Java tutorial
/* * Rajarshi Guha <rajarshi@presidency.com> * 3/4/05 * * 01/19/06 - Thanks to Noel O'Boyle for supplying a patch to update the code * 01/19/06 - Updated to produce PDF output if specified * 01/20/06 - Applied patch from Egon Willighagen to produce a PDF table of structures * 01/22/06 - Updated to allow multiple columns in tabular output * 01/22/06 - Applied patch from Egon Willighagen to output properties if present in the SDF file * 01/24/06 - Updated to improve the formatting of numbers when the properties are * included in tabular PDF output * 02/09/06 - Updated to be in sync with the latest CDK CVS * 03/20/06 - Updated to be in sync with the latest CDK CVS * 04/28/06 - Added code to perform explicity aromaticity detection and synced with latest CDK * 05/10/06 - Caught an exception, synced with latest CDK * 05/18/06 - Updated to show H's for heteroatoms - not configurable from the CLI * 06/05/08 - Updated to the latest CDK, removed SVG spport, removed JAI dependency * ---------------------------------------------------------------------------------------- * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 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 General Public License for more details. * * You should have received a copy of the GNU 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 */ import com.lowagie.text.*; import com.lowagie.text.Rectangle; import com.lowagie.text.pdf.PdfContentByte; import com.lowagie.text.pdf.PdfPCell; import com.lowagie.text.pdf.PdfPTable; import com.lowagie.text.pdf.PdfWriter; import org.apache.commons.cli.*; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.geometry.GeometryTools; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.iterator.IteratingMDLReader; import org.openscience.cdk.layout.StructureDiagramGenerator; import org.openscience.cdk.renderer.Renderer2DModel; import org.openscience.cdk.renderer.old.Renderer2D; import org.openscience.cdk.tools.CDKHydrogenAdder; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import javax.imageio.ImageIO; import javax.swing.*; import java.awt.*; import java.awt.Image; import java.awt.image.BufferedImage; import java.io.*; import java.text.DecimalFormat; import java.util.Map; class displayStructureAsPDFTable extends displayStructure { private PdfPTable table; private Document document; int ncol = 1; boolean props = false; boolean doColor = false; DecimalFormat decimalFormat; public displayStructureAsPDFTable(boolean withH, int width, int height, double scale, int ncol, boolean props, boolean doColor, String odir) { this.withH = withH; this.width = width; this.height = height; this.scale = scale; this.odir = odir; this.props = props; this.ncol = ncol; this.doColor = doColor; suffix = ".pdf"; oformat = "PDF"; decimalFormat = new DecimalFormat("0.000E00"); this.frame = new JFrame(); try { File file = new File(odir + "/output" + this.suffix); document = new Document(); PdfWriter writer = PdfWriter.getInstance(document, new FileOutputStream(file)); float[] widths = new float[ncol]; for (int i = 0; i < ncol; i += 2) { if (props) { widths[i] = 3f; widths[i + 1] = 2f; } else { widths[i] = 1.5f; widths[i + 1] = 3f; } } table = new PdfPTable(widths); document.open(); } catch (Exception exc) { exc.printStackTrace(); } } private void addTitle(IAtomContainer mol, Phrase phrase) { if (mol.getProperty(CDKConstants.TITLE) == null || mol.getProperty(CDKConstants.TITLE).toString().trim().length() == 0) return; phrase.add(new Chunk(CDKConstants.TITLE + ": ", FontFactory.getFont(FontFactory.HELVETICA_BOLD))); phrase.add( new Chunk(mol.getProperty(CDKConstants.TITLE) + "\n", FontFactory.getFont(FontFactory.HELVETICA))); } private void addProperty(Object propertyLabel, IAtomContainer mol, Phrase phrase) { if (mol.getProperty(propertyLabel) == null || mol.getProperty(propertyLabel).toString().trim().length() == 0) return; phrase.add(new Chunk(propertyLabel + ": ", FontFactory.getFont(FontFactory.HELVETICA_BOLD))); String value; try { double tmp = Double.parseDouble(mol.getProperty(propertyLabel).toString()); value = decimalFormat.format(tmp); } catch (NumberFormatException nfe) { value = mol.getProperty(propertyLabel).toString(); } phrase.add(new Chunk(value + "\n", FontFactory.getFont(FontFactory.HELVETICA))); } public IAtomContainer addHeteroHydrogens(IAtomContainer mol) { CDKHydrogenAdder ha = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance()); for (int i = 0; i < mol.getAtomCount(); i++) { try { if (!mol.getAtom(i).getSymbol().equals("C")) { ha.addImplicitHydrogens(mol, mol.getAtom(i)); } } catch (CDKException cdke) { cdke.printStackTrace(); } } return mol; } public void drawStructure(IAtomContainer mol, int cnt) { mol = addHeteroHydrogens(mol); // do aromaticity detection try { CDKHueckelAromaticityDetector.detectAromaticity(mol); } catch (CDKException cdke) { cdke.printStackTrace(); } r2dm = new Renderer2DModel(); renderer = new Renderer2D(r2dm); Dimension screenSize = new Dimension(this.width, this.height); setPreferredSize(screenSize); r2dm.setBackgroundDimension(screenSize); // make sure it is synched with the JPanel size setBackground(r2dm.getBackColor()); try { StructureDiagramGenerator sdg = new StructureDiagramGenerator(); sdg.setMolecule((IMolecule) mol); sdg.generateCoordinates(); this.mol = sdg.getMolecule(); r2dm.setDrawNumbers(false); r2dm.setUseAntiAliasing(true); r2dm.setColorAtomsByType(doColor); r2dm.setShowExplicitHydrogens(withH); r2dm.setShowImplicitHydrogens(true); r2dm.setShowAromaticity(true); r2dm.setShowReactionBoxes(false); r2dm.setKekuleStructure(false); GeometryTools.translateAllPositive(this.mol); GeometryTools.scaleMolecule(this.mol, getPreferredSize(), this.scale); GeometryTools.center(this.mol, getPreferredSize()); } catch (Exception exc) { exc.printStackTrace(); } this.frame.getContentPane().add(this); this.frame.pack(); Rectangle pageSize = new Rectangle(this.getSize().width, this.getSize().height); try { StringBuffer comment = new StringBuffer(); PdfPCell cell = new PdfPCell(); Phrase phrase = new Phrase(); addTitle(mol, phrase); if (props) { Map<Object, Object> propertyMap = mol.getProperties(); for (Object key : propertyMap.keySet()) { if (key.equals("AllRings")) continue; if (key.equals("SmallestRings")) continue; if (key.equals(CDKConstants.TITLE)) continue; addProperty(key, mol, phrase); } } cell.addElement(phrase); table.addCell(cell); Image awtImage = createImage(this.getSize().width, this.getSize().height); Graphics snapGraphics = awtImage.getGraphics(); paint(snapGraphics); com.lowagie.text.Image pdfImage = com.lowagie.text.Image.getInstance(awtImage, null); pdfImage.setAbsolutePosition(0, 0); table.addCell(pdfImage); } catch (DocumentException de) { System.err.println(de.getMessage()); } catch (IOException ioe) { System.err.println(ioe.getMessage()); } } public void paint(Graphics g) { super.paint(g); renderer.paintMolecule(this.mol, (Graphics2D) g, false, true); } public void close() throws Exception { document.add(table); document.close(); } } class displayStructure extends JPanel { protected boolean withH = false; protected int width = 300; protected int height = 300; protected double scale = .9; protected boolean doColor = false; protected String oformat = "PNG"; protected String odir = "./"; protected String suffix = ".png"; protected JFrame frame = null; IAtomContainer mol; Renderer2DModel r2dm; Renderer2D renderer; public displayStructure() { } public IAtomContainer addHeteroHydrogens(IAtomContainer mol) { CDKHydrogenAdder ha = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance()); for (int i = 0; i < mol.getAtomCount(); i++) { try { if (!mol.getAtom(i).getSymbol().equals("C")) { ha.addImplicitHydrogens(mol, mol.getAtom(i)); } } catch (CDKException cdke) { cdke.printStackTrace(); } } return mol; } public displayStructure(boolean withH, int width, int height, double scale, boolean doColor, String oformat, String odir) { this.withH = withH; this.width = width; this.height = height; this.scale = scale; this.oformat = oformat; this.odir = odir; this.doColor = doColor; if (oformat.equalsIgnoreCase("png")) { suffix = ".png"; this.oformat = "PNG"; } else if (oformat.equalsIgnoreCase("jpeg")) { suffix = ".jpg"; this.oformat = "JPEG"; } else if (oformat.equalsIgnoreCase("pdf")) { suffix = ".pdf"; this.oformat = "PDF"; } else if (oformat.equalsIgnoreCase("svg")) { suffix = ".svg"; this.oformat = "SVG"; } this.frame = new JFrame(); } public void drawStructure(IAtomContainer mol, int cnt) { // do aromaticity detection try { CDKHueckelAromaticityDetector.detectAromaticity(mol); } catch (CDKException cdke) { cdke.printStackTrace(); } mol = addHeteroHydrogens(mol); r2dm = new Renderer2DModel(); renderer = new Renderer2D(r2dm); Dimension screenSize = new Dimension(this.width, this.height); setPreferredSize(screenSize); r2dm.setBackgroundDimension(screenSize); // make sure it is synched with the JPanel size setBackground(r2dm.getBackColor()); try { StructureDiagramGenerator sdg = new StructureDiagramGenerator(); sdg.setMolecule((IMolecule) mol); sdg.generateCoordinates(); this.mol = sdg.getMolecule(); r2dm.setDrawNumbers(false); r2dm.setUseAntiAliasing(true); r2dm.setColorAtomsByType(doColor); r2dm.setShowAromaticity(true); r2dm.setShowAromaticityInCDKStyle(false); r2dm.setShowReactionBoxes(false); r2dm.setKekuleStructure(false); r2dm.setShowExplicitHydrogens(withH); r2dm.setShowImplicitHydrogens(true); GeometryTools.translateAllPositive(this.mol); GeometryTools.scaleMolecule(this.mol, getPreferredSize(), this.scale); GeometryTools.center(this.mol, getPreferredSize()); } catch (Exception exc) { exc.printStackTrace(); } this.frame.getContentPane().add(this); this.frame.pack(); String filename; if (cnt < 10) filename = this.odir + "/img00" + cnt + this.suffix; else if (cnt < 100) filename = this.odir + "/img0" + cnt + this.suffix; else filename = this.odir + "/img" + cnt + this.suffix; if (oformat.equalsIgnoreCase("png") || oformat.equalsIgnoreCase("jpeg")) { BufferedImage img; try { img = new BufferedImage(this.getSize().width, this.getSize().height, BufferedImage.TYPE_INT_RGB); // img = (BufferedImage) createImage(this.getSize().width, this.getSize().height); Graphics2D snapGraphics = (Graphics2D) img.getGraphics(); this.paint(snapGraphics); File graphicsFile = new File(filename); ImageIO.write(img, oformat, graphicsFile); } catch (NullPointerException e) { System.out.println(e.toString()); } catch (IOException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } else if (oformat.equalsIgnoreCase("pdf")) { File file = new File(filename); Rectangle pageSize = new Rectangle(this.getSize().width, this.getSize().height); Document document = new Document(pageSize); try { PdfWriter writer = PdfWriter.getInstance(document, new FileOutputStream(file)); document.open(); PdfContentByte cb = writer.getDirectContent(); Image awtImage = createImage(this.getSize().width, this.getSize().height); Graphics snapGraphics = awtImage.getGraphics(); paint(snapGraphics); com.lowagie.text.Image pdfImage = com.lowagie.text.Image.getInstance(awtImage, null); pdfImage.setAbsolutePosition(0, 0); cb.addImage(pdfImage); } catch (DocumentException de) { System.err.println(de.getMessage()); } catch (IOException ioe) { System.err.println(ioe.getMessage()); } document.close(); } else if (oformat.equalsIgnoreCase("svg")) { /* try { SVGWriter cow = new SVGWriter(new FileWriter(filename)); if (cow != null) { cow.writeAtomContainer(mol); cow.close(); } } catch (IOException ioe) { ioe.printStackTrace(); } catch (CDKException cdke) { cdke.printStackTrace(); } */ } } public void paint(Graphics g) { super.paint(g); renderer.paintMolecule(this.mol, (Graphics2D) g, false, true); } public void close() throws Exception { } } public class draw2d { private static boolean withH = false; private static int width = 300; private static int height = 300; private static double scale = 0.9; private static String oformat = "PNG"; private static String outputDirectory = "./"; private static boolean verbose = false; private static boolean tabular = false; private static int ncol = 2; private static boolean props = false; private static boolean doColor = false; private void printHelp(Options options) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("draw2d [OPTIONS] sdf_file\n", "Draws 2D images from coordinate files. Default output is PNG and input should be an SDF file.