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[Cdk-commits] SF.net SVN: cdk:[13282] jchempaint/trunk
|
From: <sh...@us...> - 2008-11-25 17:12:37
|
Revision: 13282
http://cdk.svn.sourceforge.net/cdk/?rev=13282&view=rev
Author: shk3
Date: 2008-11-25 17:12:32 +0000 (Tue, 25 Nov 2008)
Log Message:
-----------
the ant build works again
Modified Paths:
--------------
jchempaint/trunk/build.xml
Removed Paths:
-------------
jchempaint/trunk/src/main/org/openscience/jchempaint/TestEditor.java
jchempaint/trunk/src/main/org/openscience/jchempaint/TestRenderer.java
Modified: jchempaint/trunk/build.xml
===================================================================
--- jchempaint/trunk/build.xml 2008-11-25 17:00:33 UTC (rev 13281)
+++ jchempaint/trunk/build.xml 2008-11-25 17:12:32 UTC (rev 13282)
@@ -1,4 +1,4 @@
-<project name="JCPCDK" default="dist-jcp" basedir=".">
+<project name="JCPCDK" default="dist" basedir=".">
<property file="ant.properties"/>
@@ -11,6 +11,7 @@
<property name="cdk.devellib" value="${cdk.dir}/develjar" />
<property name="cdk.metainf" value="${cdk.dir}/src/META-INF" />
<property name="src" value="src" />
+ <property name="lib" value="lib" />
<property name="dist" value="dist" />
<property name="appjars.dir" value="${dist}/appjars" />
@@ -18,7 +19,7 @@
<delete dir="${dist}" />
</target>
- <target id="dist-jcp" name="dist-jcp" depends="compile-jcp, unjar-libjars, unjar-cdkjars"
+ <target id="dist" name="dist" depends="compile-jcp, unjar-libjars, unjar-cdkjars"
description="Builds the JChemPaint application">
<jar jarfile="${dist}/jchempaint-${jcp.version}.jar">
<manifest>
@@ -49,7 +50,12 @@
<includesfile name="${cdk.metainf}/render.libdepends"/>
<includesfile name="${cdk.metainf}/standard.libdepends"/>
</fileset>
- </unjar>
+ </unjar>
+ <unjar dest="${appjars.dir}">
+ <fileset dir="${lib}">
+ <include name="**/*" />
+ </fileset>
+ </unjar>
</target>
<target id="unjar-cdkjars" name="unjar-cdkjars">
@@ -94,6 +100,8 @@
</fileset>
<fileset dir="${cdk.dist}/jar">
</fileset>
+ <fileset dir="${lib}">
+ </fileset>
</classpath>
</javac>
Deleted: jchempaint/trunk/src/main/org/openscience/jchempaint/TestEditor.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/TestEditor.java 2008-11-25 17:00:33 UTC (rev 13281)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/TestEditor.java 2008-11-25 17:12:32 UTC (rev 13282)
@@ -1,314 +0,0 @@
-/* $Revision: 7636 $ $Author: nielsout $ $Date: 2007-09-02 11:46:10 +0100 (su, 02 sep 2007) $
- *
- * Copyright (C) 2007 Niels Out <nie...@us...>
- *
- * Contact: cdk...@li... or no...@sc...
- *
- * 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 I ask is that proper credit is given for my 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.jchempaint;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.Rectangle2D;
-
-import javax.swing.JComponent;
-import javax.swing.JFrame;
-import javax.swing.JPanel;
-import javax.swing.JToolBar;
-
-import org.openscience.cdk.Atom;
-import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.DefaultChemObjectBuilder;
-import org.openscience.cdk.Molecule;
-import org.openscience.cdk.controller.Controller2DHub;
-import org.openscience.cdk.controller.Controller2DModel;
-import org.openscience.cdk.controller.ExampleController2DModule;
-import org.openscience.cdk.controller.SwingEventRelay;
-import org.openscience.cdk.controller.SwingMouseEventRelay;
-import org.openscience.cdk.interfaces.IAtom;
-import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.interfaces.IChemObjectBuilder;
-import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.layout.StructureDiagramGenerator;
-import org.openscience.cdk.renderer.Renderer2DModel;
-import org.openscience.cdk.renderer.IJava2DRenderer;
-import org.openscience.cdk.renderer.Java2DRenderer;
-import org.openscience.cdk.tools.manipulator.ChemModelManipulator;
-
-/**
- * Test class for testing the new Java2DRenderer and Controller2DHub.
