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

ifs = oemolistream()
ifs.open('g_create_derivatives.sdf')
ofs_1 = oemolostream()
ofs_1.open('h_react_derivatives_ln.ism')
ofs_2 = oemolostream()
ofs_2.open('h_react_derivatives_ln.sdf')
ofs_3 = oemolostream()
ofs_3.open('h_react_derivatives_lp.ism')
ofs_4 = oemolostream()
ofs_4.open('h_react_derivatives_lp.sdf')

# Hydantoin, Succinyl, Acetyl, Formyl
# Reaction: OH- nucleophilic attack at X-C=O (peptide) -OH
mol_hyd = OEGraphMol()
OEParseSmiles(mol_hyd, "[OH]")
libgen1 = OELibraryGen("[C,#1:4][C:1](=[O:3])[NH0,NH1:2].[OH:100]>>[*:4][C:1]([O-:3])([OH:100])[N:2]")
mol_wat = OEGraphMol()
OEParseSmiles(mol_wat, "O(H)H")
libgen2 = OELibraryGen("[C,#1:4][C:1](=[O:3])[NH0,NH1:2].[O:100]([H:101])[H:102]>>[*:4][C:1]([O-:3])([O:100][H:101])[*+:2][H:102]")

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_hyd.Clear()
    mol_wat.Clear()

for products in libgen1.GetProducts():
    title = products.GetTitle()[:-1]
    products.SetTitle(title)
    OEWriteMolecule(ofs_1, products)
    OEWriteMolecule(ofs_2, products)

for products in libgen2.GetProducts():
    title = products.GetTitle()[:-1]+'1'
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)

ifs.close()


#Formimino
# Reaction: OH- nucleophilic attack at X-C=O (peptide) -OH
ifs.open('g_create_derivatives.sdf')
mol_wat = OEGraphMol()
OEParseSmiles(mol_wat, "O(H)H")
mol_hyd = OEGraphMol()
OEParseSmiles(mol_hyd, "[OH]")
libgen1 = OELibraryGen("[NH:3]=[CH:4][NH0,NH1:2].[O:100][H:101]>>[*:3]([H:101])[CH:4]([O-:100])[NH0,NH1:2]")
libgen2 = OELibraryGen("[NH:3]=[CH:4][NH0,NH1:2].[O:100]([H:101])[H:102]>>[*:3]([H:101])[CH:4]([O-:100])[*+:2][H:102]")
libgen3 = OELibraryGen("[NH:3]=[CH:4][NH0,NH1:2].[O:100]([H:101])[H:102]>>[*+:3]([H:101])([H:102])[CH:4]([O-:100])[*:2]")

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)
    mol.Clear()
    mol_hyd.Clear()
    mol_wat.Clear()

for products in libgen1.GetProducts():
    title = products.GetTitle()[:-1]
    products.SetTitle(title)
    OEWriteMolecule(ofs_1, products)
    OEWriteMolecule(ofs_2, products)

for products in libgen2.GetProducts():
    title = products.GetTitle()[:-1]+'1'
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)

for products in libgen3.GetProducts():
    title = products.GetTitle()[:-1]+'2'
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)

ifs.close()


#Carbamoyl
# Reaction: OH- nucleophilic attack at X-C=O (peptide) -OH
ifs.open('g_create_derivatives.sdf')
mol_wat = OEGraphMol()
OEParseSmiles(mol_wat, "O(H)H")
mol_hyd = OEGraphMol()
OEParseSmiles(mol_hyd, "[OH]")
libgen1 = OELibraryGen("[NH2:1][C:2](=[O:3])[NH1,NH0:4].[OH:100]>>[NH2:1][C:2]([O-:3])([OH:100])[N:4]")
libgen2 = OELibraryGen("[NH2:1][C:2](=[O:3])[NH1,NH0:4].[O:100]([H:101])[H:102]>>[NH2:1][C:2]([O-:3])([O:100][H:101])[*+:4][H:102]")
libgen3 = OELibraryGen("[NH2:1][C:2](=[O:3])[NH1,NH0:4].[O:100]([H:101])[H:102]>>[NH2+:1]([H:102])[C:2]([O-:3])([O:100][H:101])[*:4]")

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)
    mol.Clear()
    mol_hyd.Clear()
    mol_wat.Clear()

for products in libgen1.GetProducts():
    title = products.GetTitle()[:-1]
    products.SetTitle(title)
    OEWriteMolecule(ofs_1, products)
    OEWriteMolecule(ofs_2, products)

for products in libgen2.GetProducts():
    title = products.GetTitle()[:-1]+'1'
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)

for products in libgen3.GetProducts():
    title = products.GetTitle()[:-1]+'2'
    products.SetTitle(title)
    OEWriteMolecule(ofs_3, products)
    OEWriteMolecule(ofs_4, products)

ifs.close()

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