Molecule Tutorials - Herong's Tutorial Examples - v1.26, by Herong Yang
Convert SDF to SVG using Open Babel
Provides a tutorial example on how to convert a molecule structure in a SDF file to a SVG (Scalable Vector Graphics) file using 'Open Babel'.
If you want to see the molecule structure specified in a SDF file, you can convert it to a SVG (Scalable Vector Graphics) file using the "Open Babel" tool.
1. Download and install "Open Babel" 2.3.1 from sourceforge.net/projects/openbabel.
2. Run the following "babel" command to convert SDF to SVG:
herong$ babel Molecule-HY-001.sdf Molecule-HY-001.svg 1 molecule converted 29 audit log messages
3. Open the SVG file, Molecule-HY-001.svg, in a text editor to review:
<?xml version="1.0"?> <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:cml="http://www.xml-cml.org/schema" width="149.961" height="333.147" x="0" y="0" font-family="sans-serif" font-size="16" stroke="rgb(0,0,0)" stroke-width="1" stroke-linecap="round"> <rect x="0%" y="0%" width="100%" height="100%" stroke-width="0" fill="rgb(255,255,255)" /> <line x1="75.4" y1="213.5" x2="75.4" y2="186.5"/> <line x1="107.2" y1="74.5" x2="87.9" y2="110.4"/> <line x1="92.8" y1="51.1" x2="107.2" y2="74.5"/> <line x1="85.0" y1="164.7" x2="95.3" y2="155.1"/> <line x1="99.3" y1="134.5" x2="87.9" y2="110.4"/> <line x1="91.9" y1="135.7" x2="83.9" y2="118.9"/> <line x1="87.9" y1="110.4" x2="49.2" y2="114.6"/> <line x1="49.2" y1="114.6" x2="43.7" y2="140.8"/> <line x1="55.0" y1="121.9" x2="51.1" y2="140.3"/> <line x1="52.2" y1="160.2" x2="64.2" y2="167.0"/> <line x1="75.4" y1="213.5" x2="110.0" y2="233.3"/> <line x1="110.0" y1="233.3" x2="110.0" y2="273.4"/> <line x1="102.8" y1="239.3" x2="102.8" y2="267.4"/> <line x1="110.0" y1="273.4" x2="75.4" y2="293.1"/> <line x1="75.4" y1="293.1" x2="40.0" y2="272.9"/> <line x1="73.8" y1="283.9" x2="48.8" y2="269.6"/> <line x1="40.0" y1="272.9" x2="40.5" y2="233.3"/> <line x1="40.5" y1="233.3" x2="75.4" y2="213.5"/> <line x1="49.2" y1="236.6" x2="73.8" y2="222.7"/> <text x="69.440616" y="181.477643" stroke="rgb(12,12,255)">N</text> <text x="98.897751" y="154.321847" stroke="rgb(12,12,255)">N</text> <text x="34.920535" y="161.686130" stroke="rgb(12,12,255)">N</text> <text x="68.026773" y="48.000000" stroke="rgb(30,239,30)">Cl</text> <text font-size="18.000000" fill ="black" font-family="sans-serif" x="10.000000" y="20.000000" >HY-001</text> <title>HY-001 - OBDepict</title> </svg>
4. Open the SVG file, Molecule-HY-001.svg, in a Web browser. You see the molecule structure:
Table of Contents
Molecule Names and Identifications
Nucleobase, Nucleoside, Nucleotide, DNA and RNA
What Is SDF (Structure Data File)
►Convert SDF to SVG using Open Babel
"sdf2svg" - PHP Script to Convert SDF to SVG
ChEMBL Database - European Molecular Biology Laboratory
PubChem Database - National Library of Medicine
INSDC (International Nucleotide Sequence Database Collaboration)
HGNC (HUGO Gene Nomenclature Committee)