Examples with IDCodeParser com.actelion.research.chem.IDCodeParser used on opensource projects

Example 1 with IDCodeParser

use of com.actelion.research.chem.IDCodeParser in project openchemlib by Actelion.

the class HoseCodeCreator method getHoseCodesFromDiaID.

public static String[] getHoseCodesFromDiaID(String diastereotopicID, int maxSphereSize, int type) {
    // We need atom coordinates to properly determine stereo features of fragments later
    StereoMolecule molecule = new IDCodeParser(true).getCompactMolecule(diastereotopicID);
    // One of the atom has to be marked !
    int atomID = -1;
    for (int i = 0; i < molecule.getAllAtoms(); i++) {
        // we need to find the marked atom
        String atomCustomLabel = molecule.getAtomCustomLabel(i);
        if (atomCustomLabel != null && atomCustomLabel.endsWith("*"))
            ;
        atomID = i;
        break;
    }
    if (atomID >= 0) {
        return HoseCodeCreator.getHoseCodesForAtom(molecule, atomID, maxSphereSize, type);
    }
    return new String[0];
}

Example 2 with IDCodeParser

use of com.actelion.research.chem.IDCodeParser in project openchemlib by Actelion.

the class DruglikenessPredictor method getDruglikenessString.

public String getDruglikenessString(StereoMolecule testMolecule) {
    if (!sInitialized)
        return "Druglikeness predictor not properly initialized.";
    double incrementSum = 0.0;
    int fragmentCount = 0;
    SSSearcher sss = new SSSearcher(SSSearcher.cMatchAtomCharge);
    StereoMolecule fragment = new StereoMolecule();
    for (int i = 0; i < sIncrementTable.getSize(); i++) {
        new IDCodeParser(false).parse(fragment, sIncrementTable.getFragment(i));
        sss.setMol(fragment, testMolecule);
        if (sss.isFragmentInMolecule()) {
            incrementSum += sIncrementTable.getIncrement(i);
            fragmentCount++;
        }
    }
    double druglikeness = (fragmentCount == 0) ? -1 : incrementSum / Math.sqrt(fragmentCount);
    return druglikeness + "\t" + fragmentCount + "\t" + testMolecule.getAtoms();
}

Example 3 with IDCodeParser

use of com.actelion.research.chem.IDCodeParser in project openchemlib by Actelion.

the class ToxicityPredictor method assessRisk.

public int assessRisk(StereoMolecule testMolecule, int riskType, ThreadMaster threadMaster) {
    if (!sInitialized)
        return cUnknownRisk;
    if (sRiskMolecules[riskType].contains(new Canonizer(testMolecule).getIDCode()))
        return cHighRisk;
    SSSearcher sss = new SSSearcher(SSSearcher.cMatchAtomCharge);
    StereoMolecule fragment = new StereoMolecule();
    for (int i = 0; i < sHighRiskFragments[riskType].size(); i++) {
        if (threadMaster != null && threadMaster.threadMustDie())
            return cUnknownRisk;
        Thread.yield();
        new IDCodeParser(false).parse(fragment, sHighRiskFragments[riskType].get(i));
        sss.setMol(fragment, testMolecule);
        if (sss.isFragmentInMolecule())
            return cHighRisk;
    }
    for (int i = 0; i < sLowRiskFragments[riskType].size(); i++) {
        if (threadMaster != null && threadMaster.threadMustDie())
            return cUnknownRisk;
        Thread.yield();
        new IDCodeParser(false).parse(fragment, sLowRiskFragments[riskType].get(i));
        sss.setMol(fragment, testMolecule);
        if (sss.isFragmentInMolecule())
            return cLowRisk;
    }
    return cNoRisk;
}

Example 4 with IDCodeParser

use of com.actelion.research.chem.IDCodeParser in project openchemlib by Actelion.

the class ReactionEncoder method decodeProducts.

