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From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

Wibe A de Jong, Andrew M Walker, Marcus D Hanwell
2013 Journal of Cheminformatics  
In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework.  ...  Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization.  ...  Visualisation and analysis of semantically rich NWChem data with Avogadro In order to read in the CML produced by NWChem or any other computational chemistry code, a new reader was developed for Avogadro  ... 
doi:10.1186/1758-2946-5-25 pmid:23705910 pmcid:PMC3764975 fatcat:khi6cl2wpzgpffer5eq5yz37wi

The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age

Sam Adams, Pablo de Castro, Pablo Echenique, Jorge Estrada, Marcus D Hanwell, Peter Murray-Rust, Paul Sherwood, Jens Thomas, Joe Townsend
2011 Journal of Cheminformatics  
The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with  ...  In the early stages, searching and indexing can be performed on the chemical subject of the calculations, and well defined calculation meta-data.  ...  Both ZCAM and Daresbury are nodes of CECAM. Finally, thanks to Charlotte Bolton for the careful editing of the manuscript. P.  ... 
doi:10.1186/1758-2946-3-38 pmid:21999363 pmcid:PMC3206452 fatcat:v62urvg22rdurbgum6eg4ballq