Examples with AmbitException net.idea.modbcum.i.exceptions.AmbitException used on opensource projects

Example 21 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class AbstractFinder method process.

@Override
public IStructureRecord process(IStructureRecord target) throws AmbitException {
    try {
        if (target == null)
            return null;
        if ((AbstractFinder.MODE.emptyonly.equals(mode) || AbstractFinder.MODE.emptyadd.equals(mode)) && !STRUC_TYPE.NA.equals(target.getType()))
            return null;
        Iterator<Property> keys = profile.getProperties(true);
        Object value = null;
        while (keys.hasNext()) {
            Property key = keys.next();
            try {
                value = retrieveValue(target, key);
                if ((value == null) || "".equals(value.toString().trim()))
                    continue;
                RESULT content = query(value.toString());
                if (content != null) {
                    STRUC_TYPE originalType = target.getType();
                    target = transform(target, content);
                    switch(mode) {
                        case emptyonly:
                            {
                                if (!STRUC_TYPE.NA.equals(originalType)) {
                                    target.setIdstructure(-1);
                                }
                                break;
                            }
                        case emptyadd:
                            {
                                target.setIdstructure(-1);
                                target.setUsePreferedStructure(false);
                                break;
                            }
                        case replace:
                            {
                                target.setUsePreferedStructure(false);
                                break;
                            }
                        case propertyonly:
                            {
                                break;
                            }
                        default:
                            // add
                            target.setIdstructure(-1);
                            target.setUsePreferedStructure(false);
                            break;
                    }
                    return target;
                }
            } catch (HttpException x) {
                if (x.getCode() == 404)
                    logger.log(Level.WARNING, value == null ? x.getMessage() : value.toString(), x);
            } catch (Exception x) {
                logger.log(Level.SEVERE, value == null ? x.getMessage() : value.toString(), x);
            }
        }
    } catch (Exception x) {
        logger.log(Level.SEVERE, x.getMessage(), x);
    }
    return null;
}

Example 22 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class DXParser method verifyDXProperty.

protected Property verifyDXProperty(Property property, Object value, ILiteratureEntry reference) throws AmbitException {
    property.setReference(reference);
    String[] split = property.getName().split("\\.");
    JsonNode endpoint = (split.length > 1) ? dxRoot.get(json_fields.endpoints.name()).get(split[1]) : null;
    JsonNode superEndpoint = endpoint == null ? null : endpoint.get("super");
    JsonNode species = (split.length > 2) ? dxRoot.get(json_fields.species.name()).get(split[2]) : null;
    if (species == null)
        return null;
    JsonNode ontology = null;
    PropertyAnnotations pa = new PropertyAnnotations();
    if (species != null) {
        PropertyAnnotation a = new PropertyAnnotation();
        a.setPredicate("species");
        a.setObject(split[2]);
        pa.add(a);
    }
    if (superEndpoint != null) {
        PropertyAnnotation a = new PropertyAnnotation();
        a.setPredicate("DX Superendpoint");
        a.setObject(superEndpoint.textValue());
        pa.add(a);
        try {
            ontology = dxRoot.get(json_fields.endpoints.name()).get(superEndpoint.textValue()).get(json_fields.ot.name());
        } catch (Exception x) {
            logger.log(Level.WARNING, x.getClass().getName() + " " + superEndpoint);
        }
    }
    if (endpoint != null) {
        PropertyAnnotation a = new PropertyAnnotation();
        a.setPredicate("DX endpoint");
        a.setObject(split[1]);
        pa.add(a);
        try {
            if (endpoint.get(json_fields.ot.name()) != null)
                ontology = endpoint.get(json_fields.ot.name());
        } catch (Exception x) {
            logger.log(Level.WARNING, x.getClass().getName() + " " + endpoint);
        }
    }
    if (ontology != null)
        property.setLabel(ontology.textValue());
    for (PropertyAnnotation a : categories) pa.add(a);
    property.setAnnotations(pa);
    return property;
}

Example 23 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class Structure2DBuilder method process.

