Tools for Working with Chemical Markup Language (Continued)

Previous Eclipse Modelling Framework The Eclipse Modelling Framework (EMF) is part of the Eclipse Project13.  This is a Java development toolkit for working with data models and representations, including XML. The article Generating an EMF Model using XML Schema (XSD)14 descibes how to generate an object model, validator, and and editor can be generated.  The EMF framework can then be used to serialize back and forth from the object model and Java code.  Using the steps in the article I generated an object model, validator, and editor in several minutes.  To enable EMF to accept the schema I had to remove two regular expression restriction statements by hand editor the schema file.  A screenshot of the generated editor is shown below. Eclipse EMF Generated Editor

Bioclipse

The Bioclipse ¹⁷ is a Java-based, open source, visual platform for chemo- and bioinformatics.  It is an Eclipse plug-in based on the Eclipse Rich Client Platform (RCP).  The present version of Bioclipse, version 0.2,  includes a CDK-plugin to provide a chemoinformatic backend and a Jmol-plugin for 3D-visualization.   The project is a collaboration between the Department of Pharmaceutical Biosciences, Uppsala University, Sweden, and the Research Group for Molecular Informatics at Cologne University Bioinformatics Center (CUBIC).

There are a number of other plug-ins under development, including

• CML - adds CML support
• Spectrum - functionality for handling spectrums
• JChemPaint - the two-dimensional editor discussed above
  
• Convertor - conversion between many file formats
• Biojava - Sequence functionality based on the Biojava project¹⁸
  
• Phylo - tree / Network visualization, editing, phylogenetic inference, and phylogeny based analyses
• CMLRSS - a view on CMLRSS feeds
  

Scalable Vector Graphics

Johanne Jean-Baptiste¹⁵ describes the use of Scalable Vector Graphics (SVB) with SVG's XML Binding Language (sXBL).  The runtime framework is the Mozilla browser.

Open Babel

Open Babel¹⁶ is an open source project to convert between various file formats used in molecular modeling, computational chemistry, and related areas.

About the Author

Related Reading

1. Alex Amies, 2006.  Introduction to Extensible Markup Language for Chemistry and Biosciences, www.medicalcomputing.net/xml_biosciences.html.
2. Alex Amies, 2006.  Basic Biological Chemistry with Chemical Markup Language, www.medicalcomputing.net/biological_chem_computer.html.
   

References

1. Chemical Markup Language is a SourceForge project hosted at  cml.sourceforge.net.  This includes the CML Schema, links to tools, documentation, and source code.  There is a discussion list at cml.sourceforge.net/list/index.html.  The CML Wiki is at cml.sourceforge.net/wiki/index.php/Main_Page.
2. The Jumbo project is also at cml.sourceforge.net in the files section and in cvs.
3. CML Molecules, www.ch.ic.ac.uk/rzepa/chimeral/resources/cml/drugs/index.html.  This includes a collection of a hundred of so molecules.
4. Marvin 4.04 by ChemAxon, www.chemaxon.com/marvin.
5. Jmol is an open source project hosted on SourceForge at jmol.sourceforge.net.  It also has a wiki at wiki.jmol.org/WebsitesUsingJmol.
6. ChemExper has a database with thousands of chemicals, their structural diagrams, and some properties.
7. JChemPaint is a SourceForge project hosted at sourceforge.net/projects/jchempaint.  The home page is at almost.cubic.uni-koeln.de/cdk/jcp.  User documentation is at almost.cubic.uni-koeln.de/cdk/jcp/application/user_guide.
8. CompChem is COMPutational CHEMistry markup language.   See www.nesc.ac.uk/talks/394/Murray-Rust.html.
9. MDL June 2005.  CTFile Formats White Paper. MDL is a company (www.mdl.com).  MOL is one of these file formats.  It is documented in Chapter 4 of this white paper at http://www.mdl.com/solutions/white_papers/ctfile_formats.jsp.  The fomat is not XML.
10. SMILES home page at www.daylight.com/smiles/index.html.
11. XDrawChem is a SourceForge project hosted at xdrawchem.sourceforge.net.
12. Adobe Chemical Markup Language demo at www.adobe.com/svg/demos/main.html.
    
13. Eclipse Foundation, Eclipse Modelling Framework page at www.eclipse.org/emf.
14. Eclipse Foundation, 2005.  Generating an EMF Model using XML Schema (XSD) at www.eclipse.org/emf/docs.php.
15. Jean-Baptiste, J 2005.  Applying sXBL to display Chemical Markup Language (CML) for the SVG Open 2005 conference and at www.svgopen.org/2005/papers/sXBLandCML.
16. Open Babel is hosted by SourceForge at openbabel.sourceforge.net/wiki/Main_Page.
17. The International Bioclipse Association, Bioclipse Project at www.bioclipse.net.
18. The BioJava Project at biojava.org.
19. JOELib2 open source project at joelib.sourceforge.net.