Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
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
►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