Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
"obabel ... -o svg -xS" - Ball/Stick Depiction in SVG
This section provides a tutorial example how to generate a SVG picture of a molecule structure in ball-stick style using the Open Babel 'obabel ... -o svg -xS' command.
If you want to see a ball and stick depiction of a molecule in SVG format, you can use the "-o svg -xS" option with the "obabel" command.
For example, the following command generates a ball and stick depiction of of the tyrosine molecule in SVG format:
herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine-ball.svg --gen2D -xS 1 molecule converted
As a comparison, running the following command generates a normal skeleton depiction of of the same molecule in SVG format:
herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine-skeleton.svg 1 molecule converted
Open both output files, tyrosine-skeleton.svg and tyrosine-ball.svg, in a Web browser, you see the differences:
Note that the above ball and stick depiction was generated by Open Babel 2.4. The ball and stick depiction generated by Open Babel 3.1.0 does not look good. See the picture 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
"obabel -o svg" - Molecule Picture in SVG
"obabel -:... -o svg" - Generate SVG from SMILES
"obabel ... -o svg -xi" - Show Atom Indices in SVG
►"obabel ... -o svg -xS" - Ball/Stick Depiction in SVG
"obabel ... -o svg -xX" - Hide Implicit H in SVG
"obabel ... -o svg -xC" - Hide Terminal C in SVG
"obabel ... -o svg -xP300" - Control Image Size
"obabel ... -o svg" - Two "svg" XML Tag Levels
"obabel ... -o svg -xd" - Hide Molecule Name
"babel ... -o svg -xd -xP300" - Open Babel 2.4 Bug
Scale SVG Images using "viewBox" Attribute
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