Examples with SMIRKSProcessor ambit2.smarts.processors.SMIRKSProcessor used on opensource projects

Example 1 with SMIRKSProcessor

use of ambit2.smarts.processors.SMIRKSProcessor in project ambit-mirror by ideaconsult.

the class StdzBatchProcessor method process.

@Override
public IStructureRecord process(IStructureRecord record) throws Exception {
    IAtomContainer mol;
    IAtomContainer processed = null;
    try {
        mol = molReader.process(record);
        if (mol != null) {
            for (Property p : record.getRecordProperties()) {
                Object v = record.getRecordProperty(p);
                // already parsed
                if (tags_to_keep != null && Arrays.binarySearch(tags_to_keep, p.getName()) < 0)
                    continue;
                if (p.getName().startsWith("http://www.opentox.org/api/1.1#"))
                    continue;
                else
                    mol.setProperty(p, v);
            }
            if (tags_to_keep != null) {
                List<String> toRemove = null;
                Iterator pi = mol.getProperties().keySet().iterator();
                while (pi.hasNext()) {
                    Object p = pi.next();
                    if (Arrays.binarySearch(tags_to_keep, p.toString()) < 0) {
                        if (toRemove == null)
                            toRemove = new ArrayList<String>();
                        toRemove.add(p.toString());
                    }
                }
                if (toRemove != null)
                    for (String propertyToRemove : toRemove) mol.removeProperty(propertyToRemove);
            }
        } else {
            logger.log(Level.SEVERE, "MSG_STANDARDIZE", new Object[] { "Empty molecule See the ERROR tag in the output file", getIds(record) });
            return record;
        }
    } catch (Exception x) {
        x.printStackTrace();
        logger.log(Level.SEVERE, "MSG_ERR_MOLREAD", new Object[] { getIds(record), x.toString() });
        return record;
    } finally {
    }
    processed = mol;
    // CDK adds these for the first MOL line
    if (!writesdf) {
        // mol.removeProperty(CDKConstants.TITLE);
        if (mol.getProperty(CDKConstants.REMARK) != null)
            mol.removeProperty(CDKConstants.REMARK);
    }
    if ((smirksProcessor != null) && smirksProcessor.isEnabled()) {
        processed = smirksProcessor.process(processed);
    }
    try {
        processed = standardprocessor.process(processed);
    } catch (Exception x) {
        String err = processed.getProperty(StructureStandardizer.ERROR_TAG);
        logger.log(Level.SEVERE, x.getMessage(), x);
        if (processed != null) {
            err = processed.getProperty(StructureStandardizer.ERROR_TAG);
            processed.setProperty(StructureStandardizer.ERROR_TAG, String.format("%s %s %s", err == null ? "" : err, x.getClass().getName(), x.getMessage()));
        }
    } finally {
        if (processed != null) {
            Iterator<Entry<Object, Object>> p = mol.getProperties().entrySet().iterator();
            // molecule
            while (p.hasNext()) {
                Entry<Object, Object> entry = p.next();
                Object value = processed.getProperty(entry.getKey());
                if (value == null || "".equals(value.toString().trim()))
                    processed.setProperty(entry.getKey(), entry.getValue());
            }
        }
    }
    if (processed != null)
        try {
            if (writesdf && sdf_title != null) {
                for (Entry<Object, Object> p : processed.getProperties().entrySet()) if (sdf_title.equals(p.getKey().toString().toLowerCase())) {
                    processed.setProperty(CDKConstants.TITLE, p.getValue());
                    break;
                }
            }
            if (debugatomtypes) {
                Object debug = (processed == null) ? null : processed.getProperty("AtomTypes");
                if (debug != null && !"".equals(debug))
                    writer.write(processed);
            } else
                writer.write(processed);
        } catch (Exception x) {
            logger.log(Level.SEVERE, x.getMessage());
        }
    return record;
}

Example 2 with SMIRKSProcessor

use of ambit2.smarts.processors.SMIRKSProcessor in project ambit-mirror by ideaconsult.

the class SmirksProcessorTest method test.

