Examples with SMIRKSManager ambit2.smarts.SMIRKSManager used on opensource projects

Example 1 with SMIRKSManager

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

the class SMIRKSDepict method getImage.

@Override
protected BufferedImage getImage(String smiles, int w, int h, String recordType, QueryType type) throws ResourceException {
    try {
        String smirks = getSmirks();
        if (smirks == null || "".equals(smirks))
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST);
        depict.setImageSize(new Dimension(w, h));
        SMIRKSManager smrkMan = new SMIRKSManager(SilentChemObjectBuilder.getInstance());
        smrkMan.setFlagProcessResultStructures(true);
        smrkMan.setSSMode(SmartsConst.SSM_MODE.SSM_NON_IDENTICAL_FIRST);
        SMIRKSReaction smr = smrkMan.parse(smirks);
        SmilesParser parser = new SmilesParser(SilentChemObjectBuilder.getInstance());
        IAtomContainer reactant = parser.parseSmiles(smiles);
        reactant = AtomContainerManipulator.removeHydrogens(reactant);
        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactant);
        CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(SilentChemObjectBuilder.getInstance());
        CDKHueckelAromaticityDetector.detectAromaticity(reactant);
        adder.addImplicitHydrogens(reactant);
        HydrogenAdderProcessor.convertImplicitToExplicitHydrogens(reactant);
        BufferedImage image = null;
        if (smrkMan.applyTransformation(reactant, this, smr)) {
            image = depict.getImage(reactant, null, true, false);
        } else {
            list.add("Not applicable");
            image = depict.getImage(list);
        }
        smr = null;
        smrkMan = null;
        return image;
    } catch (ResourceException x) {
        throw x;
    } catch (Exception x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x.getMessage(), x);
    }
}

Example 2 with SMIRKSManager

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

the class TestUtilities method testSMIRKS.

public void testSMIRKS(String smirks, String targetSmiles) throws Exception {
    System.out.println("Testing SMIRKS: " + smirks);
    SMIRKSManager smrkMan = new SMIRKSManager(SilentChemObjectBuilder.getInstance());
    smrkMan.setFlagSSMode(FlagSSMode);
    // Product processing flags
    smrkMan.setFlagProcessResultStructures(FlagProductPreprocessing);
    smrkMan.setFlagClearHybridizationBeforeResultProcess(FlagClearHybridizationOnProductPreProcess);
    smrkMan.setFlagClearImplicitHAtomsBeforeResultProcess(this.FlagClearImplicitHAtomsBeforeProductPreProcess);
    smrkMan.setFlagClearAromaticityBeforeResultProcess(this.FlagClearAromaticityBeforePreProcess);
    smrkMan.setFlagAddImplicitHAtomsOnResultProcess(this.FlagAddImplicitHAtomsOnProductPreProcess);
    smrkMan.setFlagConvertAddedImplicitHToExplicitOnResultProcess(this.FlagImplicitHToExplicitOnProductPreProcess);
    smrkMan.setFlagConvertExplicitHToImplicitOnResultProcess(this.FlagExplicitHToImplicitOnProductPreProcess);
    smrkMan.setFlagApplyStereoTransformation(FlagApplyStereoTransformation);
    smrkMan.setFlagHAtomsTransformation(FlagHAtomsTransformation);
    smrkMan.setFlagHAtomsTransformationMode(FlagHAtomsTransformationMode);
    smrkMan.setFlagAromaticityTransformation(FlagAromaticityTransformation);
    smrkMan.getSmartsParser().mSupportSingleBondAromaticityNotSpecified = FlagSingleBondAromaticityNotSpecified;
    smrkMan.getSmartsParser().mSupportDoubleBondAromaticityNotSpecified = FlagDoubleBondAromaticityNotSpecified;
    SMIRKSReaction reaction = smrkMan.parse(smirks);
    if (!smrkMan.getErrors().equals("")) {
        System.out.println(smrkMan.getErrors());
        // System.out.println("\n" + reaction.transformationDataToString());
        return;
    }
    if (FlagPrintTransformationData)
        System.out.println(reaction.transformationDataToString());
    if (targetSmiles.equals(""))
        return;
    IAtomContainer target = SmartsHelper.getMoleculeFromSmiles(targetSmiles);
    if (FlagTargetPreprocessing)
        this.preProcess(target);
    if (FlagPrintAtomAttributes) {
        System.out.println("Target (reactant):");
        System.out.println("Reactant atom attributes:\n" + SmartsHelper.getAtomsAttributes(target));
        System.out.println("Reactant bond attributes:\n" + SmartsHelper.getBondAttributes(target));
    }
    switch(FlagReactionOperation) {
        case APPLY:
            boolean res = smrkMan.applyTransformation(target, reaction);
            if (FlagPrintAtomAttributes) {
                System.out.println("Product:");
                System.out.println("Product atom attributes:\n" + SmartsHelper.getAtomsAttributes(target));
                System.out.println("Product bond attributes:\n" + SmartsHelper.getBondAttributes(target));
            }
            System.out.println("    " + SmartsHelper.moleculeToSMILES(target, true));
            String transformedSmiles = SmartsHelper.moleculeToSMILES(target, true);
            if (res) {
                System.out.println("Reaction application: " + targetSmiles + "  -->  " + transformedSmiles + "    abs. smiles res " + SmilesGenerator.absolute().create(target));
            } else
                System.out.println("Reaction not appicable!");
            break;
        case CombinedOverlappedPos:
            IAtomContainerSet resSet = smrkMan.applyTransformationWithCombinedOverlappedPos(target, null, reaction);
            if (resSet == null)
                System.out.println("Reaction not appicable!");
            else {
                System.out.println("Reaction application With Combined Overlapped Positions: ");
                for (int i = 0; i < resSet.getAtomContainerCount(); i++) System.out.println(SmartsHelper.moleculeToSMILES(resSet.getAtomContainer(i), true));
            }
            break;
        case SingleCopyForEachPos:
            IAtomContainerSet resSet2 = smrkMan.applyTransformationWithSingleCopyForEachPos(target, null, reaction, FlagSSModeForSingleCopyForEachPos);
            if (resSet2 == null)
                System.out.println("Reaction not appicable!");
            else {
                System.out.println("Reaction application With Single Copy For Each Position: ");
                for (int i = 0; i < resSet2.getAtomContainerCount(); i++) System.out.println(SmartsHelper.moleculeToSMILES(resSet2.getAtomContainer(i), true));
            }
            break;
    }
    System.out.println();
}

