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The HELM project team is happy to announce the release of an open source web-editor to complement it's existing suite of software. This web-editor is designed to support organisations that do not wish to deploy a thick client. This is an initial release and the functionality will be extended in further releases during 2017.
HELM Web Editor brings HELM’s industry standard biomolecular representation to the browser, greatly enhancing the deployability of the technology for its adopters
Current functionality includes:
- HELM 1 support
- The ability to use the supplied monomer libraries to draw macromolecules, visualise them as sequences or atom/bond structures and calculate properties.
- Import/export of HELM and xHELM.
- A limited set of rules that allow you to manipulate the structure.
The authors kindly supply a demo web page demonstrating different chart types and functions of the SpeckTackle library. Example data is embedded in the web page (800 kb file size). Click on the buttons at the top of the page to see the data displayed. For the Chromatogram, Difference Chart and Spectral Match click the button then the Add Data button.
Highlighting a section of the spectra expands the view and mouseover on the 2D NMR spectra provides a tooltip giving chemical shifts
I've added this to the spectroscopy resources page
Un1Chem is a new web resource provided by the EBI, it is a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between databases. Currently the uniChem contains data from 21 different data sources.
This script originally created by Sune Askjær first calculates the InChiKey for molecules in a workspace and then uses Un1Chem to search for information in multiple databases, then it provides a summary and a link to a locally generated summary table.
Full details are here Scripting Vortex 18.
Henry Rzepa has used his blog to offer insights into reaction mechanisms. However the issues of security have made the use of java plugins an onerous task to maintain. His solution:-
One of the most important changes from a developers point of view is the external libs (jQuery, jQuey UI, jQuery plugins, glMatrix) are now included into the ChemDoodle scope. This offers several advantages, including eliminating all library conflicts, reducing the number of files required to be installed, and controls the versions used by ChemDoodle. You can now include these libraries yourself at any version and not worry about conflicts. To use the libraries inside of ChemDoodle, call them from the ChemDoodle.lib closure. When I created the interactive graph using FLOT this was one of the issues.
There is also a new EditorCanvas3D canvas which is the 3D component allowing you to interact with and alter chemical data as the 2D Sketcher does in 2D. The 3D editor supports many new WebGL features including picking, highlighting and measurements (distances, angles and torsions).
Lewis Dot Structure style bonds can now be rendered.
As well as editing and drawing structures ChemDoodle web components provides an means to simulate NMR and mass spectra in a web browser
There are also a number of bug fixes and other improvements.
This update includes some major refactors, such as the renaming of the sketcher files and packages and inclusion of the external libraries internal to the ChemDoodle scope, so pay careful attention when upgrading.
The six libraries are FusionCharts Suite XT, HighCharts, Google Chart Tools, Sencha ExtJS, Charts, Chart.js, Flot, jqPlot. I’ve used Flot a couple of times and found it a very useful lightweight library. But as they say choice is good.
Once the molecule has been built and minimised using the MMFF force field you can then use GAMESS to calculate a range of molecular properties.
I’ve previously highlighted the use of ChemDoodle web components to display molecular structures within a web page, and a recent publication DOI by Henry Rzepa lead me to explore some of the newer additions to the means to render molecules within a web page without the use of applets or plugins.