Hydrogen Representations in SMILES

This section provides a quick introduction on hydrogen representations in SMILES. Hydrogens are represented explicitly as atoms 'O([H])[H]', explicitly as counts '[OH2]', or implicitly like 'O'.

How Hydrogens Are Represented in SMILES? - Hydrogen are represented according to the following rules:

1. Explicitly as Atoms - A hydrogen can be represented by its atomic symbol in square brackets [H]. For example, [H][O][H] for water; [2H]O[2H] for heavy water; [H][H] for hydrogen molecule.

2. Explicitly as Counts - When hydrogens are connected to an atom, which is represented in square brackets, those hydrogens must be represented a count in the form of [xHn]. For example, "[OH2]" is the same as "O([H])[H]"

3. Implicitly - When hydrogens are connected to an atom, which is represented without square brackets, those hydrogens are implicitly represented according to normal valence assumptions. For example, "O" is the same as "O([H])[H]"

Table of Contents

 About This Book

SMILES (Simplified Molecular-Input Line-Entry System)

 What Is SMILES

 What Is Canonical SMILES

 Atom Represenations in SMILES

 Bond Represenations in SMILES

 Branch Represenations in SMILES

 Ring Represenations in SMILES

 Disconnected Structures in SMILES

 Charge Represenations in SMILES

 Isotope Represenations in SMILES

 Directional Bonds 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

 Resources and Tools

 Cheminformatics Related Terminologies

 References

 Full Version in PDF/EPUB