Technical Report 117, c4e-Preprint Series, Cambridge

The Semantics of Chemical Markup Language (CML) for Computational Chemistry: CompChem

ref: Technical Report 117, c4e-Preprint Series, Cambridge

Authors: Weerapong Phadungsukanan, Markus Kraft, Joe Townsend, and Peter Murray-Rust

Associated Theme: Quantum Chemistry

Abstract

This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repository. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are being discussed. The use of CompChem is illustrated on two practical applications.

Material from this preprint has been published in: Journal of Cheminformatics 4, 15, (2012)

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