Example usage for java.lang Error Error

List of usage examples for java.lang Error Error

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Introduction

In this page you can find the example usage for java.lang Error Error.

Prototype

public Error(Throwable cause)

Source Link

Document

Constructs a new error with the specified cause and a detail message of (cause==null ?

Usage

From source file:edu.berkeley.compbio.phyloutils.NearestNodeFinder.java

public static void main(String[] argv) throws IOException, NoSuchNodeException {
    //service.setGreengenesRawFilename(argv[0]);
    service.setHugenholtzFilename(argv[0]);
    //service.setSynonymService(NcbiTaxonomyClient.getInstance());
    service.init();//w  w w.ja  v  a  2  s. c  o  m

    final int[] targetIds = IntArrayReader.read(argv[1]);
    int[] queryIds = IntArrayReader.read(argv[2]);
    final double minDistance = Double.parseDouble(argv[3]); // implement leave-one-out at any level

    Map<Integer, Double> results = Parallel.map(new ArrayIterator(queryIds), new Function<Integer, Double>() {
        public Double apply(Integer queryId) {
            try {
                double best = Double.MAX_VALUE;
                for (int targetId : targetIds) {
                    double d = service.minDistanceBetween(queryId, targetId);
                    if (d >= minDistance) {
                        best = Math.min(best, d);
                    }
                }
                return best;
            } catch (NoSuchNodeException e) {
                throw new Error(e);
            }
        }
    });

    String outfileName = argv[4];
    PrintWriter out = new PrintWriter(outfileName);
    out.println("id\tdist");

    for (Map.Entry<Integer, Double> entry : results.entrySet()) {
        out.println(entry.getKey() + "\t" + entry.getValue());
    }
    out.close();
}

From source file:com.genentech.struchk.sdfNormalizer.java

public static void main(String[] args) {
    long start = System.currentTimeMillis();
    int nMessages = 0;
    int nErrors = 0;
    int nStruct = 0;

    // create command line Options object
    Options options = new Options();
    Option opt = new Option("in", true, "input file [.ism,.sdf,...]");
    opt.setRequired(true);//from ww  w.j  a v  a 2s.c  o m
    options.addOption(opt);

    opt = new Option("out", true, "output file");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("mol", true, "molFile used for output: ORIGINAL(def)|NORMALIZED|TAUTOMERIC");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("shortMessage", false,
            "Limit message to first 80 characters to conform with sdf file specs.");
    opt.setRequired(false);
    options.addOption(opt);

    CommandLineParser parser = new PosixParser();
    CommandLine cmd;
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        exitWithHelp(options, e.getMessage());
        throw new Error(e); // avoid compiler errors
    }
    args = cmd.getArgs();

    if (args.length != 0) {
        System.err.print("Unknown options: " + args + "\n\n");
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("sdfNormalizer", options);
        System.exit(1);
    }

    String molOpt = cmd.getOptionValue("mol");
    OUTMolFormat outMol = OUTMolFormat.ORIGINAL;
    if (molOpt == null || "original".equalsIgnoreCase(molOpt))
        outMol = OUTMolFormat.ORIGINAL;
    else if ("NORMALIZED".equalsIgnoreCase(molOpt))
        outMol = OUTMolFormat.NORMALIZED;
    else if ("TAUTOMERIC".equalsIgnoreCase(molOpt))
        outMol = OUTMolFormat.TAUTOMERIC;
    else {
        System.err.printf("Unkown option for -mol: %s\n", molOpt);
        System.exit(1);
    }

    String inFile = cmd.getOptionValue("in");
    String outFile = cmd.getOptionValue("out");
    boolean limitMessage = cmd.hasOption("shortMessage");

    try {
        oemolistream ifs = new oemolistream(inFile);
        oemolostream ofs = new oemolostream(outFile);

        URL cFile = OEStruchk.getResourceURL(OEStruchk.class, "Struchk.xml");

        // create OEStruchk from config file
        OEStruchk strchk = new OEStruchk(cFile, CHECKConfig.ASSIGNStructFlag, false);

