a_aa_outofkegg.sdf')
form = OEGraphMol()
OEParseSmiles(form, "ClC=O")
libgen4 = OELibraryGen("[N:1][C:2][C:3](=[O:4])[O:5].[Cl:10][C:7]=[O:8]>>[C:7](=[O:8])[N:1][C:2][C:3](=[O:4])[O:5]")
libgen4.SetExplicitHydrogens(False)
libgen4.SetValenceCorrection(True)
for mol in ifs.GetOEMols():
    libgen4.AddStartingMaterial(mol, 0)
    libgen4.AddStartingMaterial(form, 1)
    mol.Clear()
    form.Clear()
for products in libgen4.GetProducts():
    num = 1
    title = products.GetTitle()+'nformyl_'+str(num)
    while title in title_list:
        num+=1
        title = products.GetTitle()+'nformyl_'+str(num)
    title_list.append(title)
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)
ifs.close()
                                                                                                                                  
ifs.open('a_aa_outofkegg.sdf')
form = OEGraphMol()
OEParseSmiles(form, "ClC=O")
libgen5 = OELibraryGen("[Nh3,Nh2:101][Ch2&!R:102][Ch2:103].[Cl:10][C:7]=[O:8]>>[C:7](=[O:8])[N:101][*:102][*:103]")
libgen5.SetExplicitHydrogens(False)
libgen5.SetValenceCorrection(True)
for mol in ifs.GetOEMols():
    libgen5.AddStartingMaterial(mol, 0)
    libgen5.AddStartingMaterial(form, 1)
    mol.Clear()
    form.Clear()
for products in libgen5.GetProducts():
    num = 1
    title = products.GetTitle()+'nformyl_'+str(num)
    while title in title_list:
        num+=1
        title = products.GetTitle()+'nformyl_'+str(num)
    title_list.append(title)
    products.SetTitle(title)
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)
ifs.close()

#N-Carbamoyl
ifs.open('a_aa_outofkegg.sdf')
carbam = OEGraphMol()
OEParseSmiles(carbam, "[NH2]C(=O)Cl")
libgen6 = OELibraryGen("[N:1][C:2][C:3](=[O:4])[O:5].[NH2:9][C:7](=[O:8])[Cl:10]>>[NH2:9][C:7](=[O:8])[N:1][C:2][C:3](=[O:4])[O:5]")
libgen6.SetExplicitHydrogens(False)
libgen6.SetValenceCorrection(True)
for mol in ifs.GetOEMols():
    libgen6.AddStartingMaterial(mol, 0)
    libgen6.AddStartingMaterial(carbam, 1)
    mol.Clear()
    carbam.Clear()
for products in libgen6.GetProducts():
    num = 1
    title = products.GetTitle()+'ncarbamoyl_'+str(num)
    while title in title_list:
        num+=1
        title = products.GetTitle()+'ncarbamoyl_'+str(num)
    title_list.append(title)
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)
ifs.close()

ifs.open('a_aa_outofkegg.sdf')
carbam = OEGraphMol()
OEParseSmiles(carbam, "[NH2]C(=O)Cl")
libgen7 = OELibraryGen("[Nh3,Nh2:101][Ch2&!R:102][Ch2:103].[NH2:9][C:7](=[O:8])[Cl:10]>>[NH2:9][C:7](=[O:8])[N:101][*:102][*:103]")
libgen7.SetExplicitHydrogens(False)
libgen7.SetValenceCorrection(True)
for mol in ifs.GetOEMols():
    libgen7.AddStartingMaterial(mol, 0)
    libgen7.AddStartingMaterial(carbam, 1)
    mol.Clear()
    carbam.Clear()
for products in libgen7.GetProducts():
    num = 1
    title = products.GetTitle()+'ncarbamoyl_'+str(num)
    while title in title_list:
        num+=1
        title = products.GetTitle()+'ncarbamoyl_'+str(num)
    title_list.append(title)
    products.SetTitle(title)
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)

