Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Directional Bonds in SMILES
This section provides a quick introduction on directional bonds in SMILES. Directional bonds, '/' and '\', are used to identify different configurations on additional atoms connected a pair of double-bond connected atoms.
How Directional Bonds Are Represented in SMILES? - Directional bonds are used to identify different configurations on additional atoms connected a pair of double-bond connected atoms. Directional bonds are represented in SMILES according to one single rule:
1. '/' and '\' are used as directional bonds to indicate relative directions of the connected atoms.
For example, "F/C=C\F" or "F\C=C/F" indicates that both "F" atoms are on the same side relative the double bond.
While, "F/C=C/F" or "F\C=C\F" indicates that two "F" atoms are on different sides relative the double bond.
Note that if directional bonds are not provided on double-bond connected atoms, then the molecule structure conformation is unspecified.
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