        OEGraphMol mol = new OEGraphMol();
        StringBuilder sb = new StringBuilder(2000);
        while (oechem.OEReadMolecule(ifs, mol)) {
            if (!strchk.applyRules(mol, null))
                nErrors++;

            switch (outMol) {
            case NORMALIZED:
                mol.Clear();
                oechem.OEAddMols(mol, strchk.getTransformedMol("parent"));
                break;
            case TAUTOMERIC:
                mol.Clear();
                oechem.OEAddMols(mol, strchk.getTransformedMol(null));
                break;
            case ORIGINAL:
                break;
            }

            oechem.OESetSDData(mol, "CTISMILES", strchk.getTransformedIsoSmiles(null));
            oechem.OESetSDData(mol, "CTSMILES", strchk.getTransformedSmiles(null));
            oechem.OESetSDData(mol, "CISMILES", strchk.getTransformedIsoSmiles("parent"));
            oechem.OESetSDData(mol, "Strutct_Flag", strchk.getStructureFlag().getName());

            List<Message> msgs = strchk.getStructureMessages(null);
            nMessages += msgs.size();
            for (Message msg : msgs)
                sb.append(String.format("\t%s:%s", msg.getLevel(), msg.getText()));
            if (limitMessage)
                sb.setLength(Math.min(sb.length(), 80));

            oechem.OESetSDData(mol, "NORM_MESSAGE", sb.toString());

            oechem.OEWriteMolecule(ofs, mol);

            sb.setLength(0);
            nStruct++;
        }
        strchk.delete();
        mol.delete();
        ifs.close();
        ifs.delete();
        ofs.close();
        ofs.delete();

    } catch (Exception e) {
        throw new Error(e);
    } finally {
        System.err.printf("sdfNormalizer: Checked %d structures %d errors, %d messages in %dsec\n", nStruct,
                nErrors, nMessages, (System.currentTimeMillis() - start) / 1000);
    }
}

From source file:MondrianService.java

public static void main(String[] arg) {
    System.out.println("Starting Mondrian Connector for Infoveave");
    Properties prop = new Properties();
    InputStream input = null;/*  w  w  w  . ja  v a2  s  . c  o  m*/
    int listenPort = 9998;
    int threads = 100;
    try {
        System.out.println("Staring from :" + getSettingsPath());
        input = new FileInputStream(getSettingsPath() + File.separator + "MondrianService.properties");
        prop.load(input);
        listenPort = Integer.parseInt(prop.getProperty("port"));
        threads = Integer.parseInt(prop.getProperty("maxThreads"));
        if (input != null) {
            input.close();
        }
        System.out.println("Found MondrianService.Properties");
    } catch (FileNotFoundException e) {
    } catch (IOException e) {
    }

    port(listenPort);
    threadPool(threads);
    enableCORS("*", "*", "*");

    ObjectMapper mapper = new ObjectMapper();
    MondrianConnector connector = new MondrianConnector();
    get("/ping", (request, response) -> {
        response.type("application/json");
        return "\"Here\"";
    });

    post("/cubes", (request, response) -> {
        response.type("application/json");
        try {
            Query queryObject = mapper.readValue(request.body(), Query.class);
            response.status(200);
            return mapper.writeValueAsString(connector.GetCubes(queryObject));
        } catch (JsonParseException ex) {
            response.status(400);
            return mapper.writeValueAsString(new Error(ex.getMessage()));
        } catch (Exception ex) {
            response.status(400);
            return mapper.writeValueAsString(new Error(ex.getMessage()));
        }
    });

    post("/measures", (request, response) -> {
        response.type("application/json");
        try {
            Query queryObject = mapper.readValue(request.body(), Query.class);
            response.status(200);
            return mapper.writeValueAsString(connector.GetMeasures(queryObject));
        } catch (JsonParseException ex) {
            response.status(400);
            return mapper.writeValueAsString(new Error(ex.getMessage()));
        } catch (Exception ex) {
            response.status(400);
            return mapper.writeValueAsString(new Error(ex.getMessage()));
        }
    });