@Test
public void test() throws Exception {
    URL config = this.getClass().getClassLoader().getResource("ambit2/smirks/smirks.json");
    SMIRKSProcessor p = new SMIRKSProcessor(logger);
    p.setLoadExamples(true);
    p.loadReactionsFromJSON(new File(config.getFile()));
    p.setTransformationasproperties(true);
    Assert.assertEquals(51, p.getTransformations().size());
    Assert.assertFalse(p.isAtomtypeasproperties());
    p.setAtomtypeasproperties(true);
    SMIRKSManager m = new SMIRKSManager(SilentChemObjectBuilder.getInstance());
    SmilesParser parser = new SmilesParser(SilentChemObjectBuilder.getInstance());
    for (SMIRKSTransformation t : p.getTransformations()) {
        if (t.getExample() != null) {
            IAtomContainer mol = parser.parseSmiles(t.getExample());
            Assert.assertNotNull(mol);
            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
            mol = p.process(mol);
            logger.log(Level.INFO, String.format("%s\t%s", t.getName(), mol.getProperties()));
            Assert.assertNotNull(String.format("%s\t%s", t.getName(), t.getExample()), mol.getProperty("Transformed"));
            Assert.assertTrue((int) mol.getProperty("Transformed") > 0);
            Assert.assertEquals(1, (int) mol.getProperty("T." + t.getName()));
            Object atomsadded = mol.getProperty("AtomTypes.added");
            if (atomsadded != null)
                Assert.assertEquals("[]", mol.getProperty("AtomTypes.added").toString());
        }
    }
}

Example 3 with SMIRKSProcessor

use of ambit2.smarts.processors.SMIRKSProcessor in project ambit-mirror by ideaconsult.

the class AmbitPipeline method parseCommandStandardize.

public void parseCommandStandardize(String subcommand, long now) throws Exception {
    int page = parsePageParam();
    int pagesize = parsePageSizeParam();
    Object tmpTag = parseSdfTitleParam();
    String smiles_header = parseInputTag_Param("smiles", IteratingDelimitedFileReader.defaultSMILESHeader);
    String inchi_header = parseInputTag_Param("inchi", "InChI");
    String inchikey_header = parseInputTag_Param("inchikey", "InChIKey");
    final String sdf_title = tmpTag == null ? null : tmpTag.toString().toLowerCase();
    final StructureStandardizer standardprocessor = new StructureStandardizer(logger_cli);
    standardprocessor.setGenerate2D(parseBooleanParam(":generate2D", false));
    standardprocessor.setGenerateTautomers(parseBooleanParam(":tautomers", false));
    SMIRKSProcessor tmp = null;
    try {
        Object o = options.getParam(":smirks");
        if (o != null) {
            File smirksConfig = new File(o.toString());
            if (smirksConfig.exists()) {
                tmp = new SMIRKSProcessor(smirksConfig, logger_cli);
                tmp.setEnabled(true);
            } else
                logger_cli.log(Level.WARNING, "SMIRKS transformation file not found");
        }
    } catch (Exception x) {
        logger_cli.log(Level.SEVERE, x.getMessage());
        tmp = null;
    }
    final SMIRKSProcessor smirksProcessor = tmp;
    standardprocessor.setSplitFragments(parseBooleanParam(":splitfragments", false));
    standardprocessor.setImplicitHydrogens(parseBooleanParam(":implicith", false));
    standardprocessor.setNeutralise(parseBooleanParam(":neutralise", false));
    final String[] tags_to_keep = parsetags_to_keep();
    standardprocessor.setRankTag(parseStringParam(":tag_rank", "RANK"));
    standardprocessor.setInchiTag(parseStringParam(":tag_inchi", "InChI"));
    standardprocessor.setInchiKeyTag(parseStringParam(":tag_inchikey", "InChIKey"));
    standardprocessor.setSMILESTag(parseStringParam(":tag_smiles", "SMILES"));
    standardprocessor.setGenerateInChI(parseBooleanParam(":inchi", true));
    standardprocessor.setGenerateSMILES(parseBooleanParam(":smiles", true));
    standardprocessor.setGenerateSMILES_Canonical(parseBooleanParam(":smilescanonical", false));
    standardprocessor.setGenerateSMILES_Aromatic(parseBooleanParam(":smilesaromatic", false));
    standardprocessor.setGenerateStereofrom2D(parseBooleanParam(":generatestereofrom2d", false));
    standardprocessor.setClearIsotopes(parseBooleanParam(":setClearIsotopes", false));
    final boolean debugatomtypes = parseBooleanParam(":debugatomtypes", false);
    final int startRecord = pagesize > 0 ? (page * pagesize + 1) : 1;
    final int maxRecord = pagesize > 0 ? ((page + 1) * pagesize + 1) : pagesize;
    final File file = getInputFile();
    FileInputState in = new FileInputState(file);
    in.setOptionalInChIHeader(inchi_header);
    in.setOptionalInChIKeyHeader(inchikey_header);
    in.setOptionalSMILESHeader(smiles_header);
    if (options.output == null)
        throw new FileNotFoundException("Output file not specified. Please use -o {file}");
    final File outfile = new File(options.output);
    logger_cli.log(Level.INFO, "MSG_INFO_READINGWRITING", new Object[] { file.getAbsoluteFile(), outfile.getAbsolutePath() });
    FileOutputState out = new FileOutputState(outfile);
    final IChemObjectWriter writer = out.getWriter();
    if (writer instanceof FilesWithHeaderWriter)
        ((FilesWithHeaderWriter) writer).setAddSMILEScolumn(false);
    final BatchDBProcessor<IStructureRecord> batch = new BatchDBProcessor<IStructureRecord>() {

