Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Bond Represenations in SMILES
This section provides a quick introduction on bond represenations in SMILES. Single, double, triple, and aromatic bonds are represented by the symbols -, =, #, and :, respectively.
How Bonds Are Represented in SMILES? - Bonds are represented in SMILES according to the following rules:
1. Single bond is represented by symbol "-" between two atoms. Single bond symbol can be omitted. For example, CC is the same as C-C; [H][H] is the same as [H]-[H].
2. Double bond is represented by symbol "=" between two atoms. For example, C=C, C=O, O=C=O, etc.
3. Triple bond is represented by symbol "#" between two atoms. For example, C#N.
4. Aromatic bond is represented by symbol ":" between two atoms. Aromatic bond symbol can be omitted, if atoms are represented by lower case letters. For example, c1ccccc1 is the same as C1:C:C:C:C:C1.
Table of Contents
►SMILES (Simplified Molecular-Input Line-Entry System)
►Bond Represenations in SMILES
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