Example 3 with SMIRKSManager

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

the class TestUtilities method testSMIRKS_.

// This is the old variant
public void testSMIRKS_(String smirks, String targetSmiles) throws Exception {
    System.out.println("Testing SMIRKS: " + smirks);
    SMIRKSManager smrkMan = new SMIRKSManager(SilentChemObjectBuilder.getInstance());
    smrkMan.setFlagSSMode(FlagSSMode);
    smrkMan.getSmartsParser().mSupportSingleBondAromaticityNotSpecified = FlagSingleBondAromaticityNotSpecified;
    smrkMan.getSmartsParser().mSupportDoubleBondAromaticityNotSpecified = FlagDoubleBondAromaticityNotSpecified;
    SMIRKSReaction reaction = smrkMan.parse(smirks);
    if (!smrkMan.getErrors().equals("")) {
        System.out.println(smrkMan.getErrors());
        // System.out.println("Product Atoms: "+SmartsHelper.getAtomsExpressionTokens(reaction.product));
        return;
    }
    if (FlagPrintTransformationData)
        System.out.println(reaction.transformationDataToString());
    if (targetSmiles.equals(""))
        return;
    IAtomContainer target = SmartsHelper.getMoleculeFromSmiles(targetSmiles);
    if (FlagTargetPreprocessing)
        this.preProcess(target);
    if (FlagPrintAtomAttributes) {
        System.out.println("Reactant atom attributes:\n" + SmartsHelper.getAtomsAttributes(target));
        System.out.println("Reactant bond attributes:\n" + SmartsHelper.getBondAttributes(target));
    }
    boolean res = smrkMan.applyTransformation(target, reaction);
    if (FlagPrintAtomAttributes) {
        System.out.println("Product before pre-processiong:");
        System.out.println("Product atom attributes:\n" + SmartsHelper.getAtomsAttributes(target));
        System.out.println("Product bond attributes:\n" + SmartsHelper.getBondAttributes(target));
    }
    System.out.println("    " + SmartsHelper.moleculeToSMILES(target, true));
    if (FlagProductPreprocessing)
        this.preProcessProduct(target);
    if (FlagPrintAtomAttributes) {
        System.out.println("Product after pre-processiong:");
        System.out.println("Product atom attributes:\n" + SmartsHelper.getAtomsAttributes(target));
        System.out.println("Product bond attributes:\n" + SmartsHelper.getBondAttributes(target));
    }
    String transformedSmiles = SmartsHelper.moleculeToSMILES(target, true);
    if (res)
        System.out.println("Reaction application: " + targetSmiles + "  -->  " + transformedSmiles);
    else
        System.out.println("Reaction not appicable!");
}