@Override
public IAtomContainer process(IAtomContainer molecule) throws AmbitException {
    if (molecule == null)
        return null;
    if (molecule.getAtomCount() == 1) {
        molecule.getAtom(0).setPoint2d(new Point2d(new double[] { 0.0001, 0.0001 }));
        return molecule;
    } else {
        IAtomContainerSet molecules = ConnectivityChecker.partitionIntoMolecules(molecule);
        IAtomContainer newmol = MoleculeTools.newAtomContainer(molecules.getBuilder());
        for (int i = 0; i < molecules.getAtomContainerCount(); i++) {
            IAtomContainer c = molecules.getAtomContainer(i);
            sdg.setMolecule((IAtomContainer) c, false);
            try {
                sdg.generateCoordinates(new Vector2d(0, 1));
                newmol.add(sdg.getMolecule());
            } catch (Exception x) {
                for (IAtom atom : c.atoms()) atom.setPoint2d(new Point2d(new double[] { 0.0001, 0.0001 }));
                newmol.add(c);
            }
        }
        return newmol;
    }
}

Example 24 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class StructureNormalizer method process.

public IStructureRecord process(IStructureRecord structure) throws AmbitException {
    if ((structure.getFormat() != null) && MOL_TYPE.NANO.name().equals(structure.getFormat())) {
        try {
            // fields
            return structure;
        /*
				 * Class clazz =
				 * FileInputState.class.getClassLoader().loadClass(
				 * "net.idea.ambit2.nano.NanoStructureNormalizer"); Method
				 * method = clazz.getMethod("normalizeNano",
				 * IStructureRecord.class); return (IStructureRecord)
				 * method.invoke(null, structure);
				 */
        } catch (Exception x) {
            if (x instanceof AmbitException)
                throw (AmbitException) x;
            else
                throw new AmbitException(x);
        }
    }
    // else process as chemical
    IAtomContainer molecule = molReader.process(structure);
    if ((molecule != null) && (molecule.getProperties() != null))
        structure.addRecordProperties(molecule.getProperties());
    if ((molecule == null) || (molecule.getAtomCount() == 0))
        structure.setType(STRUC_TYPE.NA);
    else {
        structure.setType(strucType.process(molecule));
        if (build2D)
            try {
                IAtomContainer newmol = build2d(molecule, structure.getType());
                if (newmol != null) {
                    molecule = newmol;
                    StringWriter w = new StringWriter();
                    SDFWriter writer = new SDFWriter(w);
                    try {
                        writer.write(molecule);
                    } catch (Exception x) {
                        logger.log(Level.WARNING, x.getMessage());
                    } finally {
                        writer.close();
                    }
                    structure.setType(strucType.process(molecule));
                    structure.setContent(w.toString());
                    structure.setFormat(MOL_TYPE.SDF.name());
                }
            } catch (Exception x) {
            }
    }
    try {
        if ((molecule != null) && (molecule.getAtomCount() > 0)) {
            structure.setSmiles(smilesKey.process(molecule));
            if ("".equals(structure.getSmiles()))
                structure.setSmiles(null);
        }
    } catch (Exception x) {
        logger.log(Level.SEVERE, x.getMessage());
        structure.setSmiles(null);
    }
    try {
        if (structure.getInchi() == null) {
            String inchi = null;
            String key = null;
            if ((molecule == null) || (molecule.getAtomCount() == 0)) {
                inchi = inchiKey.process(structure);
            } else
                try {
                    if (inchiProcessor == null)
                        inchiProcessor = new InchiProcessor();
                    boolean kekulize = false;
                    for (IBond bond : molecule.bonds()) if (bond.getFlag(CDKConstants.ISAROMATIC)) {
                        kekulize = true;
                        break;
                    }
                    IAtomContainer kekulized = (IAtomContainer) molecule;
                    if (kekulize)
                        try {
                            // inchi can't process aromatic bonds...
                            kekulized = (IAtomContainer) molecule.clone();
                            // the new kekulizer probably do not needs atom typing
                            // AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(kekulized);
                            Kekulization.kekulize(kekulized);
                            for (IBond bond : kekulized.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
                        } catch (Exception x) {
                            logger.log(Level.FINE, x.getMessage(), x);
                            ;
                        }
                    InChIGenerator gen = inchiProcessor.process(kekulized);
                    if (INCHI_RET.OKAY.equals(gen.getReturnStatus()) || INCHI_RET.WARNING.equals(gen.getReturnStatus())) {
                        inchi = gen.getInchi();
                        key = gen.getInchiKey();
                    } else {
                        inchi = null;
                        key = String.format("ERROR:%s:%s", gen.getReturnStatus(), gen.getMessage());
                    }
                } catch (Exception x) {
                    inchi = null;
                    key = null;
                }
            if ("".equals(inchi))
                inchi = null;
            structure.setInchi(inchi);
            structure.setInchiKey(key);
        }
    } catch (Exception x) {
        structure.setInchi(null);
        structure.setInchiKey("ERROR:" + x.getMessage());
    }
    if ((molecule != null) && (molecule.getAtomCount() > 0))
        try {
            IMolecularFormula formula = MolecularFormulaManipulator.getMolecularFormula(molecule);
            structure.setFormula(formula == null ? null : MolecularFormulaManipulator.getString(formula));
        } catch (Exception x) {
            structure.setFormula(null);
        }
    if (DXParser.hasDxProperties(structure)) {
        if (dxParser == null)
            dxParser = new DXParser();
        structure = dxParser.process(structure);
    }
    return structure;
}

