From: <eg...@us...> - 2006-10-25 13:29:45
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Revision: 7184 http://svn.sourceforge.net/cdk/?rev=7184&view=rev Author: egonw Date: 2006-10-25 06:29:22 -0700 (Wed, 25 Oct 2006) Log Message: ----------- Deleted very old code that I wrote, which had little functionality and never took off. Removed Paths: ------------- trunk/cdk/src/org/openscience/cdk/applications/IUPACNameGenerator.java trunk/cdk/src/org/openscience/cdk/applications/jchempaint/action/CreateIUPACNameAction.java Deleted: trunk/cdk/src/org/openscience/cdk/applications/IUPACNameGenerator.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/applications/IUPACNameGenerator.java 2006-10-25 13:27:38 UTC (rev 7183) +++ trunk/cdk/src/org/openscience/cdk/applications/IUPACNameGenerator.java 2006-10-25 13:29:22 UTC (rev 7184) @@ -1,144 +0,0 @@ -/* $RCSfile$ - * $Author$ - * $Date$ - * $Revision$ - * - * Copyright (C) 2003-2006 The Chemistry Development Kit (CDK) project - * - * Contact: cdk...@li... - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. - */ -package org.openscience.cdk.applications; - -import java.util.Locale; - -import org.openscience.cdk.Molecule; -import org.openscience.cdk.iupac.generator.IUPACName; -import org.openscience.cdk.smiles.SmilesParser; -import org.openscience.cdk.tools.FormatStringBuffer; -import org.openscience.cdk.tools.LoggingTool; - -/** - * This class implements a IUPAC name generator. - * - * @cdk.module applications - * - * @author Egon Willighagen - * @cdk.created 2003-10-22 - * @cdk.keyword IUPAC name - */ -public class IUPACNameGenerator -{ - - /** - * The main program for the IUPACNameGenerator class - * - *@param args The command line arguments - */ - public static void main(String[] args) - { - - // to make sure the CDK LoggingTool is configured - LoggingTool logger = new LoggingTool(); - LoggingTool.configureLog4j(); - logger.dumpSystemProperties(); - - Locale l = new Locale("en", "US"); - String smiles = ""; - if (args.length == 1) - { - smiles = args[0]; - } else if (args.length > 1) - { - // parse options - for (int i = 0; i < args.length - 1; i++) - { - String opt = args[i]; - if ("--dutch".equalsIgnoreCase(opt)) - { - l = new Locale("nl", "NL"); - } else if ("--german".equalsIgnoreCase(opt)) - { - l = new Locale("de", "DE"); - } else - { - /* - * This is a command line application * - * Do not convert these System.out/err.println() * - * to logger statements - */ - System.err.println("Unknown option: " + opt); - System.exit(1); - } - } - - smiles = args[args.length - 1]; - } else - { - /* - * This is a command line application * - * Do not convert these System.out/err.println() * - * to logger statements - */ - System.out.println("Syntax : java org.openscience.cdk.applications.IUPACNameGenerator <SMILES>"); - System.exit(0); - } - - SmilesParser sp = new SmilesParser(); - Molecule mol = null; - try - { - mol = sp.parseSmiles(smiles); - } catch (Exception exc) - { - /* - * This is a command line application * - * Do not convert these System.out/err.println() * - * to logger statements - */ - System.out.println("Problem parsing SMILES: " + exc.toString()); - exc.printStackTrace(System.out); - } - if (mol != null) - { - org.openscience.cdk.iupac.generator.IUPACNameGenerator gen = - new org.openscience.cdk.iupac.generator.IUPACNameGenerator(l); - int atomCount = mol.getAtomCount(); - gen.generateName(mol); - IUPACName name = (IUPACName) gen.getName(); - /* - * This is a command line application * - * Do not convert these System.out/err.println() * - * to logger statements - */ - System.out.println("IUPAC name: " + name.getName()); - System.out.println("Full (" + name.size() + " parts):"); - System.out.print(name.toString()); - int namedAtomCount = atomCount - mol.getAtomCount(); - FormatStringBuffer format = new FormatStringBuffer("%3.1lf"); - /* - * This is a command line application * - * Do not convert these System.out/err.println() * - * to logger statements - */ - System.out.println("Ratio named: " + - format.format(100.0 * (double) namedAtomCount / (double) atomCount) + - "% (" + namedAtomCount + "/" + atomCount + ")"); - } - } - -} - Deleted: trunk/cdk/src/org/openscience/cdk/applications/jchempaint/action/CreateIUPACNameAction.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/applications/jchempaint/action/CreateIUPACNameAction.java 2006-10-25 13:27:38 UTC (rev 7183) +++ trunk/cdk/src/org/openscience/cdk/applications/jchempaint/action/CreateIUPACNameAction.java 2006-10-25 13:29:22 UTC (rev 7184) @@ -1,68 +0,0 @@ -/* $RCSfile$ - * $Author$ - * $Date$ - * $Revision$ - * - * Copyright (C) 2003-2006 The JChemPaint project - * - * Contact: jch...@li... - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 - * of the License, or (at your option) any later version. - * All we ask is that proper credit is given for our work, which includes - * - but is not limited to - adding the above copyright notice to the beginning - * of your source code files, and to any copyright notice that you may distribute - * with programs based on this work. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. - */ -package org.openscience.cdk.applications.jchempaint.action; - -import java.awt.event.ActionEvent; -import java.util.Locale; - -import javax.swing.JOptionPane; - -import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.ChemModel; -import org.openscience.cdk.Molecule; -import org.openscience.cdk.iupac.generator.IUPACName; -import org.openscience.cdk.iupac.generator.IUPACNameGenerator; -import org.openscience.cdk.tools.manipulator.ChemModelManipulator; - - -/** - * Creates the IUPAC name for the active compound. It uses the - * experimental IUPAC name generator from CDK. - * - * @cdk.module jchempaint - * @author Egon Willighagen - * @cdk.created 2003-08-11 - */ -public class CreateIUPACNameAction extends JCPAction { - - private static final long serialVersionUID = -6369815894943464691L; - - public void actionPerformed(ActionEvent e) { - logger.debug("Trying to create IUPAC name: ", type); - Locale locale = new Locale("en", "US"); - IUPACNameGenerator generator = new IUPACNameGenerator(locale); - ChemModel model = (ChemModel)jcpPanel.getJChemPaintModel().getChemModel(); - IAtomContainer container = ChemModelManipulator.getAllInOneContainer(model); - Molecule molecule = new Molecule(container); - generator.generateName(molecule); - IUPACName name = (IUPACName)generator.getName(); - String message = "IUPAC name: " + name.getName(); - logger.debug(message); - JOptionPane.showMessageDialog(jcpPanel, message); - } -} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |