Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
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
►SMILES (Simplified Molecular-Input Line-Entry System)
Branch Represenations in SMILES
Disconnected Structures in SMILES
Charge Represenations in SMILES
Isotope Represenations 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