    post("/dimensions", (request, response) -> {
        response.type("application/json");
        try {
            Query queryObject = mapper.readValue(request.body(), Query.class);
            response.status(200);
            return mapper.writeValueAsString(connector.GetDimensions(queryObject));
        } catch (JsonParseException ex) {
            response.status(400);
            return mapper.writeValueAsString(new Error(ex.getMessage()));
        } catch (Exception ex) {
            response.status(400);
            return mapper.writeValueAsString(new Error(ex.getMessage()));
        }
    });

    post("/cleanCache", (request, response) -> {
        response.type("application/json");
        try {
            Query queryObject = mapper.readValue(request.body(), Query.class);
            response.status(200);
            return mapper.writeValueAsString(connector.CleanCubeCache(queryObject));
        } catch (JsonParseException ex) {
            response.status(400);
            return mapper.writeValueAsString(new Error(ex.getMessage()));
        } catch (Exception ex) {
            response.status(400);
            return mapper.writeValueAsString(new Error(ex.getMessage()));
        }
    });

    post("/executeQuery", (request, response) -> {
        response.type("application/json");
        try {
            Query queryObject = mapper.readValue(request.body(), Query.class);
            response.status(200);
            String content = mapper.writeValueAsString(connector.ExecuteQuery2(queryObject));
            return content;
        } catch (JsonParseException ex) {
            response.status(400);
            return mapper.writeValueAsString(new Error(ex.getMessage()));
        } catch (Exception ex) {
            response.status(400);
            return mapper.writeValueAsString(new Error(ex.getMessage()));
        }
    });
}

From source file:com.genentech.chemistry.openEye.apps.SDFSubRMSD.java

public static void main(String... args) throws IOException { // create command line Options object
    Options options = new Options();
    Option opt = new Option("in", true, "input file oe-supported");
    opt.setRequired(true);/*from   w  ww. ja  v  a  2s .c o  m*/
    options.addOption(opt);

    opt = new Option("out", true, "output file oe-supported");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("fragFile", true, "file with single 3d substructure query");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("isMDL", false,
            "if given the fragFile is suposed to be an mdl query file, query features are supported.");
    opt.setRequired(false);
    options.addOption(opt);

    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        System.err.println(e.getMessage());
        exitWithHelp(options);
    }
    args = cmd.getArgs();

    if (cmd.hasOption("d")) {
        System.err.println("Start debugger and press return:");
        new BufferedReader(new InputStreamReader(System.in)).readLine();
    }

    String inFile = cmd.getOptionValue("in");
    String outFile = cmd.getOptionValue("out");
    String fragFile = cmd.getOptionValue("fragFile");

    // read fragment
    OESubSearch ss;
    oemolistream ifs = new oemolistream(fragFile);
    OEMolBase mol;
    if (!cmd.hasOption("isMDL")) {
        mol = new OEGraphMol();
        oechem.OEReadMolecule(ifs, mol);
        ss = new OESubSearch(mol, OEExprOpts.AtomicNumber, OEExprOpts.BondOrder);
    } else {
        int aromodel = OEIFlavor.Generic.OEAroModelOpenEye;
        int qflavor = ifs.GetFlavor(ifs.GetFormat());
        ifs.SetFlavor(ifs.GetFormat(), (qflavor | aromodel));
        int opts = OEMDLQueryOpts.Default | OEMDLQueryOpts.SuppressExplicitH;
        OEQMol qmol = new OEQMol();
        oechem.OEReadMDLQueryFile(ifs, qmol, opts);
        ss = new OESubSearch(qmol);
        mol = qmol;
    }

    double nSSatoms = mol.NumAtoms();
    double sssCoords[] = new double[mol.GetMaxAtomIdx() * 3];
    mol.GetCoords(sssCoords);
    mol.Clear();
    ifs.close();

    if (!ss.IsValid())
        throw new Error("Invalid query " + args[0]);