/**
 * Generates an array of all products of the encoded reaction string as bytes.
 * If the string includes atom coordinates, these are used.
 * @param rxnBytes
 * @return null or StereoMolecule array with at least one molecule
 */
public static StereoMolecule[] decodeProducts(byte[] rxnBytes) {
    if (rxnBytes == null || rxnBytes.length == 0)
        return null;
    int productIndex = 1 + ArrayUtils.indexOf(rxnBytes, (byte) ReactionEncoder.PRODUCT_IDENTIFIER);
    if (productIndex == 0)
        return null;
    int productEnd = ArrayUtils.indexOf(rxnBytes, (byte) ReactionEncoder.OBJECT_DELIMITER, productIndex);
    if (productEnd == -1)
        productEnd = rxnBytes.length;
    if (productIndex == productEnd)
        return null;
    byte[] coords = null;
    int coordsIndex = 1 + ArrayUtils.indexOf(rxnBytes, (byte) ReactionEncoder.OBJECT_DELIMITER, productEnd + 1);
    if (coordsIndex != 0) {
        int reactantIndex = 0;
        while (reactantIndex < productIndex) {
            // advance coordinate index one step for every reactant
            reactantIndex = 1 + ArrayUtils.indexOf(rxnBytes, (byte) ReactionEncoder.MOLECULE_DELIMITER, reactantIndex);
            coordsIndex = 1 + ArrayUtils.indexOf(rxnBytes, (byte) ReactionEncoder.MOLECULE_DELIMITER, coordsIndex);
        }
        coords = rxnBytes;
    }
    ArrayList<StereoMolecule> productList = new ArrayList<StereoMolecule>();
    while (productIndex != -1 && productIndex < productEnd) {
        StereoMolecule product = new IDCodeParser().getCompactMolecule(rxnBytes, coords, productIndex, coordsIndex);
        if (product.getAllAtoms() != 0)
            productList.add(product);
        productIndex = 1 + ArrayUtils.indexOf(rxnBytes, (byte) ReactionEncoder.MOLECULE_DELIMITER, productIndex);
        coordsIndex = 1 + ArrayUtils.indexOf(rxnBytes, (byte) ReactionEncoder.MOLECULE_DELIMITER, coordsIndex);
    }
    return productList.size() == 0 ? null : productList.toArray(new StereoMolecule[0]);
}

Example 5 with IDCodeParser

use of com.actelion.research.chem.IDCodeParser in project openchemlib by Actelion.

the class DruglikenessPredictor method assessDruglikeness.

public double assessDruglikeness(StereoMolecule testMolecule, ThreadMaster threadMaster) {
    ParameterizedStringList detail = new ParameterizedStringList();
    if (!sInitialized) {
        detail.add("Druglikeness predictor not properly initialized.", ParameterizedStringList.cStringTypeText);
        return cDruglikenessUnknown;
    }
    detail.add("Found sub-structure fragments and their contributions:", ParameterizedStringList.cStringTypeText);
    detail.add("(yellow atoms carry at least one more substituent)", ParameterizedStringList.cStringTypeText);
    double nastyIncrementSum = 0.0;
    double incrementSum = 0.0;
    int fragmentCount = 0;
    SSSearcher sss = new SSSearcher(SSSearcher.cMatchAtomCharge);
    StereoMolecule fragment = new StereoMolecule();
    for (int i = 0; i < sIncrementTable.getSize(); i++) {
        if (threadMaster != null && threadMaster.threadMustDie())
            return cDruglikenessUnknown;
        Thread.yield();
        new IDCodeParser(false).parse(fragment, sIncrementTable.getFragment(i));
        sss.setMol(fragment, testMolecule);
        if (sss.isFragmentInMolecule()) {
            double increment = sIncrementTable.getIncrement(i);
            if (increment < -1)
                nastyIncrementSum += increment;
            else {
                incrementSum += increment;
                fragmentCount++;
            }
            detail.add(sIncrementTable.getFragment(i), ParameterizedStringList.cStringTypeIDCode);
            detail.add(Double.toString(increment), ParameterizedStringList.cStringTypeDouble);
        }
    }
    if (fragmentCount == 0)
        return -1;
    double druglikeness = nastyIncrementSum + incrementSum / Math.sqrt(fragmentCount);
    // correct cut-off by also treating molecules
    // with more than 50 found fragments as more drug-like
    druglikeness = druglikeness + 0.0625 * (fragmentCount - 40);
    mDetail = detail;
    return druglikeness;
}