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

Example 31 with StereoMolecule

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

the class MoleculeDragAdapter method drawDragImage.

public Image drawDragImage(Transferable transferable, int width, int height) {
    if (transferable instanceof MoleculeTransferable) {
        try {
            MoleculeTransferable t = (MoleculeTransferable) transferable;
            Object o = t.getTransferData(MoleculeFlavors.DF_SERIALIZEDOBJECT);
            if (o instanceof StereoMolecule) {
                StereoMolecule mol = (StereoMolecule) o;
                Depictor2D depict = new Depictor2D(mol);
                BufferedImage img = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
                Graphics g = img.getGraphics();
                ((Graphics2D) g).setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
                ((Graphics2D) g).setRenderingHint(RenderingHints.KEY_STROKE_CONTROL, RenderingHints.VALUE_STROKE_PURE);
                depict.validateView(g, new Rectangle2D.Double(0, 0, width, height), AbstractDepictor.cModeInflateToMaxAVBL);
                depict.paint(g);
                return img;
            }
        } catch (IOException e1) {
            System.err.println(e1);
        } catch (UnsupportedFlavorException e1) {
            System.err.println(e1);
        }
    }
    return null;
}

Example 32 with StereoMolecule

use of com.actelion.research.chem.StereoMolecule 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;
}

Example 33 with StereoMolecule

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

the class ToxicityPredictor method getDetail.

public ParameterizedStringList getDetail(StereoMolecule testMolecule, int riskType) {
    ParameterizedStringList theDetail = new ParameterizedStringList();
    if (!sInitialized) {
        theDetail.add("Toxicity predictor not properly initialized.", ParameterizedStringList.cStringTypeText);
        return theDetail;
    }
    String idcode = new Canonizer(testMolecule).getIDCode();
    if (sRiskMolecules[riskType].contains(idcode)) {
        theDetail.add("This molecule is known to be " + cRiskNameA[riskType] + ":", ParameterizedStringList.cStringTypeText);
        theDetail.add(idcode, ParameterizedStringList.cStringTypeIDCode);
        return theDetail;
    }
    SSSearcher sss = new SSSearcher(SSSearcher.cMatchAtomCharge);
    boolean found = false;
    StereoMolecule fragment = new StereoMolecule();
    for (int i = 0; i < sHighRiskFragments[riskType].size(); i++) {
        new IDCodeParser(false).parse(fragment, sHighRiskFragments[riskType].get(i));
        sss.setMol(fragment, testMolecule);
        if (sss.isFragmentInMolecule()) {
            if (!found)
                theDetail.add("High-risk fragments indicating " + cRiskNameN[riskType] + ":", ParameterizedStringList.cStringTypeText);
            found = true;
            theDetail.add(sHighRiskFragments[riskType].get(i), ParameterizedStringList.cStringTypeIDCode);
        }
    }
    found = false;
    for (int i = 0; i < sLowRiskFragments[riskType].size(); i++) {
        new IDCodeParser(false).parse(fragment, sLowRiskFragments[riskType].get(i));
        sss.setMol(fragment, testMolecule);
        if (sss.isFragmentInMolecule()) {
            if (!found)
                theDetail.add("Medium-risk fragments indicating " + cRiskNameN[riskType] + ":", ParameterizedStringList.cStringTypeText);
            found = true;
            theDetail.add(sLowRiskFragments[riskType].get(i), ParameterizedStringList.cStringTypeIDCode);
        }
    }
    if (theDetail.getSize() == 0)
        theDetail.add("No indication for " + cRiskNameN[riskType] + " found.", ParameterizedStringList.cStringTypeText);
    return theDetail;
}

Example 34 with StereoMolecule

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

the class FragmentSpec method matchFragments.

private void matchFragments() {
    // locate disconnected unmapped areas as fragments
    for (int atom = 0; atom < mMol.getAtoms(); atom++) mMol.setAtomMarker(atom, mMol.getAtomMapNo(atom) == 0);
    for (int atom = mMol.getAtoms(); atom < mMol.getAllAtoms(); atom++) mMol.setAtomMarker(atom, false);
    int[] fragmentNo = new int[mMol.getAllAtoms()];
    // TODO: check metal bond behaviour
    int fragmentCount = mMol.getFragmentNumbers(fragmentNo, true, false);
    mMol.removeAtomMarkers();
    if (fragmentCount == 0)
        return;
    StereoMolecule[] fragment = mMol.getFragments(fragmentNo, fragmentCount);
    FragmentSpec[] spec = new FragmentSpec[fragmentCount];
    for (int i = 0; i < fragmentCount; i++) {
        fragment[i].ensureHelperArrays(Molecule.cHelperRings);
        spec[i] = new FragmentSpec();
        spec[i].atomMap = new int[fragment[i].getAtoms()];
        spec[i].rank = new int[fragment[i].getAtoms()];
    }
    // create mapping from fragment's atom indices to mMol atom index
    int[] fragmentAtom = new int[fragmentCount];
    for (int atom = 0; atom < mMol.getAtoms(); atom++) {
        if (mMol.getAtomMapNo(atom) == 0) {
            int fNo = fragmentNo[atom];
            int fAtom = fragmentAtom[fNo]++;
            String label = encodeMappedNeighbors(atom);
            if (label != null) {
                fragment[fNo].setAtomCustomLabel(fAtom, label);
                int highNeighbor = getHighestMappedNeighbor(atom);
                if (spec[fNo].highestMappedNeighbor < highNeighbor)
                    spec[fNo].highestMappedNeighbor = highNeighbor;
            }
            spec[fNo].atomMap[fAtom] = atom;
        }
    }
    for (int i = 0; i < fragmentCount; i++) {
        Canonizer canonizer = new Canonizer(fragment[i], Canonizer.ENCODE_ATOM_CUSTOM_LABELS);
        spec[i].code = canonizer.getIDCode();
        for (int a = 0; a < fragment[i].getAtoms(); a++) spec[i].rank[a] = canonizer.getFinalRank()[a];
    }
    for (int i = 0; i < fragmentCount - 1; i++) {
        if (!spec[i].isMapped) {
            for (int j = i + 1; j < fragmentCount; j++) {
                if (!spec[j].isMapped && spec[i].code.equals(spec[j].code) && spec[i].highestMappedNeighbor != spec[j].highestMappedNeighbor) {
                    mapFragments(spec[i], spec[j]);
                    break;
                }
            }
        }
    }
}

Example 35 with StereoMolecule

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

the class Reaction method normalize.

public void normalize() {
    int size = mReactant.size();
    for (int i = size - 1; i >= 0; i--) {
        StereoMolecule mol = mReactant.get(i);
        if (mol.getAllAtoms() == 0) {
            mReactant.remove(i);
        }
    }
    size = mProduct.size();
    for (int i = size - 1; i >= 0; i--) {
        StereoMolecule mol = mProduct.get(i);
        if (mol.getAllAtoms() == 0) {
            mProduct.remove(i);
        }
    }
}