pKa plugin

Is it possible to bring up the pKa plugin showing the macrospecies distribution graph through the api without the user having to go to the tools menu themselves?

Yes, it is possible.

Code:

// import a molecule and clean it in 2D
// Note: clean is not required if the input mol has 2D coordinates
Molecule mol = MolImporter.importMol("OC(=O)C1CC=CN=C1");
mol.clean(2, null);

// instantiate plugin
pKaPlugin plugin = new pKaPlugin();

// set parameters
// set pH limits and step size for microspecies distribution calculation
plugin.setpHLower(0);
plugin.setpHUpper(14);
plugin.setpHStep(0.25);

// set molecule and run the calculation
plugin.setMolecule(mol);
plugin.run();

// instantiate plugin display, and display the results
CalculatorPluginDisplay display = new pKaPluginDisplay();
display.setPlugin(plugin);
display.store();
Component component = display.getResultComponent();
component.setVisible(true);

It will display the result panel of the pKa plugin (MarvinSketch: Tools>Protonation>pKa). The full source code is attached.

Note: pKaPluginDisplay class is not part of the public Marvin API (it is not listed in the javadoc), but it is public, and can be used.

Zsolt