Computing InChIs#

About this interactive icons recipe

  • Author: Vincent Scalfani

  • Reviewer: Stuart Chalk

  • Topics: How to Calculate InChIs from SMILES, Using RDKit or Open Babel Adapted from CPCDS 2021 Digital IUPAC Session - 51st IUPAC General Assembly

  • Format: Interactive Jupyter Notebook (Python)

  • Scenarios: You need to convert a SMILES string into its equivalent InChI string.

  • Skills: You should be familiar with

  • Learning outcomes: After completing this example you should understand:

    • How to load and use RDKit to obtain and display chemical identifiers

    • How to load and use Open Babel to obtain and display chemical identifiers

  • Citation: ‘Computing InChIs’, Vincent Scalfani, The IUPAC FAIR Chemistry Cookbook, Contributed: 2024-02-14 https://w3id.org/ifcc/IFCC012.

  • Reuse: This notebook is made available under a CC-BY-4.0 license.

1. Using RDKit#

1.1 Import RDKit Modules#

from rdkit import Chem
from rdkit.Chem import Draw

1.2 Create a Molecular Object from SMILES#

# PubChem CID: 134601
m = Chem.MolFromSmiles('COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)[C@H](CC(=O)O)N')
m # to show image of molecule
../_images/18fcfcaea1d0a56ab95abf88e64b2e3750ca78cb088e00e1aa4695ccc29ceec1.png 
# Internally, we have created an RDKit molecular object
print(m)

<rdkit.Chem.rdchem.Mol object at 0x7febc5ab02e0>

1.3 Calculate InChI#

# Compute InChI from RDKit mol
Chem.MolToInchi(m)

'InChI=1S/C14H18N2O5/c1-21-14(20)11(7-9-5-3-2-4-6-9)16-13(19)10(15)8-12(17)18/h2-6,10-11H,7-8,15H2,1H3,(H,16,19)(H,17,18)/t10-,11-/m0/s1'

# Compute InChIKey from RDKit mol
Chem.MolToInchiKey(m)

'IAOZJIPTCAWIRG-QWRGUYRKSA-N'

1.4 Calculate InChIs for a List of Molecules#

# Import a file of SMILES strings
smiles_list = []
with open('../files/my_smiles.smi') as infile:
     for smi in infile:
            smiles_list.append(smi.rstrip()) # rstrip removes newline
print(smiles_list)

['COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)[C@H](CC(=O)O)N', 'COC(=O)[C@@H](CC1=CC=CC=C1)NC(=O)[C@@H](CC(=O)O)N', 'COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)C[C@@H](C(=O)O)N', 'C1=CC=C(C=C1)C[C@@H](C(=O)O)NC(=O)[C@H](CC(=O)O)NC=O', 'C[C@@H](C(=O)N[C@@H](CC1=CC=CC=C1)C(=O)O)N', 'CC(C)C[C@@H](C(=O)N[C@@H](CC1=CC=CC=C1)C(=O)O)NC(=O)C']

# Or create a list directly
smiles_list = ['COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)[C@H](CC(=O)O)N',
               'COC(=O)[C@@H](CC1=CC=CC=C1)NC(=O)[C@@H](CC(=O)O)N',
               'COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)C[C@@H](C(=O)O)N',
               'C1=CC=C(C=C1)C[C@@H](C(=O)O)NC(=O)[C@H](CC(=O)O)NC=O',
               'C[C@@H](C(=O)N[C@@H](CC1=CC=CC=C1)C(=O)O)N',
               'CC(C)C[C@@H](C(=O)N[C@@H](CC1=CC=CC=C1)C(=O)O)NC(=O)C']

# Next, loop through the smiles_list and create RDKit molecular objects
mols = []
for smi in smiles_list:
    mols.append(Chem.MolFromSmiles(smi))
    
print(mols)
# alternative solution
# mols = [Chem.MolFromSmiles(smi) for smi in smiles_list]

[<rdkit.Chem.rdchem.Mol object at 0x7febc5ab07b0>, <rdkit.Chem.rdchem.Mol object at 0x7febc5ab0890>, <rdkit.Chem.rdchem.Mol object at 0x7febc5ab0c80>, <rdkit.Chem.rdchem.Mol object at 0x7febc5ab0cf0>, <rdkit.Chem.rdchem.Mol object at 0x7febc5ab0d60>, <rdkit.Chem.rdchem.Mol object at 0x7febc5ab0dd0>]

# Display the molecules in a grid
# SVG False uses PNG
Draw.MolsToGridImage(mols, molsPerRow=3, useSVG=False)
../_images/413483a68657f0010c06d89bc7be5f51faea67c6b33bbf73321275db7b632a45.png 
# Loop through mols (molecular objects) and calculate InChIs
InChIs = [Chem.MolToInchi(mol) for mol in mols]
print(InChIs)

['InChI=1S/C14H18N2O5/c1-21-14(20)11(7-9-5-3-2-4-6-9)16-13(19)10(15)8-12(17)18/h2-6,10-11H,7-8,15H2,1H3,(H,16,19)(H,17,18)/t10-,11-/m0/s1', 'InChI=1S/C14H18N2O5/c1-21-14(20)11(7-9-5-3-2-4-6-9)16-13(19)10(15)8-12(17)18/h2-6,10-11H,7-8,15H2,1H3,(H,16,19)(H,17,18)/t10-,11-/m1/s1', 'InChI=1S/C14H18N2O5/c1-21-14(20)11(7-9-5-3-2-4-6-9)16-12(17)8-10(15)13(18)19/h2-6,10-11H,7-8,15H2,1H3,(H,16,17)(H,18,19)/t10-,11-/m0/s1', 'InChI=1S/C14H16N2O6/c17-8-15-10(7-12(18)19)13(20)16-11(14(21)22)6-9-4-2-1-3-5-9/h1-5,8,10-11H,6-7H2,(H,15,17)(H,16,20)(H,18,19)(H,21,22)/t10-,11-/m0/s1', 'InChI=1S/C12H16N2O3/c1-8(13)11(15)14-10(12(16)17)7-9-5-3-2-4-6-9/h2-6,8,10H,7,13H2,1H3,(H,14,15)(H,16,17)/t8-,10-/m0/s1', 'InChI=1S/C17H24N2O4/c1-11(2)9-14(18-12(3)20)16(21)19-15(17(22)23)10-13-7-5-4-6-8-13/h4-8,11,14-15H,9-10H2,1-3H3,(H,18,20)(H,19,21)(H,22,23)/t14-,15-/m0/s1']

