Existing XML languages with relevance to quantum chemistry

The domain of computational chemistry is fortunate in that XML representations already exist for a number of its key concepts. These have been developed as part of the Chemical Markup Language (CML) (http://cml.sourceforge.net). This includes a number of XML schemas that specify the representations for concepts that relate to various chemistry domains. One schema specifies common concepts (CMLCore) and the others (known an extensions) focus on particular areas, such as computational chemistry (CMLComp) and chemical reactions (CMLReact). The XML schemas and example documents can be downloaded from the CML site. CML has excellent support for the representation of small molecule structures, and is now supported by a number of tools (such a Jmol (http://jmol.sourceforge.net), JChemPaint (http://jchempaint.sourceforge.net) and Marvin (http://www.chemaxon.com/marvin/)). CMLComp is under development and eCCP1 has found that some extensions are required to enable better coverage of computational chemistry concepts. This has resulted from discussions at a number of meetings, identifying further necessary support for concepts including basis sets (e.g. Gaussian atomic), properties on grids (such as charge density maps), molecular vibrations and macromolecules. Some of these extensions can be taken from other XML languages, while others will be too specific to computational chemistry and will need to be created. For example, the Visualisation Tool Kit (VTK) (http://public.kitware.com/VTK/) has XML representations for properties on grids (regular, rectilinear, irregular). As with the use of the Chemical Markup Language, the adoption of representations from other XML languages provides benefits through the availability of tools that understand data in this format. The use of VTK markup for grids results in simple visualisation of this data using the APIs made available through VTK. The atomic basis set is an example of a concept that will need to have a representation designed, something that is being addressed within the eCCP1 project.

Question: What CML markup would be useful for quantum chemistry?
Question: What does CML not cover?

-- PhilipCouch - 08 Nov 2004

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Topic revision: r2 - 09 Nov 2004 - PhilipCouch
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