Plugins/Blocktype/ChemNIH

From Mahara Wiki
Jump to: navigation, search

Chem 2D NIH plugin

Chemistry.png

Structure of Aspirin displayed with the Chem 2D NIH plugin (left: skeletal and full) and Jmol NIH plugin (right: stick, ball and stick and spacefill)



This plugin relies on the remarkable Chemical Identifier Resolver service developed by the Computer-Aided Drug Design (CADD) Group of the Chemical Biology Laboratory (CBL), National Cancer Institute (NCI), National Institute of Health (NIH) located at NCI-Frederick.

http://cactus.nci.nih.gov/chemical/structure

Use

When editing the contents of a View, drag the Chem 2D NIH icon (thumb.png, below) from the 'External feeds' tab into your view

Thumb-chem2d.png For Mahara 1.5 and 1.6

Chemnih thumb.png For Mahara 1.2, 1.3 and 1.4

The Chem 2D NIH (chemnih) plugin uses the Chemical Identifier Resolver (CIR) service to return a Gif image of the 2D structure of any meaningful chemical search term. Valid search terms include a trivial chemical name, systematic (e.g. IUPAC) chemical name, SMILES, InChI or InChIKey. You can set the height and width of the embedded image. You can also select whether the structure is shown in skeletal format (without explicit carbon atom labels or hydrogen atoms) or as a fully displayed structure (with all atoms and atom labels).

So, just type in an appropriate term (e.g. ethanol, morphine, buckyball, Cl/C=C\Cl) and you get an (almost) instant image of the 2D structure.

Installation

The latest version of the plugin, for Mahara 1.2, 1.3, 1.4, 1.5 and 1.6, can be downloaded from Github

https://github.com/geoffrowland/mahara-blocktype_chemnih

After unpacking, the /chemnih folder (and its contents) is simply copied into the /blocktype folder of your Mahara installation.

Remember to set appropriate Web server permissions on the new folder and contents.

Finally, visit your Site Administration > Plugin Administration page to enable the plugin.

To Do

  • Improve 'fallover' behaviour when the NIH NCI/CADD Chemical Identifier Resolver service is not available. It is still in beta and so is occasionally off line for development.
    • Ping NIH NCI/CADD server?
    • Might also be solved if the Chemical Identifier Resolver is mirrored.
    • Perhaps combine with RSC ChemSpider web service http://www.chemspider.com/