- *
- * @author nielsout
- * @author egonw
- * @cdk.module jchempaint
- * @cdk.svnrev $Revision: 9162 $
- */
-public class TestEditor extends JPanel {
-
- private static final long serialVersionUID = -4728755515648290149L;
-
- private JFrame frame;
- private SwingPainter painter = new SwingPainter();
- private StructureDiagramGenerator sdg = new StructureDiagramGenerator();
- protected IChemObjectBuilder builder;
- private Controller2DHub hub;
-
- public Controller2DHub get2DHub() {
- return hub;
- }
- private JComponent lastActionButton;
- public JComponent getActionButton() {
- return lastActionButton;
- }
- public void setActionButton(JComponent actionButton) {
- lastActionButton = actionButton;
- }
- private TestEditor() {
- builder = DefaultChemObjectBuilder.getInstance();
-
- frame = new JFrame();
- frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- frame.setName("'frame'");
-
-
- // sdg.setMolecule(makeMasstest());
- sdg.setMolecule(makeSWedgeTest());
-
- try {
- sdg.generateCoordinates();
- } catch (Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- IMolecule mol = sdg.getMolecule();
- System.out.println("molecule: " + mol);
-
- painter = new SwingPainter();
- painter.setMolecule(mol);
- painter.setName("'painter'");
-
- SwingEventRelay eventRelay = new SwingEventRelay(painter);
-
- hub = new Controller2DHub(
- new Controller2DModel(), painter.getRenderer(),
- ChemModelManipulator.newChemModel(mol),
- eventRelay
- );
- hub.registerGeneralControllerModule(
- new ExampleController2DModule()
- );
- SwingMouseEventRelay relay = new SwingMouseEventRelay(hub);
- painter.addMouseListener(relay);
- painter.addMouseMotionListener(relay);
-
- JToolBar toolbar=null;//changed shk3 = SomeToolBar.getToolbar(this, 1);
- // frame.add(toolbar);
-
- frame.add(toolbar, BorderLayout.NORTH);
- // frame.revalidate();
-
- frame.add(painter);
-
- painter.setBackground(Color.WHITE);
-
-
- }
-
- private void run() {
- frame.setSize(800, 400);
- frame.setVisible(true);
- }
-
- /**
- * @param args
- */
- public static void main(String[] args) {
- TestEditor prog = new TestEditor();
- prog.setName("'the TestEditor'");
- prog.run();
- }
-
- public class SwingPainter extends JComponent {
- private static final long serialVersionUID = 2;
-
- Renderer2DModel model = new Renderer2DModel();
- IJava2DRenderer renderer = new Java2DRenderer(model);
-
- private IMolecule molecule;
-
- Graphics2D graphic;
-
-
- public void setMolecule(IMolecule molecule) {
- this.molecule = molecule;
- }
- public IJava2DRenderer getRenderer() {
- return this.renderer;
- }
- public Renderer2DModel getModel() {
- return this.model;
- }
- public IMolecule getMolecule() {
- return this.molecule;
- }
- public Graphics2D getGraphics2D() {
- return this.graphic;
- }
- AffineTransform affinelast = new AffineTransform();
- public void update(Graphics g) {
- System.out.println("!!! Repainting molecule!!!");
-
- }
- public void update() {
- System.out.println("!!! Repainting molecule!!!");
-
- }
- private double prevZoom;
- private int windowH;
- private int windowW;
-
- public void paint(Graphics g) {
- //System.out.println("Painting molecule..!");
- super.paint(g);
- model.setZoomFactor(1);
- model.setShowAromaticity(true);
-
- //IChemModel imol = hub.getIChemModel();
- //FIXME: make sure to draw all molecules if imol has more then one..
