"obfit" - Superimpose Two Molecules

This section provides a quick introduction on the 'obfit' command provided in Open Babel package to superimpose two molecules.

What Is "obfit" Command? - "obfit" command is a command line tool provided in the Open Babel package that allows you to Superimpose Two Molecules.

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

NAME
     obfit -- superimpose two molecules based on a pattern

SYNOPSIS
     obfit SMARTS-pattern fixed-file outfile

DESCRIPTION
     Superimpose two molecules using a quaternion fit. The atoms used to fit 
     the two molecules are defined by the SMARTS pattern given by the user. It 
     is useful to align congeneric series of molecules on a common structural
     scaffold for 3D-QSAR studies. It can also be useful for displaying the 
     results of conformational generation.

     Any molecules matching the supplied SMARTS pattern will be rotated and 
     translated to provide the smallest possible RMSD between the matching regions. 
     If a molecule does not match the SMARTS pattern, it will be output with no
     transformation.

EXAMPLES
     Align all the molecules in 'testmv.sdf' on a single molecule of 'testref.sdf' 
     by superimposing them on its N-methylpiperidyl portion (and outputting a 
     new SD file to the standard output):

           obfit '[nh]1c2c(=O)n(C)c(=O)n(C)c2cc1' testref.sdf testmv.sdf

Here is an example of superimposing, or aligning, molecule structures against a reference molecule structures using the "obift" command:

1. Create a toluene molecule structure as the reference molecule with a molecule editor so that you can keep the extra carbon on top of the benzene ring. Save the the toluene molecule structure in toluene.sdf.

2. Convert toluene.sdf to toluene.svg to see the toluene molecule structure.

Upward Toluene Molecule
Upward Toluene Molecule

3. Create 4 more molecule structures similar to the toluene molecule structure, by rotating the ring and replacing C with N, O, and F. Save them in a single file, fit-input.sdf.

4. Convert fit-input.sdf to fit-input.svg to see those similar molecule structures.

Similar Molecule Structures before Alignment
Similar Molecule Structures before Alignment

5. Now fit those those similar molecule structures against the toluene molecule structure with the help of SMARTS pattern "c1cc(*)ccc1".

herong$ obfit 'c1cc(*)ccc1' toluene.sdf fit-input.sdf > fit-output.sdf 
RMSD: 0.000032
RMSD: 0.000032
RMSD: 0.000032
RMSD: 0.000000

6. Convert fit-output.sdf to fit-output.svg to see that all similar molecule structures are superimposed (aligned) to the toluene molecule structure.

herong$ obabel fit-output.sdf fit-output.svg 
4 molecules converted
110 audit log messages 
Similar Molecule Structures after Alignment
Similar Molecule Structures after Alignment

As you can see, "obfit" did a good job to superimpose or align structures of all similar molecules to the given reference molecule structure.

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