fileconvertor.java

化学图形处理软件

    private String getOutputFileName(String inputFilename, String outputFormat) {
        String outputFilename = inputFilename.substring(0,inputFilename.lastIndexOf('.'));
        outputFilename = outputFilename.substring(outputFilename.lastIndexOf(File.separatorChar) + 1);
        outputFilename = outputFilename + ".";
        if (outputFormat.equalsIgnoreCase("CML")) {
            outputFilename = outputFilename + "cml";
        } else if (outputFormat.equalsIgnoreCase("MOL")) {
            outputFilename = outputFilename + "mol";
        } else if (outputFormat.equalsIgnoreCase("SMI")) {
            outputFilename = outputFilename + "smi";
        } else if (outputFormat.equalsIgnoreCase("SHELX")) {
            outputFilename = outputFilename + "res";
        } else if (outputFormat.equalsIgnoreCase("SVG")) {
            outputFilename = outputFilename + "svg";
        } else if (outputFormat.equalsIgnoreCase("XYZ")) {
            outputFilename = outputFilename + "xyz";
        } else if (outputFormat.equalsIgnoreCase("PDB")) {
            outputFilename = outputFilename + "pdb";
        } else if (outputFormat.equalsIgnoreCase("GIN")) {
            outputFilename = outputFilename + "in";
        } else if (outputFormat.equalsIgnoreCase("CDK")) {
            outputFilename = outputFilename + "java.fragment";
        } else if (outputFormat.equalsIgnoreCase("HIN")) {
            outputFilename = outputFilename + "hin";
        }
        return outputFilename;
    }

    private void printHelp(Options options) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("FileConvertor", options);
        
        // now report on the supported formats
        System.out.println();
        System.out.println(" OUTPUT FORMATS:");
        System.out.println("  cml    Chemical Markup Language (the default)");
        System.out.println("  gin    Gaussian Input File");
        System.out.println("  hin    Hyperchem file");
        System.out.println("  mol    MDL molfile");
        System.out.println("  pdb    PDB");
        System.out.println("  shelx  ShelX");
        System.out.println("  smi    SMILES");
        System.out.println("  svg    Scalable Vector Graphics");
        System.out.println("  xyz    XYZ");
        
        System.exit(0);
    }
    
    /**
     * Parses the options in the command line arguments and returns
     * the index of the first non-option argument.
     */
    private String[] parseCommandLineOptions(String[] args) {

        Options options = new Options();
        options.addOption("h", "help", false, "give this help page");
        options.addOption(
            OptionBuilder.withLongOpt("question").
                          withDescription("level of IO questions [none|fewest|some|all]").
                          withValueSeparator('=').
                          hasArg().
                          create("q")
        );
        options.addOption(
            OptionBuilder.withLongOpt("outputformat").
                          withDescription("see below for supported formats (CML2 is default)").
                          withValueSeparator('=').
                          hasArg().
                          create("o")
        );
        options.addOption(
            OptionBuilder.withLongOpt("listoptions").
                          withDescription("lists the IO questions for the given format").
                          withValueSeparator('=').
                          hasArg().
                          create("l")
        );
        options.addOption(
            OptionBuilder.withLongOpt("properties").
                          withDescription("Java properties file with the IO settings").
                          withValueSeparator('=').
                          hasArg().
                          create("p")
        );
        options.addOption(
            OptionBuilder.withLongOpt("addHydrogens").
                          withDescription("add explicit hydrogens where missing").
                          create("a")
        );
        options.addOption(
            OptionBuilder.withLongOpt("removeHydrogens").
                          withDescription("remove all explicit hydrogens").
                          create("r")
        );
        options.addOption(
            OptionBuilder.withLongOpt("create2DCoordinates").
                          withDescription("create 2D coordinates using a layout algorithm").
                          create("2")
        );
        options.addOption(
            OptionBuilder.withLongOpt("rebondFrom3DCoordinates").
                          withDescription("calculate bonds from 3D coordinates").
                          create("b")
        );
        
        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("o")) {
            this.oformat = line.getOptionValue("o");
        }
        if (line.hasOption("q")) {
            String level = line.getOptionValue("q");
            if ("none".equals(level)) {
                settingListener = new TextGUIListener(0);
            } else if ("fewest".equals(level)) {
                settingListener = new TextGUIListener(1);
            } else if ("some".equals(level)) {
                settingListener = new TextGUIListener(2);
            } else if ("all".equals(level)) {
                settingListener = new TextGUIListener(3);
            } else {
                System.out.println("Only supported levels: none, fewest, some, all");
                System.exit(1);
            }
        }
        if (line.hasOption("l")) {
            listOptionsForIOClass(line.getOptionValue("l"));
            System.exit(0);
        }
        if (line.hasOption("p")) {
            String filename = line.getOptionValue("p");
            try {
                File file = new File(filename);
                Properties props = new Properties();
                props.load(new FileInputStream(file));
                propsListener = new PropertiesListener(props);
                settingListener = null;
            } catch (FileNotFoundException exception) {
                System.out.println("Cannot find properties file: " + filename);
                System.exit(1);
            } catch (IOException exception) {
                System.out.println("Cannot read properties file: " + filename);
                System.exit(1);
            }
        }
        if (line.hasOption("a")) {
            this.applyHAdding = true;
        }
        if (line.hasOption("r")) {
            this.applyHRemoval = true;
        }
        if (line.hasOption("2")) {
            this.apply2DCleanup = true;
        }
        if (line.hasOption("b")) {
            this.apply3DRebonding = true;
        }

        String[] filesToConvert = line.getArgs();
        
        if (filesToConvert.length == 0 || line.hasOption("h")) {
            printHelp(options);
        }
        
        return filesToConvert;
    }

    public void listOptionsForIOClass(String ioClassName) {
        logger.debug("listing IOSetting options");
        
