smilesparsertest.java

化学图形处理软件

/*
 *  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2006-04-21 10:59:31 +0200 (Fri, 21 Apr 2006) $
 *  $Revision: 6067 $
 *
 *  Copyright (C) 1997-2007  The Chemistry Development Kit (CDK) project
 *
 *  Contact: [e-mail]
 *
 *  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.test.gui.smiles;

import java.awt.Dimension;

import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.applications.swing.MoleculeListViewer;
import org.openscience.cdk.applications.swing.MoleculeViewer2D;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.tools.LoggingTool;

/**
 *@author         steinbeck
 *@cdk.module     test-gui-smiles
 *@cdk.created    2003-09-19
 */
public class SmilesParserTest {
	
	private LoggingTool logger;
	boolean standAlone = false;
	private SmilesParser sp;

	/**
	 *  Constructor for the SmilesParserTest object
	 *
	 *@param  name  Description of the Parameter
	 */
	public SmilesParserTest(String name) {
		sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		logger = new LoggingTool(this);
	}

	public void testSMILES() {
		String[] smiles =
			{
				"Nc1ncnc2[nH]cnc12",
				"C1c2c(c3c(c(O)cnc3)cc2)CC(=O)C1",
				"O=C(O3)C1=COC(OC4OC(CO)C(O)C(O)C4O)C2C1C3C=C2COC(C)=O",
				"CN1C=NC2=C1C(N(C)C(N2C)=O)=O",
				"CN(C)CCC2=CNC1=CC=CC(OP(O)(O)=O)=C12",
				"O=C(O)C1C(OC(C3=CC=CC=C3)=O)CC2N(C)C1CC2",
				"C1(C2(C)(C))C(C)=CCC2C1",
				"C1(C=C(C=C(C=C(C=C(C=CC%35=C%36)C%31=C%35C%32=C%33C%36=C%34)C%22=C%31C%23=C%32C%24=C%25C%33=C%26C%34=CC%27=CC%28=CC=C%29)C%14=C%22C%15=C%23C%16=C%24C%17=C%18C%25=C%19C%26=C%27C%20=C%28C%29=C%21)C6=C%14C7=C%15C8=C%16C9=C%17C%12=C%11C%18=C%10C%19=C%20C%21=CC%10=CC%11=CC(C=C%30)=C%12%13)=C(C6=C(C7=C(C8=C(C9=C%13C%30=C5)C5=C4)C4=C3)C3=C2)C2=CC=C1",
				"CC1(C(=C(CC(C1)O)C)C=CC(=CC=CC(=CC=CC=C(C=CC=C(C=CC1=C(CC(CC1(C)C)O)C)C)C)C)C)C",
				"NC(C(C)C)C(NC(C(C)O)C(NC(C(C)C)C(NC(CCC(N)=O)C(NC(CC([O-])[O-])C(NCC(NC(CC(N)=O)C(NC(Cc1ccccc1)C(NC(CO)C(NC(Cc2ccccc2)C(NC(CO)C(NC(CC(C)C)C(NC(CCC([O-])[O-])C(NC(CO)C(NC(C(C)C)C(NC(CCCC[N+])C(NC(CCCC[N+])C(NC(CC(C)C)C(NC(CCCC[N+])C(NC(CC([O-])[O-])C(NC(CC(C)C)C(NC(CCC(N)=O)C(NC(CCC([O-])[O-])C(N3CCCC3C(NC(CCC(N)=O)C(NC(CCC([O-])[O-])C(N4CCCC4C(NC(CCCNC([N+])[N+])C(NC(C(C)C)C(NCC(NC(CCCC[N+])C(NC(CC(C)C)C(NC(CCCNC([N+])[N+])C(NC(CC(N)=O)C(NC(Cc5ccccc5)C(NC(C)C(N6CCCC6C(NC(C(C)CC)C(N7CCCC7C(NCC(NC(CCC([O-])[O-])C(N8CCCC8C(NC(C(C)C)C(NC(C(C)C)C(N9CCCC9C(NC(C(C)CC)C(NC(CC(C)C)C(NC%19C[S][S]CC(C(NC(CCCC[N+])C(NC(CCC([O-])[O-])C(N%10CCCC%10C(NC(CC(N)=O)C(NC(C)C(NC(CCC(N)=O)C(NC(CCC([O-])[O-])C(NC(C(C)CC)C(NC(CC(C)C)C(NC(CCC(N)=O)C(NC(CCCNC([N+])[N+])C(NC(CC(C)C)C(NC(CCC([O-])[O-])C(NC(CCC([O-])[O-])C(NC(C(C)CC)C(NC(C)C(NC(CCC([O-])[O-])C(NC(CC([O-])[O-])C(N%11CCCC%11C(NCC(NC(C(C)O)C(NC%14C[S][S]CC%13C(NC(C(C)O)C(NCC(NC(C[S][S]CC(C(NC(C)C(NC(Cc%12ccc(O)cc%12)C(NC(C)C(NC(C)C(N%13)=O)=O)=O)=O)=O)NC(=O)C(C(C)CC)NC(=O)C(CCC([O-])[O-])NC%14=O)C(O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)NC(=O)C(CC(C)C)NC(=O)C%15CCCN%15C(=O)C(CCCC[N+])NC(=O)C(CC(C)C)NC(=O)C(CCC([O-])[O-])NC(=O)C(CCC([O-])[O-])NC(=O)C%16CCCN%16C(=O)C(Cc%17ccccc%17)NC(=O)C(CC(N)=O)NC(=O)C%18CCCN%18C(=O)C(CC(N)=O)NC(=O)C(CO)NC%19=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O",
				"CC(C(C8CCC(CC8)=O)C3C4C(CC5(CCC(C9=CC(C=CN%10)=C%10C=C9)CCCC5)C4)C2CCC1CCC7(CCC7)C6(CC6)C1C2C3)=O"
			};
		MoleculeListViewer mlv = new MoleculeListViewer();
		mlv.setMolViewDim(new Dimension(400, 600));
		for (int f = 0; f < smiles.length; f++) {
			try {
				IMolecule mol = sp.parseSmiles(smiles[f]);
				StructureDiagramGenerator sdg = new StructureDiagramGenerator();
				MoleculeViewer2D mv = new MoleculeViewer2D();
				//mv.getRenderer2DModel().setDrawNumbers(true);
				sdg.setMolecule((Molecule) mol.clone());
				sdg.generateCoordinates();
				mv.setAtomContainer(sdg.getMolecule());
				mlv.addStructure(mv, "Structure " + (f + 1));
			} catch (Exception exc) {
				logger.debug("Could not parse SMILES: ", smiles[f]);
				logger.debug(exc);
			}
		}
	}

}