Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
What Is SMILES
This section provides a quick introduction of SMILES (Simplified Molecular-Input Line-Entry System), which is a specification in the form of a line notation for describing molecule structures using short ASCII strings.
What Is SMILES? - SMILES (Simplified Molecular-Input Line-Entry System) is a specification in the form of a line notation for describing molecule structures using short ASCII strings.
The original specification of SMILES was provided by Daylight Chemical Information Systems in "SMILES - A Simplified Chemical Language" at https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html.
Currently, a more formal specification is provided by Craig A. James as "OpenSMILES specification" at http://opensmiles.org/opensmiles.html.
Here is a list of SMILES of some molecules.
Common Name SMILES ------ ------ Alcohol CCO Aspirin CC(=O)OC1=CC=CC=C1C(=O)O Caffeine CN1C=NC2=C1C(=O)N(C(=O)N2C)C Oxygen O=O Salt Cl.Na Soda OC(O)O[Na] Sugar OCC2OC(OC1(CO)OC(CO)C(O)C1O)C(O)C(O)C2O Water 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