- //molecule = imol.getMoleculeSet().getMolecule(0);
-
- graphic = (Graphics2D)g;
- Color bg = model.getBackColor();
- g.setColor(bg);
- g.fillRect(0, 0, getWidth(), getHeight());
-
- if (!affinelast.equals(graphic.getTransform())) {
- System.out.println("swing changed matrix to:" + graphic.getTransform());
- affinelast = graphic.getTransform();
- }
-
- if (prevZoom != model.getZoomFactor() || windowH != getSize().height || windowW != getSize().width )
- {
- //new window / size changed
- renderer.paintMolecule(molecule, (Graphics2D)g, (Rectangle2D)getBounds());
- windowH = getSize().height;
- windowW = getSize().width;
- prevZoom = model.getZoomFactor();
- }
- else { //same window (repaint triggered)
- renderer.paintMolecule(molecule, graphic);
- }
- }
- }
- public static Molecule makeAlkanetest(int chainLength)
- {
- Molecule currentChain = new Molecule();
-
- //Add the initial atom
- IAtom atom = new Atom("C");
- atom.setHydrogenCount(3);
- currentChain.addAtom(atom);
-
- //Add further atoms and bonds as needed, a pair at a time.
- int atomCount = 1;
- for (; atomCount < chainLength - 1; atomCount++) {
- atom = new Atom("C");
- atom.setHydrogenCount(2);
- currentChain.addAtom(atom);
- currentChain.addBond(atomCount, atomCount - 1, IBond.Order.SINGLE);
- }
- atom = new Atom("C");
- atom.setHydrogenCount(3);
- currentChain.addAtom(atom);
- currentChain.addBond(atomCount, atomCount - 1, IBond.Order.SINGLE);
-
- return currentChain;
- }
-
- public IMolecule makeMasstest() {
- IMolecule mol = builder.newMolecule();
- IAtom atomC0 = new Atom("C");
- atomC0.setID("C0"); atomC0.setHydrogenCount(3);
- IAtom atomC1 = new Atom("C");
- atomC1.setID("C1"); atomC1.setHydrogenCount(2);
-
- IAtom atomS = new Atom("S");
- atomS.setID("S");
- //atomC1.setHydrogenCount(1);
- atomC0.setMassNumber(10);
- atomS.setMassNumber(4);
-
- atomC1.setMassNumber(26);
-
- atomC0.setFormalCharge(-2);
- atomS.setFormalCharge(2);
- atomC1.setFormalCharge(-1);
-
- IBond bondB0 = builder.newBond(atomC0, atomC1);
- bondB0.setElectronCount(1);
- IBond bondB1 = builder.newBond(atomC1, atomS);
- bondB1.setElectronCount(1);
-
- mol.addAtom(atomC0); mol.addAtom(atomC1);
- mol.addAtom(atomS);
- mol.addBond(bondB0);
- mol.addBond(bondB1);
-
- return mol;
- }
- public IMolecule makeSWedgeTest() {
- IMolecule mol = builder.newMolecule();
- IAtom atomC0 = new Atom("C");
- atomC0.setID("C0"); atomC0.setHydrogenCount(0);
-
-
- IAtom atomO1 = new Atom("O");
- atomO1.setID("O1"); atomO1.setHydrogenCount(0);
-
- IAtom atomH0 = new Atom("H");
- atomH0.setID("H0"); atomH0.setHydrogenCount(0);
- IAtom atomH1 = new Atom("H");
- atomH1.setID("H1"); atomH1.setHydrogenCount(0);
-
- IBond bondB1 = builder.newBond(atomC0, atomO1);
- bondB1.setElectronCount(2);
- bondB1.setOrder(IBond.Order.DOUBLE);
- IBond bondB2 = builder.newBond(atomC0, atomH0);
- bondB2.setElectronCount(1);
- bondB2.setStereo(CDKConstants.STEREO_BOND_DOWN);
-
- IBond bondB3 = builder.newBond(atomC0, atomH1);
- bondB3.setElectronCount(1);
- bondB3.setStereo(CDKConstants.STEREO_BOND_UP);
-
- mol.addAtom(atomC0);
- mol.addAtom(atomO1);
- mol.addAtom(atomH0);
- mol.addAtom(atomH1);
-mol.addBond(bondB1);
- mol.addBond(bondB2);
- mol.addBond(bondB3);
-
- return mol;
- }
-}
Deleted: jchempaint/trunk/src/main/org/openscience/jchempaint/TestRenderer.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/TestRenderer.java 2008-11-25 17:00:33 UTC (rev 13281)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/TestRenderer.java 2008-11-25 17:12:32 UTC (rev 13282)
@@ -1,377 +0,0 @@
-/* $Revision: 7636 $ $Author: nielsout $ $Date: 2007-09-02 11:46:10 +0100 (su, 02 sep 2007) $
- *
- * Copyright (C) 2007 Niels Out <nie...@us...>
- *
- * Contact: cdk...@li... or no...@sc...
