Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Charge Represenations in SMILES
This section provides a quick introduction on charge represenations in SMILES. Positive/negative charges are represented by repeating '+'/'-' symbols or '+n'/'-n'.
How Charges Are Represented in SMILES? - Disconnected structures are represented in SMILES according to the following rules:
1. One unit of positive or negative charge is represented by "+" or "-" symbol following the atomic symbol in square brackets []. For example, "[Na+].[Cl-]", "[Na+].[O-]c1ccccc1".
2. Multiple units of charge can be represented by multiple "+" or "-" symbols. For example, "[Fe++]".
3. Multiple units of charge can also be represented by a single "+" or "-" symbol followed by the unit count number. For example, "[Fe+2]".
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