        @Override
        public void onItemRead(IStructureRecord input, IBatchStatistics stats) {
            super.onItemRead(input, stats);
            if ((maxRecord > 0) && stats.getRecords(RECORDS_STATS.RECORDS_READ) >= (maxRecord))
                cancel();
        }

        @Override
        public boolean skip(IStructureRecord input, IBatchStatistics stats) {
            return (stats.getRecords(RECORDS_STATS.RECORDS_READ) < startRecord) || ((maxRecord > 0) && (stats.getRecords(RECORDS_STATS.RECORDS_READ) >= maxRecord));
        }

        @Override
        public void onItemSkipped(IStructureRecord input, IBatchStatistics stats) {
            super.onItemSkipped(input, stats);
            if (stats.isTimeToPrint(getSilentInterval() * 2))
                propertyChangeSupport.firePropertyChange(PROPERTY_BATCHSTATS, null, stats);
        }

        @Override
        public void onItemProcessing(IStructureRecord input, Object output, IBatchStatistics stats) {
        }

        @Override
        public void onError(IStructureRecord input, Object output, IBatchStatistics stats, Exception x) {
            super.onError(input, output, stats, x);
            logger_cli.log(Level.SEVERE, x.getMessage());
        }

        @Override
        public long getSilentInterval() {
            return 30000L;
        }

        @Override
        public void close() throws Exception {
            try {
                writer.close();
            } catch (Exception x) {
            } finally {
            }
            super.close();
        }
    };
    batch.setProcessorChain(new ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor>());
    batch.getProcessorChain().add(new StdzBatchProcessor(standardprocessor, smirksProcessor, tags_to_keep, logger_cli, writer, sdf_title, debugatomtypes));
    batch.addPropertyChangeListener(new PropertyChangeListener() {

        @Override
        public void propertyChange(PropertyChangeEvent evt) {
            if (AbstractBatchProcessor.PROPERTY_BATCHSTATS.equals(evt.getPropertyName()))
                logger_cli.log(Level.INFO, evt.getNewValue().toString());
        }
    });
    /*
		 * standardprocessor.setCallback(new
		 * DefaultAmbitProcessor<IAtomContainer, IAtomContainer>() {
		 * 
		 * @Override public IAtomContainer process(IAtomContainer target) throws
		 * Exception { try { //writer.write(target); } catch (Exception x) {
		 * logger.log(Level.SEVERE, x.getMessage()); } return target; } });
		 */
    IBatchStatistics stats = null;
    try {
        stats = batch.process(in);
    } catch (Exception x) {
        StringWriter w = new StringWriter();
        x.printStackTrace(new PrintWriter(w));
        logger_cli.log(Level.WARNING, "MSG_ERR", new Object[] { x.getMessage() });
        logger_cli.log(Level.FINE, "MSG_ERR_DEBUG", new Object[] { x.getMessage(), w.toString() });
    } finally {
        try {
            if (batch != null)
                batch.close();
        } catch (Exception x) {
            logger_cli.log(Level.WARNING, "MSG_ERR", new Object[] { x.getMessage() });
        }
        if (stats != null)
            logger_cli.log(Level.INFO, "MSG_INFO", new Object[] { stats.toString() });
    }
}