# N-formimino
ifs.open('a_aa_outofkegg.sdf')
pattern = OEGraphMol()
OEParseSmiles(pattern, "[NH]=CCl")
libgen8 = OELibraryGen("[N:1][C:2][C:3](=[O:4])[O:5].[NH:8]=[C:7][Cl:10]>>[NH:8]=[C:7][N:1][C:2][C:3](=[O:4])[O:5]")
libgen8.SetExplicitHydrogens(False)
libgen8.SetValenceCorrection(True)
for mol in ifs.GetOEMols():
    libgen8.AddStartingMaterial(mol, 0)
    libgen8.AddStartingMaterial(pattern, 1)
    mol.Clear()
    pattern.Clear()
for products in libgen8.GetProducts():
    num = 1
    title = products.GetTitle()+'nformimino_'+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.close()
                                                                                                                                  
ifs.open('a_aa_outofkegg.sdf')
pattern = OEGraphMol()
OEParseSmiles(pattern, "[NH]=CCl")
libgen9 = OELibraryGen("[Nh3,Nh2:101][Ch2&!R:102][Ch2:103].[NH:8]=[C:7][Cl:9]>>[NH:8]=[C:7][N:101][*:102][*:103]")
libgen9.SetExplicitHydrogens(False)
libgen9.SetValenceCorrection(True)
for mol in ifs.GetOEMols():
    libgen9.AddStartingMaterial(mol, 0)
    libgen9.AddStartingMaterial(pattern, 1)
    mol.Clear()
    pattern.Clear()
for products in libgen9.GetProducts():
    num = 1
    title = products.GetTitle()+'nformimino_'+str(num)
    while title in title_list:
        num+=1
        title = products.GetTitle()+'nformimino_'+str(num)
    title_list.append(title)
    products.SetTitle(title)
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)
ifs.close()

#hydantoin
ifs.open('a_aa_outofkegg.sdf')
pattern = OEGraphMol()
OEParseSmiles(pattern, "O=C1[NH]CC1=O")
libgen10 = OELibraryGen("[N:1][C:2][C:3](=[O:4])[O:5].[C:7]1(=[O:6])[NH:8][C:9][C:10]1=[O:11]>>[C:10]1(=[O:11])[C:9][NH:8][C:7](=[O:6])[N:1]1[C:2][C:3](=[O:4])[O:5]")
libgen10.SetExplicitHydrogens(False)
libgen10.SetValenceCorrection(True)
for mol in ifs.GetOEMols():
    libgen10.AddStartingMaterial(mol, 0)
    libgen10.AddStartingMaterial(pattern, 1)
    mol.Clear()
    pattern.Clear()
for products in libgen10.GetProducts():
    num = 1
    title = products.GetTitle()+'hydantoin_'+str(num)
    while title in title_list:
        num+=1
        title = products.GetTitle()+'hydantoin_'+str(num)
    title_list.append(title)
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)
ifs.close()
                                                                                                                                  
ifs.open('a_aa_outofkegg.sdf')
pattern = OEGraphMol()
OEParseSmiles(pattern, "O=C1[NH]CC1=O")
libgen11 = OELibraryGen("[Nh3,Nh2:101][Ch2&!R:102][Ch2:103].[C:7]1(=[O:6])[NH:8][C:9][C:10]1=[O:11]>>[C:10]1(=[O:11])[C:9][NH:8][C:7](=[O:6])[N:101]1[*:102][*:103]")
libgen11.SetExplicitHydrogens(False)
libgen11.SetValenceCorrection(True)
for mol in ifs.GetOEMols():
    libgen11.AddStartingMaterial(mol, 0)
    libgen11.AddStartingMaterial(pattern, 1)
    mol.Clear()
    pattern.Clear()
for products in libgen11.GetProducts():
    num = 1
    title = products.GetTitle()+'hydantoin_'+str(num)
    while title in title_list:
        num+=1
        title = products.GetTitle()+'hydantoin_'+str(num)
    title_list.append(title)
    products.SetTitle(title)
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)
ifs.close()

ofs_3.close()
ofs_4.close()