- *
- * 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 I ask is that proper credit is given for my 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.jchempaint;
-
-import java.awt.Color;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.Rectangle2D;
-import java.awt.image.BufferedImage;
-import java.io.File;
-import java.io.IOException;
-
-import javax.imageio.ImageIO;
-import javax.swing.JComponent;
-import javax.swing.JFrame;
-import javax.swing.JPanel;
-import javax.vecmath.Point2d;
-
-import org.openscience.cdk.Atom;
-import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.DefaultChemObjectBuilder;
-import org.openscience.cdk.Molecule;
-import org.openscience.cdk.exception.InvalidSmilesException;
-import org.openscience.cdk.interfaces.IAtom;
-import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.interfaces.IChemObjectBuilder;
-import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.layout.StructureDiagramGenerator;
-import org.openscience.cdk.renderer.IJava2DRenderer;
-import org.openscience.cdk.renderer.Java2DRenderer;
-import org.openscience.cdk.renderer.Renderer2DModel;
-
-/**
- * Test class for testing the new Java2DRenderer.
- *
- * @author nielsout
- * @cdk.svnrev $Revision: 9162 $
- * @cdk.module progzjcp
- */
-public class TestRenderer extends JPanel {
-
- private static final long serialVersionUID = -4728755515648290149L;
-
- JFrame frame;
- SwingPainter painter = new SwingPainter();
- StructureDiagramGenerator sdg = new StructureDiagramGenerator();
- protected IChemObjectBuilder builder;
- public void setUp() {
- builder = DefaultChemObjectBuilder.getInstance();
- }
- public class RendererListner implements MouseListener {
- public void mouseClicked(MouseEvent e) {
- System.out.println(e);
- IMolecule molecule = painter.getMolecule();
-
- //painter.getGraphics2D(),
- Point2d ptDst = painter.renderer.getCoorFromScreen(e.getX(), e.getY());
- System.out.println("Mouse click at (" + e.getX() + ","
- + e.getY() + ") real world coordinates: " + ptDst);
- Java2DRenderer.showClosestAtomOrBond(molecule, ptDst);
- try {
- int width = 400, height = 400;
-
- // TYPE_INT_ARGB specifies the image format: 8-bit RGBA packed
- // into integer pixels
- System.out.println("\tstarting..\n");
- BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
- System.out.println("bi created\n");
-
- Graphics2D ig2 = bi.createGraphics();
- System.out.println("ig2 created\n");
-
-
- ig2.setColor(getBackground());
- ig2.fillRect(0, 0, width, height);
-
- Renderer2DModel model = painter.getModel();
- IJava2DRenderer renderer = painter.getRenderer();
-
- model.setZoomFactor(1);
- System.out.println("setZoomeFActor done\n");
-
- Rectangle2D rectangle = new Rectangle2D.Double();
- rectangle.setFrame(0, 0, width, height);
- renderer.paintMolecule(molecule, ig2, rectangle);
- System.out.println("renderer.paintMolecule done\n");
-
- ImageIO.write(bi, "PNG", new File("c:\\tmp\\yourImageName.PNG"));
- ImageIO.write(bi, "JPEG", new File("c:\\tmp\\yourImageName.JPG"));
- ImageIO.write(bi, "gif", new File("c:\\tmp\\yourImageName.GIF"));
- ImageIO.write(bi, "BMP", new File("c:\\tmp\\yourImageName.BMP"));
-
- } catch (IOException ie) {
- ie.printStackTrace();
- }
- }
- public void mouseEntered(MouseEvent e) { }
- public void mouseExited(MouseEvent e) { }
- public void mousePressed(MouseEvent e) { }
- public void mouseReleased(MouseEvent e) { }
- }
-
- private TestRenderer() throws InvalidSmilesException {
