Examples with MOL_TYPE ambit2.base.interfaces.IStructureRecord.MOL_TYPE used on opensource projects

Example 1 with MOL_TYPE

use of ambit2.base.interfaces.IStructureRecord.MOL_TYPE in project ambit-mirror by ideaconsult.

the class MoleculeReader method handleFormat.

protected IAtomContainer handleFormat(MOL_TYPE format, IStructureRecord target) throws AmbitException {
    switch(format) {
        case SDF:
            {
                try {
                    IAtomContainer ac = MoleculeTools.readMolfile(target.getContent());
                    if ((ac != null) && (ac.getProperties() != null)) {
                        Object title = ac.getProperty(CDKConstants.TITLE);
                        if (title != null) {
                            if (CASProcessor.isValidFormat(title.toString()))
                                try {
                                    if (casTransformer == null)
                                        casTransformer = new CASProcessor();
                                    ac.setProperty(AmbitCONSTANTS.CASRN, casTransformer.process(title.toString()));
                                    ac.removeProperty(CDKConstants.TITLE);
                                } catch (Exception x) {
                                }
                            if (removeCDKTitle)
                                ac.removeProperty(CDKConstants.TITLE);
                        }
                        // CAS transformation was moved from MyIterating MDLReader
                        Iterator props = ac.getProperties().entrySet().iterator();
                        while (props.hasNext()) {
                            Map.Entry entry = (Map.Entry) props.next();
                            Object key = entry.getKey();
                            Object value = entry.getValue();
                            if (Property.test4CAS(key.toString().toLowerCase())) {
                                if (casTransformer == null)
                                    casTransformer = new CASProcessor();
                                ac.setProperty(key, casTransformer.process(value.toString()));
                            }
                        }
                        /* !%&$* PubChem */
                        Object sid = ac.getProperty("PUBCHEM_SUBSTANCE_ID");
                        if (sid != null) {
                            ac.setProperty("PUBCHEM_SID", sid);
                            ac.removeProperty("PUBCHEM_SUBSTANCE_ID");
                        }
                        Object cid = ac.getProperty("PUBCHEM_COMPOUND_CID");
                        if (cid != null) {
                            ac.setProperty("PUBCHEM_CID", cid);
                            ac.removeProperty("PUBCHEM_COMPOUND_CID");
                        }
                        Object synonyms = ac.getProperty("PUBCHEM_SUBSTANCE_SYNONYM");
                        if (synonyms != null) {
                            BufferedReader reader = new BufferedReader(new StringReader(synonyms.toString()));
                            String line = null;
                            while ((line = reader.readLine()) != null) {
                                String type = "PUBCHEM Name";
                                String value = line;
                                if (value.startsWith("DSSTox_RID_")) {
                                    type = "DSSTox_RID";
                                    value = value.substring(11);
                                } else if (value.startsWith("DSSTox_GSID_")) {
                                    type = "DSSTox_GSID";
                                    value = value.substring(12);
                                } else if (value.startsWith("DSSTox_CID_")) {
                                    type = "DSSTox_CID";
                                    value = value.substring(11);
                                } else if (value.startsWith("Tox21_")) {
                                    type = "Tox21";
                                    value = value.substring(6);
                                } else if (value.startsWith("CAS-")) {
                                    type = "CASRN";
                                    value = value.substring(4);
                                } else if (value.startsWith("NCGC")) {
                                    type = "NCGC";
                                } else {
                                    value = value.toLowerCase();
                                }
                                ac.setProperty(type, value);
                            }
                            reader.close();
                            ac.removeProperty("PUBCHEM_SUBSTANCE_SYNONYM");
                        }
                        ac.removeProperty(CDKConstants.REMARK);
                    }
                    if (ac != null) {
                        if (MoleculeTools.repairBondOrder4(ac)) {
                        // ok, all set
                        } else {
                            try {
                                AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);
                            } catch (Exception x) {
                                ac.setProperty("ERROR.atomtypes", String.format("%s\t%s", x.getClass().getName(), x.getMessage()));
                            }
                            try {
                                hadder.addImplicitHydrogens(ac);
                            } catch (Exception x) {
                                ac.setProperty("ERROR.implicith", String.format("%s\t%s", x.getClass().getName(), x.getMessage()));
                            }
                        }
                    }
                    return ac;
                } catch (Exception x) {
                    throw new AmbitException(x);
                }
            }
        case CML:
            try {
                IAtomContainer ac = MoleculeTools.readCMLMolecule(target.getContent());
                if ((ac != null) && (ac.getProperties() != null)) {
                    Object title = ac.getProperty(CDKConstants.TITLE);
                    if (title != null) {
                        if (CASProcessor.isValidFormat(title.toString()))
                            try {
                                if (casTransformer == null)
                                    casTransformer = new CASProcessor();
                                ac.setProperty(AmbitCONSTANTS.CASRN, casTransformer.process(title.toString()));
                            } catch (Exception x) {
                            }
                        ac.removeProperty(CDKConstants.TITLE);
                    }
                    ac.removeProperty(CDKConstants.REMARK);
                }
                AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);
                hadder.addImplicitHydrogens(ac);
                return ac;
            } catch (Exception x) {
                throw new AmbitException(x);
            }
        case INC:
            try {
                if (target.getContent().startsWith("InChI=")) {
                    if (inchiFactory == null)
                        inchiFactory = InChIGeneratorFactory.getInstance();
                    InChIToStructure c = inchiFactory.getInChIToStructure(target.getContent(), SilentChemObjectBuilder.getInstance());
                    return c.getAtomContainer();
                } else {
                    // smiles
                    if (smiParser == null)
                        smiParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
                    IAtomContainer mol = smiParser.parseSmiles(target.getContent());
                    // atom typing will drop aromatic flags ...
                    if (atomtypingonsmiles) {
                        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
                        for (IBond b : mol.bonds()) if (b.isAromatic())
                            for (IAtom a : b.atoms()) a.setFlag(CDKConstants.ISAROMATIC, true);
                    }
                    return mol;
                }
            } catch (Exception x) {
                throw new AmbitException(x);
            }
        case NANO:
            try {
                Class clazz = FileInputState.class.getClassLoader().loadClass("net.idea.ambit2.rest.nano.MoleculeNanoReader");
                Method method = clazz.getMethod("nm2atomcontainer", IStructureRecord.class);
                return (IAtomContainer) method.invoke(null, target);
            } catch (Exception x) {
                if (x instanceof AmbitException)
                    throw (AmbitException) x;
                else
                    throw new AmbitException(x);
            }
        case PDB:
            try {
                IAtomContainer ac = MoleculeTools.readPDBfile(target.getContent());
                for (IAtom atom : ac.atoms()) {
                    if (atom.getImplicitHydrogenCount() == null)
                        atom.setImplicitHydrogenCount(0);
                }
                return ac;
            } catch (Exception x) {
                throw new AmbitException(x);
            }
        default:
            {
                throw new AmbitException("Unknown format " + target.getFormat());
            }
    }
}