Example 4 with SMIRKSManager

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

the class TestStrVisualizer method testSMIRKS.

public void testSMIRKS(String smirks, IAtomContainer target) throws Exception {
    System.out.println("Testing SMIRKS: " + smirks);
    SMIRKSManager smrkMan = new SMIRKSManager(SilentChemObjectBuilder.getInstance());
    smrkMan.setFlagFilterEquivalentMappings(filterEqMaps);
    smrkMan.setSSMode(SmartsConst.SSM_MODE.SSM_NON_IDENTICAL);
    SMIRKSReaction reaction = smrkMan.parse(smirks);
    if (!smrkMan.getErrors().equals("")) {
        System.out.println(smrkMan.getErrors());
        return;
    }
    System.out.println(reaction.transformationDataToString());
    setFrame();
    String targetSmiles = SmartsHelper.moleculeToSMILES(target, true);
    addStructure((IAtomContainer) target.clone());
    smrkMan.applyTransformation(target, reaction);
    String transformedSmiles = SmartsHelper.moleculeToSMILES(target, true);
    addStructure(target);
    System.out.println("Reaction application: " + targetSmiles + "  -->  " + transformedSmiles);
}

Example 5 with SMIRKSManager

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

the class AutomaticSmirksTestUtilities method applySmirks.

public List<String> applySmirks(String smrk, String smi) {
    try {
        SMIRKSManager smrkMan = new SMIRKSManager(SilentChemObjectBuilder.getInstance());
        smrkMan.setFlagSSMode(SmartsConst.SSM_MODE.SSM_NON_IDENTICAL_FIRST);
        smrkMan.setFlagProcessResultStructures(true);
        smrkMan.setFlagClearHybridizationBeforeResultProcess(true);
        smrkMan.setFlagClearImplicitHAtomsBeforeResultProcess(true);
        smrkMan.setFlagClearAromaticityBeforeResultProcess(true);
        smrkMan.setFlagAddImplicitHAtomsOnResultProcess(true);
        smrkMan.setFlagConvertAddedImplicitHToExplicitOnResultProcess(false);
        smrkMan.setFlagConvertExplicitHToImplicitOnResultProcess(true);
        smrkMan.getSmartsParser().mSupportDoubleBondAromaticityNotSpecified = false;
        smrkMan.setFlagApplyStereoTransformation(true);
        SMIRKSReaction reaction = smrkMan.parse(smrk);
        if (!smrkMan.getErrors().equals(""))
            throw new RuntimeException("Invalid SMIRKS: " + smrkMan.getErrors());
        IAtomContainer target = smilesParser.parseSmiles(smi);
        for (IAtom atom : target.atoms()) if (atom.getFlag(CDKConstants.ISAROMATIC))
            atom.setFlag(CDKConstants.ISAROMATIC, false);
        for (IBond bond : target.bonds()) if (bond.getFlag(CDKConstants.ISAROMATIC))
            bond.setFlag(CDKConstants.ISAROMATIC, false);
        // do not add Hs: https://sourceforge.net/p/cdk/mailman/message/34608714/
        // AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(target);
        // CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(SilentChemObjectBuilder.getInstance());
        // adder.addImplicitHydrogens(target);
        MoleculeTools.convertImplicitToExplicitHydrogens(target);
        // for our project, we want to use daylight aromaticity
        // CDKHueckelAromaticityDetector.detectAromaticity(target);
        Aromaticity aromaticity = new Aromaticity(ElectronDonation.daylight(), Cycles.or(Cycles.all(), Cycles.edgeShort()));
        aromaticity.apply(target);
        IAtomContainerSet resSet2 = smrkMan.applyTransformationWithSingleCopyForEachPos(target, null, reaction, SmartsConst.SSM_MODE.SSM_ALL);
        List<String> result = new ArrayList<String>();
        if (resSet2 != null)
            for (int i = 0; i < resSet2.getAtomContainerCount(); i++) {
                IAtomContainer mol = resSet2.getAtomContainer(i);
                AtomContainerManipulator.suppressHydrogens(mol);
                String smiles = SmilesGenerator.absolute().create(mol);
                result.add(smiles);
            }
        return result;
    } catch (Exception e) {
        System.err.println(e.getMessage());
        System.err.println("SMIRKS " + smrk);
        System.err.println("SMILES " + smi);
        // e.printStackTrace();
        return null;
    }
}