- frame = new JFrame();
- frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-
- painter = new SwingPainter();
- //painter.addMouseMotionListener(new TestRendererMouseE());
- //only react on mouse clicks for now
- painter.addMouseListener(new RendererListner());
- setUp();
-
- IMolecule mol;
-
- //mol = MoleculeFactory.makeAlphaPinene();
- //mol = MoleculeFactory.makeThiazole();
- //mol = MoleculeFactory.makeAlkane(5);
- //mol = makeAlkanetest(5);
- //mol = makeMasstest();
-
- //mol = MoleculeFactory.makeBenzene();
- mol = makeBenzene();
-
- //mol = makeSWedgeTest();
-//System.out.println("molecule: " + mol);
-
-
- sdg.setMolecule(mol);
- try {
- sdg.generateCoordinates();
- } catch (Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- painter.setMolecule(sdg.getMolecule());
- frame.add(painter);
-
- painter.setBackground(Color.WHITE);
-
-
- }
-
- private void run() {
- frame.setSize(400, 400);
-
-// frame.show();
- frame.setVisible(true);
-
- }
-
- /**
- * @param args
- */
- public static void main(String[] args) throws InvalidSmilesException {
- TestRenderer prog = new TestRenderer();
- prog.run();
- }
-
- public class SwingPainter extends JComponent {
- private static final long serialVersionUID = 2;
-
- Renderer2DModel model = new Renderer2DModel();
-
- //IRenderer2D renderer = new Java2DRenderer(model);
- IJava2DRenderer renderer = new Java2DRenderer(model);
-
- private IMolecule molecule;
-
- Graphics2D graphic;
-
- public void setMolecule(IMolecule molecule) {
- this.molecule = molecule;
- }
- public IJava2DRenderer getRenderer() {
- return this.renderer;
- }
- public Renderer2DModel getModel() {
- return this.model;
- }
- public IMolecule getMolecule() {
- return this.molecule;
- }
- public Graphics2D getGraphics2D() {
- return this.graphic;
- }
- AffineTransform affinelast = new AffineTransform();
- public void paint(Graphics g) {
- //if (isOpaque()) { //paint background
- // g.setColor(getBackground());
-
- // }
- super.paint(g);
- //System.out.println("Painting molecule..!");
- graphic = (Graphics2D)g;
- model.setZoomFactor(1);
- Color bg = model.getBackColor();
- g.setColor(bg);
- g.fillRect(0, 0, getWidth(), getHeight());
-
- if (!affinelast.equals(graphic.getTransform())) {
- System.out.println("swing changed matrix to:" + graphic.getTransform());
- affinelast = graphic.getTransform();
- }
-
- renderer.paintMolecule(molecule, (Graphics2D)g, (Rectangle2D)getBounds());
- }
- }
- public static Molecule makeAlkanetest(int chainLength)
- {
- Molecule currentChain = new Molecule();
-
- //Add the initial atom
- IAtom atom = new Atom("C");
- atom.setHydrogenCount(3);
- currentChain.addAtom(atom);
-
- //Add further atoms and bonds as needed, a pair at a time.
- int atomCount = 1;
- for (; atomCount < chainLength - 1; atomCount++) {
- atom = new Atom("C");
- atom.setHydrogenCount(2);
- currentChain.addAtom(atom);
- currentChain.addBond(atomCount, atomCount - 1, IBond.Order.SINGLE);
- }
- atom = new Atom("C");
- atom.setHydrogenCount(3);
- currentChain.addAtom(atom);
- currentChain.addBond(atomCount, atomCount - 1, IBond.Order.SINGLE);
-
- return currentChain;
- }
- public IMolecule makeSWedgeTest() {
- IMolecule mol = builder.newMolecule();
- IAtom atomC0 = new Atom("C");
- atomC0.setID("C0"); atomC0.setHydrogenCount(0);
-
-
- IAtom atomO1 = new Atom("O");
- atomO1.setID("O1"); atomO1.setHydrogenCount(0);
-
- IAtom atomH0 = new Atom("H");
