index

XML/CML Exercises

XML/CML Exercises

Prerequisites

The examples here use portable OpenSource tools so that you can re-run these at home. Most assume:

• Java. Java1.4 SDK should be installed on your machine.
• ant. ant1.5 should be installed on your machine.
• Saxon. saxon7.jar (supplied) should be in your CLASSPATH

Basic XML

• XML Schema and document validation. Run Xerces to validate a simple document against a simple schema.
• XSLT. Use Saxon to transform documents
• XSLT. Run simple stylesheets (chemstyle) within a browser (unfortunately only Microsoft)
• XSLT. Use Saxon to transform documents

Jumbo

• cmlAll. compile the complete CML Schema, generate CMLDOM and ancillary information
• creating and compiling a schema. Edit your own CML schema and compile CMLDOM and related components
• JumboMarker. Run example transforming MOPAC to XML (inc. GUI)
• JumboMarker. Create a simple Marker to extract XML from your favourite code. For the avdenturous

Servlets

• sdf2cml. upload an SDF or MOL file and convert to CML
• sdf2inchi. upload an SDF or MOL file and convert to INChI
• sdf2cmlrss. upload an SDF or MOL file and convert to a CMLRSS feed
• mopac2cml. upload a raw MOPAC output and convert to CML

Transformations

• mopac2html. Transform MOPAC-XML to HTML
• cml2mopac. Create MOPAC input from cml and params

Legacy converters

A variety of converters from legacy to CML

• OpenBabel. Convert between MOL, SDF, Gaussian, PDB, Mol2, CML-1 and CML-2
• JumboLegacy. Convert MOL, SDF, to CML
• Jumbo-CIF. Convert CIF to CML (inc. GUI)

Dictionaries

• dictionary. Create dictionary entry and run stylesheet linking to it.
• scientific units.

Database

• wwmmMopacHtml. High-throughput MOPAC results
• cmlXindice. set up and search your own Xindice database on MOPAC results

CMLRSS

• cmlrssClient. install your own CMLRSS client and view multiple CMLRSS feeds on the WWW

OpenSource software

Products of a closely coordinated community, to whom many thanks. Java, unless indicated. We may be able to make examples available

• OpenBabel. See above. C++.
• Jmol. Java application/applet for viewing 3D molecules, including animation, vibrations and output of computational chemistry. Used in CMLRSS client.
• JChempaint. Java application/applet for viewing and editing 2D molecules (structure diagrams), including reactions. Used in CMLRSS client.
• CDK. Java library for molecular manipulation, legacy conversion, chemoinformatics, etc. Interoperates with CML-DOM. Used as engine for Jmol and JChempaint and in JumboTools
• JOELib. Java library for molecular manipulation, legacy conversion, chemoinformatics, etc. Interoperates with CML-DOM. Java version of OELib (used in OpenBabel). Strong on substructure searching, molecular descriptors, etc.

Software required

A checklist ...

• java. from http://www.javasoft.com. The JRE is sufficient if you just need to run it - type java -version to check. You need the Java SDK to compile Java or create Javadoc. Type javac to check.
• ant. from http://www.apache.org/jakarta. Needs to be on your PATH.
• Tomcat. from http://www.apache.org/jakarta. Needs to be on your PATH.