Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
"obrotate" - Rotate Dihedral Angles with SMARTS
This section provides a quick introduction on the 'obrotamer' command provided in Open Babel package to rotate dihedral angles with SMARTS.
What Is "obrotate" command? - "obrotate" command is a command line tool provided in the Open Babel package that allows you to batch-rotate dihedral angles matching SMARTS patterns.
Here is the user manual of the "obrotamer" command.
NAME
obrotate -- batch-rotate dihedral angles matching SMARTS patterns
SYNOPSIS
obrotate 'SMARTS-pattern' filename atom1 atom2 atom3 atom4 angle
DESCRIPTION
The obrotate program rotates the torsional (dihedral) angle of a specified
bond in molecules to that defined by the user. In other words, it does the
same as a user setting an angle in a molecular modeling package, but much
faster and in batch mode (i.e. across multiple molecules in a file).
The four atom IDs required are indexes into the SMARTS pattern, which starts
at atom 0 (zero). The angle supplied is in degrees. The two atoms used to
set the dihedral angle <atom1> and <atom4> do not need to be connected to
the atoms of the bond <atom2> and <atom3> in any way.
The order of the atoms matters -- the portion of the molecule attached to
<atom1> and <atom2> remain fixed, but
the portion bonded to <atom3> and & <atom4> moves.
EXAMPLES
Let's say that you want to define the conformation of a large number of
molecules with a pyridyl scaffold and substituted with an aliphatic chain
at the 3-position, for example for docking or 3D-QSAR purposes.
To set the value of the first dihedral angle to 90 degrees:
obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90
Here 6 and 7 define the bond to rotate in the SMARTS pattern, i.e., c1-C
and atoms 5 and 8 define the particular dihedral angle to rotate.
Since the atoms to define the dihedral do not need to be directly connected,
the nitrogen in the pyridine can be used:
obrotate 'c1ccncc1CCC' pyridines.sdf 4 6 7 8 90
Keep the pyridyl ring fixed and moves the aliphatic chain:
obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90
Keep the aliphatic chain fixed and move the pyridyl ring:
obrotate 'c1ccncc1CCC' pyridines.sdf 8 7 6 5 90
1. Create a molecule with a pyridyl ring and an aliphatic chain.
herong$ obabel -:c1ccncc1CCC -O pyridine.sdf --gen3D -d 1 molecule converted
2. Move the aliphatic chain with the "obrotate" command:
herong$ obrotate 'c1ccncc1CCC' pyridine.sdf 5 6 7 8 90 > pyridine-rotate-chain.sdf
3. Move the pyridyl ring with the "obrotate" command:
herong$ obrotate 'c1ccncc1CCC' pyridine.sdf 8 7 6 5 90 > pyridine-rotate-ring.sdf
To see differences of the rotated structures, you can open them in the PubChem 3D Viewer at https://pubchem.ncbi.nlm.nih.gov/pc3d/.
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