"obrotamer" - Generate Random Rotational Isomers

This section provides a quick introduction on the 'obrotamer' command provided in Open Babel package to generate random rotational isomers.

What Is "obrotamer" command? - "obrotamer" command is a command line tool provided in the Open Babel package that allows you to Generate Random Rotational Isomers for a given molecule.

Here is the user manual of the "obrotamer" command.

NAME
     obrotamer -- generate conformer/rotamer coordinates

SYNOPSIS
     obrotamer filename

DESCRIPTION
     The obrotamer tool can be used as part of a conformational search by generating 
     random isomers based on rotating dihedral angles. These rotamers are not 
     conformers -- that is, obrotamer does not perform geometry optimization
     after generating the rotamer structure. The obminimize tool can do geometry 
     optimization using molecular mechanics.

EXAMPLES
           obrotamer baseconformer.sdf >rotamer1.sdf

     Generate a random rotational isomer of baseconformer.sdf and write it to rotamer1.sdf

Here is an example of generating random Rotational Isomers with the "obminimize" command:

1. Create a sample molecule with some rotatable bonds:

herong$ obabel "-:CC(N)CCC(C)O" -O sample.sdf --gen2D 
1 molecule converted

2. Generate 3 random rotational isomers from the sample molecule:

herong$ obrotamer sample.sdf > sample-isomer-1.sdf 
 Number of rotatable bonds: 3
 
herong$ obrotamer sample.sdf > sample-isomer-2.sdf 
 Number of rotatable bonds: 3
 
herong$ obrotamer sample.sdf > sample-isomer-3.sdf 
 Number of rotatable bonds: 3 

3. Put the sample molecule and it isomers together in a single SVG picture:

herong$ obabel sample.sdf sample-*.sdf sample-isomers.svg -xcols2 
4 molecules converted

4. Compare rotational isomers against the original molecule structure, which is the first one in the first row:

Sample Molecule and Its Rotational Isomers
Sample Molecule and Its Rotational Isomers

Table of Contents

 About This Book

 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

 Resources and Tools

 Cheminformatics Related Terminologies

 References

 Full Version in PDF/EPUB