\n", options, ""); System.exit(0); } private String[] parseCommandLineOptions(String[] args) { Options options = new Options(); options.addOption("c", "scale", true, "Scale factor (default is 0.9)"); options.addOption("f", "format", true, "Output format (PNG, JPEG, PDF)"); options.addOption("t", "table", false, "Output structures as a tabular PDF. This option overrides the format option and the output\nfile is called output.pdf"); options.addOption("n", "ncol", true, "How many molecule columns should tabular output have. The number must be 1 or more"); options.addOption("p", "props", false, "If present output properties in the PDF table. Default is no"); options.addOption("h", "help", false, "Give this help page"); options.addOption("s", "showH", false, "Show explicit hydrogens (default is no)"); options.addOption("l", "color", false, "Color atoms"); options.addOption("o", "outputDir", true, "Where to dump images (default is current directory)"); options.addOption("x", "x", true, "Width of the images (default is 300)"); options.addOption("y", "y", true, "Height of the images (default is 300)"); options.addOption("v", "verbose", false, "Verbose output"); CommandLine line = null; try { CommandLineParser parser = new PosixParser(); line = parser.parse(options, args); } catch (ParseException exception) { System.err.println("Unexpected exception: " + exception.toString()); } if (line.hasOption("l")) { this.doColor = true; } if (line.hasOption("s")) { this.withH = true; } if (line.hasOption("t")) { this.tabular = true; } if (line.hasOption("v")) { this.verbose = true; } if (line.hasOption("p")) { this.props = true; } if (line.hasOption("o")) { this.outputDirectory = line.getOptionValue("o"); } if (line.hasOption("x")) { this.width = Integer.parseInt(line.getOptionValue("x")); } if (line.hasOption("y")) { this.height = Integer.parseInt(line.getOptionValue("y")); } if (line.hasOption("c")) { this.scale = Double.parseDouble(line.getOptionValue("c")); } if (line.hasOption("n")) { this.ncol = Integer.parseInt(line.getOptionValue("n")); if (this.ncol <= 0) { printHelp(options); System.exit(0); } this.ncol = 2 * this.ncol; } if (line.hasOption("f")) { this.oformat = line.getOptionValue("f"); if (!oformat.equalsIgnoreCase("PNG") && !oformat.equalsIgnoreCase("JPEG") && !oformat.equalsIgnoreCase("SVG") && !oformat.equalsIgnoreCase("PDF")) oformat = "PNG"; } String[] filesToDraw = line.getArgs(); if (filesToDraw.length == 0 || line.hasOption("h")) { printHelp(options); } return filesToDraw; } public static void main(String args[]) { draw2d mk = new draw2d(); String[] filesToDraw = mk.parseCommandLineOptions(args); displayStructure ds = null; IteratingMDLReader imdlr; if (tabular) oformat = "PDF"; if (verbose) System.out.println("Output format is " + oformat); if (tabular) { if (verbose) System.out.println("Making a tabular PDF with " + ncol + " columns"); ds = new displayStructureAsPDFTable(withH, width, height, scale, ncol, props, doColor, outputDirectory); } try { imdlr = new IteratingMDLReader(new BufferedReader(new FileReader(filesToDraw[0])), DefaultChemObjectBuilder.getInstance()); int cnt = 1; while (imdlr.hasNext()) { if (verbose) { System.out.println("Processing molecule " + cnt); } IMolecule m = (IMolecule) imdlr.next(); // do atom typing AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(m); if (!tabular) { ds = new displayStructure(withH, width, height, scale, doColor, oformat, outputDirectory); } assert ds != null; ds.drawStructure(m, cnt); cnt = cnt + 1; } if (ds != null) ds.close(); System.exit(0); } catch (FileNotFoundException fnf) { System.out.println(fnf.toString()); } catch (Exception fnf) { System.out.println(fnf.toString()); fnf.printStackTrace(); } } }