2. Using Open Babel#

2.1 Import Open Babel Modules#

# Open Babel v3.1.1
from openbabel import pybel

2.2 Create a Molecular Object from SMILES#

m = pybel.readstring("smi", "COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)[C@H](CC(=O)O)N")
m # to show image of molecule
../_images/12f48eb44fb5bea53d85ed905d40c3ea6f4b07b9b48796b87b8e83e30cc31be0.svg
# Internally, we have created an Open Babel molecular object
print(type(m))

<class 'openbabel.pybel.Molecule'>

2.3 Calculate InChI#

# Set up InChI conversion
conv = pybel.ob.OBConversion()
conv.SetOutFormat("inchi")

True

# Calculate InChI
inchi_output = conv.WriteString(m.OBMol)
print(inchi_output)

InChI=1S/C14H18N2O5/c1-21-14(20)11(7-9-5-3-2-4-6-9)16-13(19)10(15)8-12(17)18/h2-6,10-11H,7-8,15H2,1H3,(H,16,19)(H,17,18)/t10-,11-/m0/s1

# Set up InChIKey conversion
conv = pybel.ob.OBConversion()
conv.SetOutFormat("inchikey")

True

# Calculate InChIKey
inchikey_output = conv.WriteString(m.OBMol)
print(inchikey_output)

IAOZJIPTCAWIRG-QWRGUYRKSA-N

2.4 Calculate InChIs for a List of Molecules#

# Import a file of SMILES
smiles_list =[]
with open('../files/my_smiles.smi') as infile:
     for smi in infile:
            smiles_list.append(smi.rstrip()) # rstrip removes newline
print(smiles_list)

['COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)[C@H](CC(=O)O)N', 'COC(=O)[C@@H](CC1=CC=CC=C1)NC(=O)[C@@H](CC(=O)O)N', 'COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)C[C@@H](C(=O)O)N', 'C1=CC=C(C=C1)C[C@@H](C(=O)O)NC(=O)[C@H](CC(=O)O)NC=O', 'C[C@@H](C(=O)N[C@@H](CC1=CC=CC=C1)C(=O)O)N', 'CC(C)C[C@@H](C(=O)N[C@@H](CC1=CC=CC=C1)C(=O)O)NC(=O)C']

# Next,loop through the smiles_list and create OB molecular objects
ms = [pybel.readstring("smi", m) for m in smiles_list]
print(ms)

[<openbabel.pybel.Molecule object at 0x7febc550edd0>, <openbabel.pybel.Molecule object at 0x7febc4242ed0>, <openbabel.pybel.Molecule object at 0x7febc438d690>, <openbabel.pybel.Molecule object at 0x7febc438da50>, <openbabel.pybel.Molecule object at 0x7febc438da90>, <openbabel.pybel.Molecule object at 0x7febc438db50>]

# Set up InChI conversion
conv = pybel.ob.OBConversion()
conv.SetOutFormat("inchi")

# Loop through mols (molecular objects) and calculate InChIs
InChIs = [conv.WriteString(m.OBMol).rstrip() for m in ms]
print(InChIs)

['InChI=1S/C14H18N2O5/c1-21-14(20)11(7-9-5-3-2-4-6-9)16-13(19)10(15)8-12(17)18/h2-6,10-11H,7-8,15H2,1H3,(H,16,19)(H,17,18)/t10-,11-/m0/s1', 'InChI=1S/C14H18N2O5/c1-21-14(20)11(7-9-5-3-2-4-6-9)16-13(19)10(15)8-12(17)18/h2-6,10-11H,7-8,15H2,1H3,(H,16,19)(H,17,18)/t10-,11-/m1/s1', 'InChI=1S/C14H18N2O5/c1-21-14(20)11(7-9-5-3-2-4-6-9)16-12(17)8-10(15)13(18)19/h2-6,10-11H,7-8,15H2,1H3,(H,16,17)(H,18,19)/t10-,11-/m0/s1', 'InChI=1S/C14H16N2O6/c17-8-15-10(7-12(18)19)13(20)16-11(14(21)22)6-9-4-2-1-3-5-9/h1-5,8,10-11H,6-7H2,(H,15,17)(H,16,20)(H,18,19)(H,21,22)/t10-,11-/m0/s1', 'InChI=1S/C12H16N2O3/c1-8(13)11(15)14-10(12(16)17)7-9-5-3-2-4-6-9/h2-6,8,10H,7,13H2,1H3,(H,14,15)(H,16,17)/t8-,10-/m0/s1', 'InChI=1S/C17H24N2O4/c1-11(2)9-14(18-12(3)20)16(21)19-15(17(22)23)10-13-7-5-4-6-8-13/h4-8,11,14-15H,9-10H2,1-3H3,(H,18,20)(H,19,21)(H,22,23)/t14-,15-/m0/s1']

References

[1] RDKit Documentation: https://www.rdkit.org/docs/index.html

[2] Open Babel Python Documentation: https://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python.html