    ifs = new oemolistream(inFile);
    oemolostream ofs = new oemolostream(outFile);
    int count = 0;

    while (oechem.OEReadMolecule(ifs, mol)) {
        count++;
        double rmsd = Double.MAX_VALUE;
        double molCoords[] = new double[mol.GetMaxAtomIdx() * 3];
        mol.GetCoords(molCoords);

        for (OEMatchBase mb : ss.Match(mol, false)) {
            double r = 0;
            for (OEMatchPairAtom mp : mb.GetAtoms()) {
                OEAtomBase asss = mp.getPattern();
                double sx = sssCoords[asss.GetIdx() * 3];
                double sy = sssCoords[asss.GetIdx() * 3];
                double sz = sssCoords[asss.GetIdx() * 3];

                OEAtomBase amol = mp.getTarget();
                double mx = molCoords[amol.GetIdx() * 3];
                double my = molCoords[amol.GetIdx() * 3];
                double mz = molCoords[amol.GetIdx() * 3];

                r += Math.sqrt((sx - mx) * (sx - mx) + (sy - my) * (sy - my) + (sz - mz) * (sz - mz));
            }
            r /= nSSatoms;
            rmsd = Math.min(rmsd, r);
        }

        if (rmsd != Double.MAX_VALUE)
            oechem.OESetSDData(mol, "SSSrmsd", String.format("%.3f", rmsd));

        oechem.OEWriteMolecule(ofs, mol);
        mol.Clear();
    }

    ifs.close();
    ofs.close();

    mol.delete();
    ss.delete();
}

From source file:com.genentech.struchk.OEMDLPercieveChecker.java

public static void main(String[] args) throws ParseException, JDOMException, IOException {
    // create command line Options object
    Options options = new Options();
    Option opt = new Option("i", true, "input file [.ism,.sdf,...]");
    opt.setRequired(true);/*from  w w  w.j  av  a  2s.c o  m*/
    options.addOption(opt);

    opt = new Option("o", true, "output file");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("d", false, "debug: wait for user to press key at startup.");
    opt.setRequired(false);
    options.addOption(opt);

    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        System.err.println(e.getMessage());
        exitWithHelp(options);
    }
    args = cmd.getArgs();

    if (cmd.hasOption("d")) {
        System.err.println("Start debugger and press return:");
        new BufferedReader(new InputStreamReader(System.in)).readLine();
    }

    if (args.length != 0) {
        exitWithHelp(options);
    }

    String inFile = cmd.getOptionValue("i");
    String outFile = cmd.getOptionValue("o");

    OEMDLPercieveChecker checker = null;
    try {
        checker = new OEMDLPercieveChecker();

        oemolostream out = new oemolostream(outFile);
        oemolistream in = new oemolistream(inFile);

        OEGraphMol mol = new OEGraphMol();
        while (oechem.OEReadMolecule(in, mol)) {
            if (!checker.checkMol(mol))
                oechem.OEWriteMolecule(out, mol);
        }
        checker.delete();
        in.close();
        in.delete();

        out.close();
        out.delete();

    } catch (Exception e) {
        throw new Error(e);
    }
    System.err.println("Done:");
}

From source file:com.genentech.retrival.tabExport.TABExporter.java

public static void main(String[] args) throws ParseException, JDOMException, IOException {
    long start = System.currentTimeMillis();
    int nStruct = 0;

    // create command line Options object
    Options options = new Options();
    Option opt = new Option("sqlFile", true, "sql-xml file");
    opt.setRequired(true);/* w w  w  .  j  av  a2 s  . c o  m*/
    options.addOption(opt);

    opt = new Option("sqlName", true, "name of SQL element in xml file");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("o", true, "output file");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("newLineReplacement", true,
            "If given newlines in fields will be replaced by this string.");
    options.addOption(opt);

    opt = new Option("noHeader", false, "Do not output header line");
    options.addOption(opt);

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        System.err.println(e.getMessage());
        exitWithHelp(options);
    }
    args = cmd.getArgs();

