Examples with SMILESWriter org.openscience.cdk.io.SMILESWriter used on opensource projects

Example 1 with SMILESWriter

use of org.openscience.cdk.io.SMILESWriter in project ambit-mirror by ideaconsult.

the class FileOutputState method getWriter.

public static IChemObjectWriter getWriter(OutputStream stream, String ext) throws AmbitIOException {
    String fname = ext.toLowerCase();
    IChemObjectWriter writer = null;
    try {
        if (fname.endsWith(_FILE_TYPE.SDF_INDEX.getExtension())) {
            writer = new SDFWriter(stream);
        } else if (fname.endsWith(_FILE_TYPE.CSV_INDEX.getExtension()))
            writer = new DelimitedFileWriter(stream);
        else if ((fname.endsWith(_FILE_TYPE.TXT_INDEX.getExtension())))
            writer = new DelimitedFileWriter(stream, new DelimitedFileFormat("\t", '"'));
        else if ((fname.endsWith(_FILE_TYPE.SMI_INDEX.getExtension())))
            writer = new SMILESWriter(stream);
        else /*
			else if ((fname.endsWith(extensions[HTML_INDEX]))) 
				writer = new HTMLTableWriter(stream);
			else if ((fname.endsWith(extensions[JPG_INDEX]))) 			
				writer = new ImageWriter(stream);
			else if ((fname.endsWith(extensions[PNG_INDEX])))  
				writer = new ImageWriter(stream);
				*/
        if ((fname.endsWith(_FILE_TYPE.PDF_INDEX.getExtension()))) {
            try {
                writer = createWriterByReflection("ambit2.core.io.PDFWriter", stream);
            } catch (Exception x) {
                throw new AmbitIOException(x);
            }
        } else if ((fname.endsWith(_FILE_TYPE.XYZ_INDEX.getExtension())))
            writer = new XYZWriter(stream);
        else if ((fname.endsWith(_FILE_TYPE.HIN_INDEX.getExtension())))
            writer = new HINWriter(stream);
        else if ((fname.endsWith(_FILE_TYPE.MOL_INDEX.getExtension())))
            writer = new SDFWriter(stream);
        else if ((fname.endsWith(_FILE_TYPE.VW_INDEX.getExtension()))) {
            writer = new DelimitedFileWriter(stream, new DelimitedFileFormat("|", '"'));
            ((DelimitedFileWriter) writer).setAddSMILEScolumn(false);
        } else /*
			else if ((fname.endsWith(extensions[SVG_INDEX]))) 
				writer = new SVGWriter(stream);
				*/
        if ((fname.endsWith(_FILE_TYPE.XLS_INDEX.getExtension())))
            try {
                writer = createXLSXWriterByReflection("ambit2.core.io.XLSFileWriter", stream, true);
            } catch (Exception x) {
                throw new AmbitIOException(x);
            }
        else if ((fname.endsWith(_FILE_TYPE.XLSX_INDEX.getExtension())))
            try {
                writer = createXLSXWriterByReflection("ambit2.core.io.XLSFileWriter", stream, false);
            } catch (Exception x) {
                throw new AmbitIOException(x);
            }
        else
            throw new AmbitIOException(MSG_UNSUPPORTEDFORMAT + ext);
    } catch (Exception x) {
        // logger.error(MSG_ERRORSAVE,filename);
        throw new AmbitIOException(MSG_ERRORSAVE, x);
    }
    return writer;
}

Example 2 with SMILESWriter

use of org.openscience.cdk.io.SMILESWriter in project ambit-mirror by ideaconsult.

the class AutomaticTautomerTests method processNCILine.

int processNCILine(String line) {
    // System.out.println(line);
    List<String> tokens = filterTokens(line.split(" "));
    if (tokens.size() < 2) {
        System.out.println("Line " + curLine + "  has less than 2 tokens.");
        return (-1);
    }
    if (tokens.size() > 2) {
        System.out.println("Line " + curLine + "  has more than 2 tokens.");
    }
    try {
        // Create molecule from SMILES
        IAtomContainer mol = null;
        SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
        mol = sp.parseSmiles(tokens.get(1));
        // Generate new SMILES
        java.io.StringWriter result = new java.io.StringWriter();
        SMILESWriter writer = new SMILESWriter(result);
        writer.write(mol);
        writer.close();
        // System.out.println(tokens.get(1) + "  -->  " + result.toString());
        String smiles = result.toString();
        int dot_index = smiles.indexOf(".");
        if (dot_index == -1)
            output(smiles);
        else
            output(smiles.substring(0, dot_index));
    } catch (Exception e) {
    }
    return (0);
}

Example 3 with SMILESWriter

use of org.openscience.cdk.io.SMILESWriter in project ambit-mirror by ideaconsult.

the class VegaShell method transform_input.

@Override
protected synchronized IAtomContainer transform_input(IAtomContainer mol) throws ShellException {
    final String msg = "Empty molecule after %s processing";
    if ((mol == null) || (mol.getAtomCount() == 0))
        throw new ShellException(this, "Empty molecule");
    String homeDir = getHomeDir(null);
    File dir = new File(homeDir);
    if (!dir.exists()) {
        logger.log(Level.INFO, String.format("%s do not exist, mkdir", dir.getAbsolutePath()));
        dir.mkdirs();
    }
    String molfile = String.format("%s%s%s", homeDir, File.separator, inFile[1]);
    String predfile = String.format("%s%s%s", homeDir, File.separator, outFile[0]);
    try (SMILESWriter writer = new SMILESWriter(new FileOutputStream(molfile))) {
        writer.write(mol);
    } catch (Exception x) {
        throw new ShellException(this, x);
    }
    // reading the script from resource
    String script = null;
    try (InputStream in = VegaShell.class.getClassLoader().getResourceAsStream("ambit2/vega/script.xml")) {
        script = String.format(IOUtils.toString(in), molfile, predfile);
    } catch (Exception x) {
        throw new ShellException(this, x);
    }
    // writing the script with proper file name
    try (FileWriter writer = new FileWriter(new File(String.format("%s/%s", homeDir, inFile[0])))) {
        writer.write(script);
    } catch (Exception x) {
        throw new ShellException(this, String.format("Can't write Vega script! %s", x.getMessage()));
    }
    for (int i = 0; i < outFile.length; i++) {
        File file = new File(homeDir + "/" + outFile[i]);
        if (file.exists())
            file.delete();
    }
    return mol;
}