Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
"obchiral" - Print Chirality Information
This section provides a quick introduction on the 'obchiral' command provided in Open Babel package to print chirality information.
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
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
List of Open Babel Command Line Tools
►"obchiral" - Print Chirality Information
"obconformer" - Generate Best Conformer
"obenergy" - Calculate Molecule Energy
"obfit" - Superimpose Two Molecules
"obgen" - Generate Molecule 3D Structures
"obgrep" - Search Molecules using SMARTS
"obminimize" - Optimize Geometry/Energy of Molecule
"obprobe" - Create Electrostatic Probe Grid
"obrotamer" - Generate Random Rotational Isomers
"obrotate" - Rotate Dihedral Angles with SMARTS
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
Cheminformatics Related Terminologies
What Is "obchiral" command? - "obchiral" command is a command line tool provided in the Open Babel package that allows you to calculate and print molecule chirality information.
"obchiral" command was removed since Open Babel 3.1.0.
Here is the user manual of the "obchiral" command provided in Open Babel 2.4.1.
NAME
obchiral -- print molecular chirality information
SYNOPSIS
obchiral filename
DESCRIPTION
The obchiral program is a tool to print the chirality information for
all molecules in a file. It also serves as example code for using the
Open Babel library (libopenbabel).
EXAMPLES
obchiral pyridines.sdf
Here is an example of calculating molecule chirality using the "obchiral" command.
herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine.sdf --gen2D 1 molecule converted herong$ obchiral tyrosine.sdf Molecule 1: Atom 8 Is Chiral C3
You can validate the above calculation result by looking at the tyrosine molecule structure below:
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
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
List of Open Babel Command Line Tools
►"obchiral" - Print Chirality Information
"obconformer" - Generate Best Conformer
"obenergy" - Calculate Molecule Energy
"obfit" - Superimpose Two Molecules
"obgen" - Generate Molecule 3D Structures
"obgrep" - Search Molecules using SMARTS
"obminimize" - Optimize Geometry/Energy of Molecule
"obprobe" - Create Electrostatic Probe Grid
"obrotamer" - Generate Random Rotational Isomers
"obrotate" - Rotate Dihedral Angles with SMARTS
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