- atomH0.setID("H0"); atomH0.setHydrogenCount(0);
- IAtom atomH1 = new Atom("H");
- atomH1.setID("H1"); atomH1.setHydrogenCount(0);
-
- IBond bondB1 = builder.newBond(atomC0, atomO1);
- bondB1.setElectronCount(2);
- IBond bondB2 = builder.newBond(atomC0, atomH0);
- bondB2.setElectronCount(1);
- bondB2.setStereo(CDKConstants.STEREO_BOND_DOWN);
-
- IBond bondB3 = builder.newBond(atomC0, atomH1);
- bondB3.setElectronCount(1);
- bondB3.setStereo(CDKConstants.STEREO_BOND_UP);
-
- mol.addAtom(atomC0);
- mol.addAtom(atomO1);
- mol.addAtom(atomH0);
- mol.addAtom(atomH1);
-mol.addBond(bondB1);
- mol.addBond(bondB2);
- mol.addBond(bondB3);
-
- return mol;
- }
- public IMolecule makeMasstest() {
- IMolecule mol = builder.newMolecule();
- IAtom atomC0 = new Atom("C");
- atomC0.setID("C0"); atomC0.setHydrogenCount(3);
- IAtom atomC1 = new Atom("C");
- atomC1.setID("C1"); atomC1.setHydrogenCount(2);
-
- IAtom atomS = new Atom("S");
- atomS.setID("S");
- //atomC1.setHydrogenCount(1);
- atomC0.setMassNumber(10);
- atomS.setMassNumber(4);
-
- atomC1.setMassNumber(26);
-
- atomC0.setFormalCharge(-2);
- atomS.setFormalCharge(2);
- atomC1.setFormalCharge(-1);
-
- IBond bondB0 = builder.newBond(atomC0, atomC1);
- bondB0.setElectronCount(1);
- IBond bondB1 = builder.newBond(atomC1, atomS);
- bondB1.setElectronCount(1);
-
- mol.addAtom(atomC0); mol.addAtom(atomC1);
- mol.addAtom(atomS);
- mol.addBond(bondB0);
- mol.addBond(bondB1);
-
- return mol;
- }
- public IMolecule makeBenzene() {
- IMolecule benzene = builder.newMolecule();
-
- System.out.println("testing..");
- IAtom atomC0 = new Atom("C");
- atomC0.setID("C0"); atomC0.setHydrogenCount(1);
- IAtom atomC1 = new Atom("C");
- atomC1.setID("C1"); atomC1.setHydrogenCount(1);
- IAtom atomC2 = new Atom("C");
- atomC2.setID("C2"); atomC2.setHydrogenCount(1);
- IAtom atomC3 = new Atom("C");
- atomC3.setID("C3"); atomC3.setHydrogenCount(1);
- IAtom atomC4 = new Atom("C");
- atomC4.setID("C4"); atomC4.setHydrogenCount(1);
- IAtom atomC5 = new Atom("C");
- atomC5.setID("C5"); atomC5.setHydrogenCount(1);
-
- atomC0.setFlag(CDKConstants.ISAROMATIC, true);
- atomC1.setFlag(CDKConstants.ISAROMATIC, true);
- atomC2.setFlag(CDKConstants.ISAROMATIC, true);
- atomC3.setFlag(CDKConstants.ISAROMATIC, true);
- atomC4.setFlag(CDKConstants.ISAROMATIC, true);
- atomC5.setFlag(CDKConstants.ISAROMATIC, true);
-
- IBond bondB0 = builder.newBond(atomC0, atomC1);
- bondB0.setElectronCount(2);
- IBond bondB1 = builder.newBond(atomC1, atomC2);
- bondB1.setElectronCount(2);
- IBond bondB2 = builder.newBond(atomC2, atomC3);
- bondB2.setElectronCount(2);
- IBond bondB3 = builder.newBond(atomC3, atomC4);
- bondB3.setElectronCount(2);
- IBond bondB4 = builder.newBond(atomC4, atomC5);
- bondB4.setElectronCount(2);
- IBond bondB5 = builder.newBond(atomC0, atomC5);
- bondB5.setElectronCount(2);
-
- IBond bondingSystem = builder.newBond();
- bondingSystem.setElectronCount(6);
- bondingSystem.setAtoms(
- new IAtom[] { atomC0, atomC1, atomC2,
- atomC3, atomC4, atomC5}
- );
-
- benzene.addAtom(atomC0); benzene.addAtom(atomC1);
- benzene.addAtom(atomC2); benzene.addAtom(atomC3);
- benzene.addAtom(atomC4); benzene.addAtom(atomC5);
-
- benzene.addBond(bondB0); benzene.addBond(bondB1);
- benzene.addBond(bondB2); benzene.addBond(bondB3);
- benzene.addBond(bondB4); benzene.addBond(bondB5);
- benzene.addBond(bondingSystem);
-
- return benzene;
- }
-}
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