    String outFile = cmd.getOptionValue("o");
    String sqlFile = cmd.getOptionValue("sqlFile");
    String sqlName = cmd.getOptionValue("sqlName");
    String newLineReplacement = cmd.getOptionValue("newLineReplacement");

    args = cmd.getArgs();

    try {
        PrintStream out = System.out;
        if (outFile != null)
            out = new PrintStream(outFile);

        SQLStatement stmt = SQLStatement.createFromFile(new File(sqlFile), sqlName);
        Object[] sqlArgs = args;
        if (stmt.getParamTypes().length != args.length) {
            System.err.printf(
                    "\nWarining sql statement needs %d parameters but got only %d. Filling up with NULLs.\n",
                    stmt.getParamTypes().length, args.length);
            sqlArgs = new Object[stmt.getParamTypes().length];
            System.arraycopy(args, 0, sqlArgs, 0, args.length);
        }

        Selecter sel = Selecter.factory(stmt);
        if (!sel.select(sqlArgs)) {
            System.err.println("No rows returned!");
            System.exit(0);
        }

        String[] fieldNames = sel.getFieldNames();
        if (fieldNames.length == 0) {
            System.err.println("Query did not return any columns");
            exitWithHelp(options);
        }

        if (!cmd.hasOption("noHeader")) {
            StringBuilder sb = new StringBuilder(200);
            for (String f : fieldNames)
                sb.append(f).append('\t');
            if (sb.length() > 1)
                sb.setLength(sb.length() - 1); // chop last \t
            String header = sb.toString();

            out.println(header);
        }

        StringBuilder sb = new StringBuilder(200);
        while (sel.hasNext()) {
            Record sqlRec = sel.next();
            sb.setLength(0);

            for (int i = 0; i < fieldNames.length; i++) {
                String fld = sqlRec.getStrg(i);
                if (newLineReplacement != null)
                    fld = NEWLinePattern.matcher(fld).replaceAll(newLineReplacement);

                sb.append(fld).append('\t');
            }

            if (sb.length() > 1)
                sb.setLength(sb.length() - 1); // chop last \t
            String row = sb.toString();

            out.println(row);

            nStruct++;
        }

    } catch (Exception e) {
        throw new Error(e);
    } finally {
        System.err.printf("TABExporter: Exported %d records in %dsec\n", nStruct,
                (System.currentTimeMillis() - start) / 1000);
    }
}

From source file:com.genentech.chemistry.tool.align.SDFAlign.java

public static void main(String... args) {
    Options options = new Options();
    Option opt = new Option("in", true, "input sd file");
    opt.setRequired(true);//from  www.  j a v a 2 s .  c o  m
    options.addOption(opt);

    opt = new Option("out", true, "output file");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("method", true, "fss|sss|MCS|clique (default mcs).");
    options.addOption(opt);

    opt = new Option("ref", true,
            "reference molecule if not given first in file is used. If multiple ref molecules are read the min RMSD is reported");
    options.addOption(opt);

    opt = new Option("mirror", false, "If given and the molecule is not chiral, return best mirror image.");
    options.addOption(opt);

    opt = new Option("rmsdTag", true, "Tagname for output of rmsd, default: no output.");
    options.addOption(opt);

    opt = new Option("atomMatch", true,
            "Sequence of none|default|hcount|noAromatic specifing how atoms are matched cf. oe document.\n"
                    + "noAromatic can be used to make terminal atoms match aliphatic and aromatic atoms.\n"
                    + "Queryfeatures are considered only if default is used.");
    options.addOption(opt);

    opt = new Option("bondMatch", true,
            "Sequence of none|default specifing how bonds are matched cf. oe document.");
    options.addOption(opt);

    opt = new Option("keepCoreHydrogens", false,
            "If not specified the hydrigen atoms are removed from the core.");
    options.addOption(opt);

    opt = new Option("outputMol", true, "aligned|original (def: aligned) use original to just compute rmsd.");
    options.addOption(opt);

    opt = new Option("doNotOptimize", false,
            "If specified the RMSD is computed without moving optimizing the overlay.");
    options.addOption(opt);

    opt = new Option("quiet", false, "Reduced warining messages");
    options.addOption(opt);