Example 25 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class AtomConfigurator method process.

public IAtomContainer process(IAtomContainer mol) throws AmbitException {
    if (mol == null)
        throw new AmbitException("Null molecule!");
    if (mol.getAtomCount() == 0)
        throw new AmbitException("No atoms!");
    logger.fine("Configuring atom types ...");
    // AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
    CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(mol.getBuilder());
    Iterator<IAtom> atoms = mol.atoms().iterator();
    List<String> errors = null;
    while (atoms.hasNext()) {
        IAtom atom = atoms.next();
        if (!(atom instanceof IPseudoAtom))
            try {
                IAtomType matched = matcher.findMatchingAtomType(mol, atom);
                if (matched != null) {
                    AtomTypeManipulator.configure(atom, matched);
                    atom.setValency(matched.getValency());
                    atom.setAtomicNumber(matched.getAtomicNumber());
                    atom.setExactMass(matched.getExactMass());
                } else {
                    if (errors == null)
                        errors = new ArrayList<String>();
                    if (errors.indexOf(atom.getSymbol()) < 0)
                        errors.add(String.format("%s", atom.getSymbol()));
                }
            } catch (Exception x) {
                if (errors == null)
                    errors = new ArrayList<String>();
                if (errors.indexOf(atom.getSymbol()) < 0) {
                    errors.add(String.format("%s", atom.getSymbol()));
                }
            }
    }
    if ((errors != null) && "true".equals(Preferences.getProperty(Preferences.STOP_AT_UNKNOWNATOMTYPES))) {
        Collections.sort(errors);
        throw new AmbitException(errors.toString());
    }
    /*
            CDKHueckelAromaticityDetector.detectAromaticity(molecule);    		
	        CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(mol.getBuilder());
	        Iterator<IAtom> atoms = mol.atoms();
	        while (atoms.hasNext()) {
	           IAtom atom = atoms.next();
	           IAtomType type = matcher.findMatchingAtomType(mol, atom);
	           try {
	        	   AtomTypeManipulator.configure(atom, type);
                   logger.debug("Found " + atom.getSymbol() + " of type " + type.getAtomTypeName());                   
	           } catch (Exception x) {
	        	   logger.error(x.getMessage() + " " + atom.getSymbol(),x);
                   
                   if ("true".equals(Preferences.getProperty(Preferences.STOP_AT_UNKNOWNATOMTYPES))) {
                       throw new AmbitException(atom.getSymbol(),x);
                   }
                   
	           }
	        }    	   
	        */
    atoms = mol.atoms().iterator();
    while (atoms.hasNext()) {
        IAtom atom = atoms.next();
        if ((atom.getAtomicNumber() == null) || (atom.getAtomicNumber() == 0)) {
            Integer no = PeriodicTable.getAtomicNumber(atom.getSymbol());
            if (no != null)
                atom.setAtomicNumber(no.intValue());
        }
    }
    return mol;
}