/* * Copyright (c) 1998-2014 ChemAxon Ltd. All Rights Reserved. */ import java.io.IOException; import chemaxon.marvin.calculations.MajorMicrospeciesPlugin; import chemaxon.marvin.calculations.TPSAPlugin; import chemaxon.marvin.calculations.logDPlugin; import chemaxon.marvin.calculations.IUPACNamingPlugin; import chemaxon.marvin.plugin.PluginException; import chemaxon.struc.Molecule; import chemaxon.formats.MolExporter; import chemaxon.formats.MolImporter; /** * In this example MajorMicrospeciesPlugin is used to generate the major * microspecies at pH 7.4,TPSAPlugin to calculate the polar surface areas, * loDPlugin to to calculate the logD values, and IUPACNamingPlugin to * generate the names of molecules read from a molfile. The results of the * calculations are written to an SDfile, the molecules in the file are the * major microspecies of the input molecules, IUPAC names, surface area * values and logD values are saved in SDF property fields. * *

Usage: *

   java PluginExample [molFile]
* * For the detailed description of this example, please visit * http://www.chemaxon.com/marvin/examples/plugin/index.html#example1 * * @version 5.0.4 04/22/2008 * @since Marvin 5.0.4 * @author Zsolt Mohacsi */ public class PluginExample { public static void main(String[] args) { try { // instantiate the plugin objects MajorMicrospeciesPlugin mmsPlugin = new MajorMicrospeciesPlugin(); TPSAPlugin tpsaPlugin = new TPSAPlugin(); logDPlugin logDPlugin = new logDPlugin(); IUPACNamingPlugin iupacNamingPlugin = new IUPACNamingPlugin(); // set the parameters for the calculations // MajorMicrospeciesPlugin parameters mmsPlugin.setpH(7.4); // major microspecies generation at pH = 7.4 // TPSAPlugin parameters tpsaPlugin.setpH(7.4); // surface area calculation at pH = 7.4 // logDPlugin parameters // set the Cl- and Na+/K+ concentration logDPlugin.setCloridIonConcentration(0.15); logDPlugin.setNaKIonConcentration(0.15); // set the pH range and pH step size logDPlugin.setpHLower(5.4); logDPlugin.setpHUpper(9.4); logDPlugin.setpHStep(2.0); // (there are no parameters to set for IUPACNamingPlugin) // create a MolExporter for writing the result molecules MolExporter exporter = new MolExporter(System.out, "sdf"); // read the input molecules and perform the calculations MolImporter importer = new MolImporter(args[0]); Molecule mol; while ((mol = importer.read()) != null) { // Perform major microspecies, polar surface area and logD // calulations // set the input molecule for MajorMicrospeciesPlugin, // TPSAPlugin and logDPlugin mmsPlugin.setMolecule(mol); tpsaPlugin.setMolecule(mol); logDPlugin.setMolecule(mol); // run the major microspecies, TPSA and logD calculations mmsPlugin.run(); tpsaPlugin.run(); logDPlugin.run(); // get the results of the calculations // get the result of the major microspecies calculation Molecule majorms = mmsPlugin.getMajorMicrospecies(); // get the result of the polar surface area calculation double surfaceArea = tpsaPlugin.getSurfaceArea(); // get the results of the logD calculation // get the pH values double[] pHs = logDPlugin.getpHs(); // get the logD values double[] logDs = logDPlugin.getlogDs(); // Generate the IUPAC name of the major microspecies // generated by the MajorMicrospeciesPlugin. // set majorms as input molecule for IUPACNamingPlugin iupacNamingPlugin.setMolecule(majorms); // run the IUPACNamingPlugin iupacNamingPlugin.run(); // get the preferred IUPAC name String name = iupacNamingPlugin.getPreferredIUPACName(); // Format and display the results // store the pH - logD pairs in a string in format // "[pH1]:logD1 [pH2]:logD2 ..." String logDresult = ""; for (int i = 0; i < pHs.length; i++) { double pH = pHs[i]; double logD = logDs[i]; logD = Math.rint(logD * 100)/100; // round logDresult += ("[" + pH + "]:" + logD + " "); } // write the result molecules (the major microspecies at // pH 7.4) with other results in SDF fields majorms.setProperty("NAME", name); majorms.setProperty("TPSA at pH 7.4", new Double(surfaceArea).toString()); majorms.setProperty("logD ([pH]:value)", logDresult); exporter.write(majorms); } importer.close(); exporter.close(); } catch (IOException e) { System.err.println("I/O error has occurred."); e.printStackTrace(); } catch (PluginException e) { System.err.println("Plugin processing or calculation error."); e.printStackTrace(); } } }