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        exitWithHelp(e.getMessage(), options);
    }

    if (cmd.getArgs().length > 0)
        exitWithHelp("To many arguments", options);

    // do not check aromaticity on atoms so that a terminal atom matches aromatic and non aromatic atoms
    int atomExpr = OEExprOpts.DefaultAtoms;
    int bondExpr = OEExprOpts.DefaultBonds;

    String atomMatch = cmd.getOptionValue("atomMatch");
    if (atomMatch == null)
        atomMatch = "";
    atomMatch = '|' + atomMatch.toLowerCase() + '|';

    String bondMatch = cmd.getOptionValue("bondMatch");
    if (bondMatch == null)
        bondMatch = "";
    bondMatch = '|' + bondMatch.toLowerCase() + '|';

    String inFile = cmd.getOptionValue("in");
    String outFile = cmd.getOptionValue("out");
    String refFile = cmd.getOptionValue("ref");
    String method = cmd.getOptionValue("method");
    String rmsdTag = cmd.getOptionValue("rmsdTag");
    String oMol = cmd.getOptionValue("outputMol");
    boolean doMirror = cmd.hasOption("mirror");
    boolean doOptimize = !cmd.hasOption("doNotOptimize");
    boolean quiet = cmd.hasOption("quiet");

    OUTType outputMol = oMol == null ? OUTType.ALIGNED : OUTType.valueOf(oMol.toUpperCase());

    if (atomMatch.startsWith("|none"))
        atomExpr = 0;
    if (atomMatch.contains("|hcount|"))
        atomExpr |= OEExprOpts.HCount;
    if (atomMatch.contains("|noAromatic|"))
        atomExpr &= (~OEExprOpts.Aromaticity);

    if (bondMatch.startsWith("|none"))
        bondExpr = 0;

    ArrayList<OEMol> refmols = new ArrayList<OEMol>();
    if (refFile != null) {
        oemolistream reffs = new oemolistream(refFile);
        if (!is3DFormat(reffs.GetFormat()))
            oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates");
        reffs.SetFormat(OEFormat.MDL);

        int aromodel = OEIFlavor.Generic.OEAroModelOpenEye;
        int qflavor = reffs.GetFlavor(reffs.GetFormat());
        reffs.SetFlavor(reffs.GetFormat(), (qflavor | aromodel));

        OEMol rmol = new OEMol();
        while (oechem.OEReadMDLQueryFile(reffs, rmol)) {
            if (!cmd.hasOption("keepCoreHydrogens"))
                oechem.OESuppressHydrogens(rmol);
            refmols.add(rmol);
            rmol = new OEMol();
        }
        rmol.delete();

        if (refmols.size() == 0)
            throw new Error("reference file had no entries");

        reffs.close();
    }

    oemolistream fitfs = new oemolistream(inFile);
    if (!is3DFormat(fitfs.GetFormat()))
        oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates");

    oemolostream ofs = new oemolostream(outFile);
    if (!is3DFormat(ofs.GetFormat()))
        oechem.OEThrow.Fatal("Invalid output format: need 3D coordinates");

    AlignInterface aligner = null;
    OEGraphMol fitmol = new OEGraphMol();

    if (oechem.OEReadMolecule(fitfs, fitmol)) {
        if (refmols.size() == 0) {
            OEMol rmol = new OEMol(fitmol);
            if (!cmd.hasOption("keepCoreHydrogens"))
                oechem.OESuppressHydrogens(rmol);

            refmols.add(rmol);
        }

        if ("sss".equalsIgnoreCase(method)) {
            aligner = new SSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr,
                    quiet);

        } else if ("clique".equalsIgnoreCase(method)) {
            aligner = new CliqueAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr,
                    quiet);

