Cheminformatics Tutorials - Herong's Tutorial Examples

∟SMILES (Simplified Molecular-Input Line-Entry System)

∟What Is Canonical SMILES

This section provides a quick introduction of Canonical SMILES, uniquely identifies each molecule structure with single unique SMILE string.

What Is Canonical SMILES? - Canonical SMILES is a special version of SMILES where each SMILES string uniquely identifies a single molecule structure.

Currently, there are multiple algorithms used to generate different flavors of Canonical SMILES. And they are not 100% compatible.

Here is some examples of Canonical SMILES of some molecules. 

                  Canonical
SMILES            SMILES
----------------  ----------------
OCC               CCO
[CH3][CH2][OH]    CCO
C-C-O             CCO
C(O)C             CCO
OC(=O)C(Br)(Cl)N  NC(Cl)(Br)C(=O)O
ClC(Br)(N)C(=O)O  NC(Cl)(Br)C(=O)O
O=C(O)C(N)(Br)Cl  NC(Cl)(Br)C(=O)O
...

Table of Contents

 About This Book

►SMILES (Simplified Molecular-Input Line-Entry System)

 What Is SMILES

►What Is Canonical SMILES

 Atom Represenations in SMILES

 Bond Represenations in SMILES

 Branch Represenations in SMILES

 Ring Represenations in SMILES

 Disconnected Structures in SMILES

 Charge Represenations in SMILES

 Isotope Represenations in SMILES

 Directional Bonds in SMILES

 Tetrahedral Centers in SMILES

 Chirality Representations in SMILES

 Hydrogen Representations in SMILES

 Open Babel: The Open Source Chemistry Toolbox

 Using Open Babel Command: "obabel"

 Generating SVG Pictures with Open Babel

 Substructure Search with Open Babel

 Similarity Search with Open Babel

 Fingerprint Index for Fastsearch with Open Babel

 Stereochemistry with Open Babel

 Command Line Tools Provided by Open Babel

 RDKit: Open-Source Cheminformatics Software

 rdkit.Chem.rdchem - The Core Module

 rdkit.Chem.rdmolfiles - Molecular File Module

 rdkit.Chem.rdDepictor - Compute 2D Coordinates

 rdkit.Chem.Draw - Handle Molecule Images

 Molecule Substructure Search with RDKit

 rdkit.Chem.rdmolops - Molecule Operations

 Daylight Fingerprint Generator in RDKit

 Morgan Fingerprint Generator in RDKit

 RDKit Performance on Substructure Search

 Introduction to Molecular Fingerprints

 OCSR (Optical Chemical Structure Recognition)

 AlphaFold - Protein Structure Prediction

 Resources and Tools

 Cheminformatics Related Terminologies

 References

 Full Version in PDF/EPUB