        String className = "org.openscience.cdk.io." + ioClassName;
        try {
            Object readerOrWriter = this.getClass().getClassLoader().
                loadClass(className).newInstance();
            IOSetting[] settings = new IOSetting[0];
            if (readerOrWriter instanceof IChemObjectIO) {
                IChemObjectIO ioClass = (IChemObjectIO)readerOrWriter;
                settings = ioClass.getIOSettings();
            } else {
                String message = "This class is not a CDK ChemObjectIO class";
                System.out.println(message);
                logger.error(message);
                return;
            }
            TextGUIListener listener = new TextGUIListener(4); // ask all questions
            listener.setInputReader(null); // but don't really ask them
            for (int i=0; i<settings.length; i++) {
                IOSetting setting = settings[i];
                if (setting != null) {
                    listener.processIOSettingQuestion(setting);
                } else {
                    String message = "This IOSetting is null";
                    System.out.println(message);
                    logger.warn(message);
                }
            }
        } catch (ClassNotFoundException exception) {
            String message = "This Reader/Writer does not exist: " + className;
            System.out.println(message);
            logger.error(message);
            logger.debug(exception);
        } catch (InstantiationException exception) {
            String message = "Could not instantiate the class: " + className;
            System.out.println(message);
            logger.error(message);
            logger.debug(exception);
        } catch (Exception exception) {
            System.out.println("An unknown exception occured: " + exception.toString());
            logger.debug(exception);
        }
    }

    /**
    * Since we do not know what kind of IChemObject the Writer supports,
    * and we want to output as much information as possible, use
    * the generalized mechanism below.
    */
    private void write(IChemFile chemFile, String outputFilename) throws IOException {
        if (cow.accepts(chemFile.getClass())) {
            // Can write ChemFile, do so
            try {
                cow.write(chemFile);
            } catch (CDKException e) {
                logger.error("Could not write ChemFile. FIXME: I should recurse!");
            }
        } else {
            logger.info("Cannot write ChemFile, recursing into ChemSequence's.");
            int count = chemFile.getChemSequenceCount();
            boolean needMoreFiles = (cow.accepts(IChemSequence.class)) && (count > 1);
            for (int i=0; i < count; i++) {
                if (needMoreFiles) {
                    cow.close(); // possibly closing empty file
                    String fname = outputFilename + "." + (i+1);
                    FileWriter fileWriter = new FileWriter(new File(fname));
                    cow = getChemObjectWriter(this.oformat, fileWriter);
                }
                write(chemFile.getChemSequence(i), outputFilename);
            }
        }
    }

    private void write(IChemSequence sequence, String outputFilename) throws IOException {
        try {
            cow.write(sequence);
        } catch (CDKException exception) {
            int count = sequence.getChemModelCount();
            boolean needMoreFiles = (cow.accepts(IChemModel.class)) && (count > 1);
            logger.info("Cannot write ChemSequence, recursing into ChemModel's.");
            for (int i=0; i < count; i++) {
                if (needMoreFiles) {
                    cow.close(); // possibly closing empty file
                    String fname = outputFilename + "." + (i+1);
                    FileWriter fileWriter = new FileWriter(new File(fname));
                    cow = getChemObjectWriter(this.oformat, fileWriter);
                }
                write(sequence.getChemModel(i), outputFilename);
            }
        }
    }

    private void write(IChemModel cm, String outputFilename) throws IOException {
        try {
            cow.write(cm);
        } catch (CDKException exception) {
            logger.info("Cannot write ChemModel, trying Crystal.");
            ICrystal crystal = cm.getCrystal();
            if (crystal != null) {
                write(crystal, outputFilename);
            }
            IMoleculeSet som = cm.getMoleculeSet();
            if (som != null) {
                write(som, outputFilename);
            }
        }
    }

    private void write(ICrystal c, String outputFilename) throws IOException {
        try {
            cow.write(c);
        } catch (CDKException exception) {
            logger.error("Cannot write Crystal: ", exception.getMessage());
        }
    }

    private void write(IMoleculeSet som, String outputFilename) throws IOException {
        try {
	        if (apply2DCleanup) {
				logger.info("Creating 2D coordinates");
				java.util.Iterator mols = som.molecules();
				StructureDiagramGenerator sdg = new StructureDiagramGenerator();
				while (mols.hasNext()) {
					IMolecule molecule = (IMolecule)mols.next();
		            try {
		                sdg.setMolecule(molecule, false); // false -> don't make clone!
		                sdg.generateCoordinates(new Vector2d(0, 1));
		                molecule = sdg.getMolecule();
		            } catch (Exception exception) {
		                System.out.println("Could not generate coordinates for this molecule.");
		                System.exit(1);
		            }
				}
			}
            cow.write(som);
        } catch (CDKException exception) {
            int count = som.getMoleculeCount();
            boolean needMoreFiles = (cow.accepts(IMoleculeSet.class)) && (count > 1);
            logger.info("Cannot write MoleculeSet, recursing into Molecules's.");
            for (int i=0; i < count; i++) {
                if (needMoreFiles) {
                    cow.close(); // possibly closing empty file
                    String fname = outputFilename + "." + (i+1);
                    FileWriter fileWriter = new FileWriter(new File(fname));
                    cow = getChemObjectWriter(this.oformat, fileWriter);
                }
                write(som.getMolecule(i), outputFilename);
            }
        }
    }

    private void write(IMolecule molecule, String outputFilename) throws IOException {
        try {
            cow.write(molecule);
        } catch (CDKException exception) {
            logger.error("Cannot write molecule: ", exception.getMessage());
            logger.debug(exception);
        }
    }
    
}