        } else if ("fss".equalsIgnoreCase(method)) {
            if (cmd.hasOption("atomMatch") || cmd.hasOption("bondMatch"))
                exitWithHelp("method fss does not support '-atomMatch' or '-bondMatch'", options);
            aligner = new FSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror);

        } else {
            aligner = new McsAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr,
                    quiet);
        }

        do {
            aligner.align(fitmol);
            oechem.OEWriteMolecule(ofs, fitmol);
        } while (oechem.OEReadMolecule(fitfs, fitmol));

    }

    fitmol.delete();
    if (aligner != null)
        aligner.close();
    for (OEMolBase mol : refmols)
        mol.delete();
    fitfs.close();
    ofs.close();
}

From source file:com.genentech.chemistry.tool.SDFFilter.java

public static void main(String args[]) {
    String usage = "java sdfFilter [options]\n" + "Filters out molecules that contain the following:\n"
            + "1. More than maxHeavy atoms (default is 100)\n" + "2. Have more than one component\n"
            + "3. Does not have any atoms\n" + "4. Have invalid atoms, like R, * etc ...\n"
            + "5. Have atomic number greater than 53 (Iodine)";

    // create Options object
    Options options = new Options();
    // add  options
    options.addOption("h", false, "");
    options.addOption("in", true, "inFile in OE formats: Ex: a.sdf or .sdf");
    options.addOption("out", true, "outFile in OE formats. Ex: a.sdf or .sdf");
    options.addOption("filtered", true, "Optional: filteredFile in OE formats. Ex: a.sdf or .sdf");
    options.addOption("maxHeavy", true, "Number of heavy atom cutoff. Default is 100");
    CommandLineParser parser = new PosixParser();

    try {//  w w  w .  j a v  a2 s .  com
        CommandLine cmd = parser.parse(options, args);
        String inFile = cmd.getOptionValue("in");
        if (inFile == null) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp(usage, options);
            System.exit(1);
        }

        String outFile = cmd.getOptionValue("out");
        if (outFile == null) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp(usage, options);
            System.exit(1);
        }

        String filteredFile = null;
        if (cmd.hasOption("filtered")) {
            filteredFile = cmd.getOptionValue("filtered");
        }

        int maxHeavy = 100;
        if (cmd.hasOption("maxHeavy")) {
            maxHeavy = Integer.parseInt(cmd.getOptionValue("maxHeavy"));
            maxAtoms = maxHeavy;
        }

        if (cmd.hasOption("h")) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp(usage, options);
            System.exit(1);
        }

        oemolistream ifs = new oemolistream(inFile);
        oemolostream ofs = new oemolostream(outFile);
        oemolostream ffs = null;
        if (filteredFile != null) {
            ffs = new oemolostream(filteredFile);
        }
        /*it appears that we don't have license to molprop toolkit
        oeisstream iss = new oeisstream();
        OEFilter filter = new OEFilter(iss);
        filter.SetTypeCheck(true);
        oechem.OEThrow.SetLevel(OEErrorLevel.Warning);
        */

        OEGraphMol mol = new OEGraphMol();

        while (oechem.OEReadMolecule(ifs, mol)) {
            //            if (passFilters(mol, filter)) { //needs license to molprop toolkit
            if (passFilters(mol)) {
                oechem.OEWriteMolecule(ofs, mol);
            } else {
                if (ffs != null) {
                    oechem.OEWriteMolecule(ffs, mol);
                }
            }
        }

    } catch (ParseException e) { // TODO print explaination
        throw new Error(e);
    }
}

From source file:Main.java

public static String URLEncode(String string) {
    try {//from www  .jav a 2  s.c o  m
        return URLEncoder.encode(string, "UTF-8");
    } catch (UnsupportedEncodingException e) {
        throw new Error(e.getMessage());
    }
}

From source file:Main.java

public static void assertSwingThread() {
    if (!SwingUtilities.isEventDispatchThread())
        throw new Error("Must be Swing event dispatching thread, but detected '"
                + Thread.currentThread().getName() + '\'');
}