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

nucleotides_list = ['nucleic_acids/5A3X.ism','nucleic_acids/5C3X.ism','nucleic_acids/5G3X.ism','nucleic_acids/5T3X.ism']

ifs = oemolistream()
onaf = OEGraphMol()
ofs_3 = oemolostream()
ofs_3.open('na_create_oligos.ism')

# Reaction 1: Substitution of Cl with Adenine/Guanine
adenine = OEGraphMol()
OEParseSmiles(adenine, 'c1nc2c(ncnc2[nH]1)N')
guanine = OEGraphMol()
OEParseSmiles(guanine, 'c1nc2c(=O)[nH]c(nc2[nH1]1)N')
libgen1 = OELibraryGen("[nH1;r5:1][c:2][n;r6:3].[C:10][Cl:11]>>[*:10][n:1][*:2][*:3]")
libgen1.SetExplicitHydrogens(False)
libgen1.SetValenceCorrection(True)
libgen2 = OELibraryGen("[nH1;r5:1][c:2][n;r6:3].[C:10][Cl:11]>>[*:10][n:1][*:2][*:3]")
libgen2.SetExplicitHydrogens(False)
libgen2.SetValenceCorrection(True)
# Reaction 2: Substitution of Cl with Cytosine/Thymine
cytosine = OEGraphMol()
OEParseSmiles(cytosine, 'c1c[nH]c(=O)nc1N')
thymine = OEGraphMol()
OEParseSmiles(thymine, 'Cc1c[nH]c(=O)[nH]c1=O')
libgen3 = OELibraryGen("[n;r6:1][cH1:2].[C:10][Cl:11]>>[*:10][n:1][c:2]")
libgen3.SetExplicitHydrogens(False)
libgen3.SetValenceCorrection(True)
libgen4 = OELibraryGen("[n;r6:1][cH1:2].[C:10][Cl:11]>>[*:10][n:1][c:2]")
libgen4.SetExplicitHydrogens(False)
libgen4.SetValenceCorrection(True)


for ona in nucleotides_list:
    ifs.open(ona)
    OEReadMolecule(ifs, onaf)
    ifs.close()
    libgen1.SetStartingMaterial(adenine, 0)
    libgen1.SetStartingMaterial(onaf, 1)
    for products in libgen1.GetProducts():
        products.SetTitle(ona[-8:-5]+'A')
	OEWriteMolecule(ofs_3, products)

    libgen2.SetStartingMaterial(guanine, 0)
    libgen2.SetStartingMaterial(onaf, 1)
    for products in libgen2.GetProducts():
        products.SetTitle(ona[-8:-5]+'G')
        OEWriteMolecule(ofs_3, products)

    libgen3.SetStartingMaterial(thymine, 0)
    libgen3.SetStartingMaterial(onaf, 1)
    for products in libgen3.GetProducts():
        products.SetTitle(ona[-8:-5]+'T')
        OEWriteMolecule(ofs_3, products)

    libgen4.SetStartingMaterial(cytosine, 0)
    libgen4.SetStartingMaterial(onaf, 1)
    for products in libgen4.GetProducts():
        products.SetTitle(ona[-8:-5]+'C')
        OEWriteMolecule(ofs_3, products)
    onaf.Clear()

ofs_3.close()