Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Tetrahedral Centers in SMILES
This section provides a quick introduction on Tetrahedral centers in SMILES. '@' is appended to a tetrahedral center atom in square brackets [] to indicate that the next 3 branches are in anticlockwise order when looking at them from the preceding bond diretion.
How Tetrahedral Centers Are Represented in SMILES? - Tetrahedral centers are atoms bonded to four neighbors. If all four neighbors of a tetrahedral center are different atoms, there will be two different configurations known as "enantiomers". In this case, the tetrahedral center is a chiral center.
To identify a specific configurations, tetrahedral chiral centers are represented in SMILES according to the following rules:
1. '@' is appended to a tetrahedral center atom in square brackets [] to indicate that the next 3 branches are in anticlockwise order when looking at them from the preceding bond direction.
For example, "N[C@](C)(F)O" and "N[C@](C)(O)F" represent 2 different configurations and a single chiral center.
2. '@@' is appended to a tetrahedral center atom in square brackets [] to indicate that the next 3 branches are in clockwise (anti-anticlockwise) order when looking at them from the preceding bond diretion.
For example, "N[C@@](C)(F)O" and "N[C@](C)(O)F" are the same conformation represented in 2 different SMILES strings.
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
►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