Plugins/Blocktype/ChemNIH

Chem 2D NIH plugin

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)

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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 (below) from the 'External feeds' tab into your view

The Chem 2D NIH (chemnih) plugin returns 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 block. You can also select whether the structure is shown in skeletal format (without explicit carbon atom labels or hydrogen atoms) or 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 and 1.3, can be downloaded from Github

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

On unpackaging, 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 handling of the situation when 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?
  • Consider using cURL rather than PHP file_get_contents()?
  • Perhaps some form of local caching of sdf data? Might also be solved if the Chemical Identifier Resolver is mirrored.