Example 2 with MOL_TYPE

use of ambit2.base.interfaces.IStructureRecord.MOL_TYPE in project ambit-mirror by ideaconsult.

the class StructureEditorProcessor method process.

@Override
public String process(IStructureRecord record) throws AmbitException {
    try {
        MOL_TYPE mtype = MOL_TYPE.valueOf(record.getFormat());
        IAtomContainer mol = null;
        switch(mtype) {
            case SDF:
                {
                    MoleculeReader reader = new MoleculeReader();
                    mol = reader.process(record);
                    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
                    reader = null;
                    break;
                }
            case CSV:
                {
                    // smiles
                    SmilesParserWrapper p = SmilesParserWrapper.getInstance(SMILES_PARSER.CDK);
                    mol = p.parseSmiles(record.getContent());
                    break;
                }
            default:
                throw new AmbitException("Unsupported format");
        }
        // actions
        if (mol != null && mol.getAtomCount() > 0)
            switch(command) {
                case layout:
                    {
                        IAtomContainerSet molecules = new AtomContainerSet();
                        CompoundImageTools cit = new CompoundImageTools();
                        cit.generate2D(mol, true, molecules);
                        mol = MoleculeTools.newAtomContainer(mol.getBuilder());
                        for (IAtomContainer m : molecules.atomContainers()) {
                            mol.add(m);
                        }
                        break;
                    }
                case aromatize:
                    if (mol != null)
                        CDKHueckelAromaticityDetector.detectAromaticity(mol);
                    break;
                case dearomatize:
                    if (mol != null) {
                        Kekulization.kekulize(mol);
                        for (IBond bond : mol.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
                    }
                    break;
                default:
                    throw new AmbitException("Unknown command");
            }
        StringWriter w = new StringWriter();
        SDFWriter writer = new SDFWriter(w);
        writer.write(mol);
        writer.close();
        return w.toString();
    } catch (AmbitException x) {
        throw x;
    } catch (Exception x) {
        throw new AmbitException(x);
    }
}