pKa Visualization

Hi Folks,

Using Tools->Potonation->pKa  in Marvin I can create a nice structure with the pKa values overlayed.

Is there any way of recreating thus using the oracle cartridge?

Ideally I would like to feed the smiles string into a sql command / stored procedure and return a dataset into an embedded Marvinview applet that would show the structure with overlayed values.

Any ideas?

Cheers.

Peter

 

Hi,

No, this cannot be done with Cartridge.
jc_evaluate  Cartridge operator can be used for calculating pKa, but it returns only numerical values.

Examples:

select jc_evaluate(<input-molecule>, 'apka("1")') from dual;

select jc_evaluate_x(<input-molecule>, 'pka()') from dual;

Zsolt

Hi,

You seem to have something eqivalent to what we need in www.chemicalize.org in the pKa calculation module - what mechanisms did you guys use to take in the smiles string, calculate the pKa and generate the image shown in the pKa portlet?

Cheers.

Peter

Hi,

We use the pKaPlugin Java API on chemicalize.org. My colleague will provide more details.

Zsolt

Hi David,

This is an extracted version of the code we use on chemicalize.org in a java servlet, it should contain the answer to your question. 

The key function calls are:

• MolImporter.importMol(String string) which can read a smiles string and create a molecule instance 


• pKaPlugin.getResultMolecule() which returns the molecule to display after setting up and running the plugin


• Molecule.toBinFormat() which exports the structure as an image

//take the mol query argument from the URL of the page

String name = new String(request.getParameter("mol").getBytes("ISO-8859-1"), "UTF-8");

try {



	//import the string - this can be any format recognized by marvin

	Molecule m = MolImporter.importMol(name);

	try {

		

		//set up a pka calculation

		pKaPlugin plugin = new pKaPlugin();

		plugin.setMolecule(m);

		plugin.setpHLower(0);

		plugin.setpHUpper(14);

		plugin.setpHStep(0.1);

		

		if (!plugin.run()) {

			out.println(plugin.getErrorMessage());

			out.println(plugin.getWarningMessage());

		} else {	

			

			//display the result molecule

			Molecule pkamol = plugin.getResultMolecule();

			

			//the default settings of toBinFormat are good here - atom labels are set on pkaMol -, we only need dearomatization

			byte[] img = pkamol.toBinFormat("png:-a,w400,h300");

			

			//save img as file or return it to the user as dataURI

		}

		

	} catch (PluginException e) {

		e.printStackTrace(System.err);

	}

} catch (MolFormatException e) {

	e.printStackTrace(System.err);	

}

Andras