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

Example 1 with TopLayer

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

the class SpinSplitManager method generateSpinSplitting.

SpinSplitting generateSpinSplitting(IAtom at) {
    // Get simple spin splitting without JJ coupling
    TopLayer tl = (TopLayer) at.getProperty(TopLayer.TLProp);
    List<Integer> classes = new ArrayList<Integer>();
    List<Integer> classHAtNumber = new ArrayList<Integer>();
    for (int i = 0; i < tl.atoms.size(); i++) {
        IAtom neighAt = tl.atoms.get(i);
        int atIndex = molecule.indexOf(neighAt);
        int classNum = atomClasses[atIndex];
        // This code works for molecules with implicit H atoms
        int numOfHAtoms = neighAt.getImplicitHydrogenCount();
        if (numOfHAtoms == 0)
            continue;
        int k = classes.indexOf(classNum);
        if (k == -1) {
            classes.add(classNum);
            classHAtNumber.add(numOfHAtoms);
        } else {
            int new_nH = numOfHAtoms + classHAtNumber.get(k);
            classHAtNumber.set(k, new_nH);
        }
    }
    SpinSplitting spinSplit = new SpinSplitting();
    if (!classes.isEmpty()) {
        spinSplit.numSplitLevels = classes.size();
        spinSplit.splits = new int[classes.size()];
        for (int i = 0; i < classHAtNumber.size(); i++) spinSplit.splits[i] = classHAtNumber.get(i) + 1;
    }
    return spinSplit;
}

Example 2 with TopLayer

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

the class ChemComplexityUtils method getAtomXDInfo.

/**
 * @param atom
 * @return array int[2] with smarts X and D primitives values for the atom
 */
public static int[] getAtomXDInfo(IAtom atom) {
    int[] xd = new int[2];
    xd[0] = 0;
    xd[1] = 0;
    List<IAtom> neighAtoms = ((TopLayer) atom.getProperty(TopLayer.TLProp)).atoms;
    for (IAtom a : neighAtoms) {
        xd[0]++;
        if (!a.getSymbol().equals("H"))
            xd[1]++;
    }
    Integer hci = atom.getImplicitHydrogenCount();
    if (hci != null)
        xd[0] += hci.intValue();
    return xd;
}

Example 3 with TopLayer

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

the class Expander method determineFirstSheres.

void determineFirstSheres(SLNContainer container) {
    firstSphere.clear();
    int nAtom = container.getAtomCount();
    int nBond = container.getBondCount();
    for (int i = 0; i < nAtom; i++) {
        firstSphere.put(container.getAtom(i), new TopLayer());
    }
    for (int i = 0; i < nBond; i++) {
        IBond bond = container.getBond(i);
        IAtom at0 = bond.getAtom(0);
        IAtom at1 = bond.getAtom(1);
        firstSphere.get(at0).atoms.add(at1);
        firstSphere.get(at0).bonds.add(bond);
        firstSphere.get(at1).atoms.add(at0);
        firstSphere.get(at1).bonds.add(bond);
    }
}

Example 4 with TopLayer

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

the class SLNHelper method nodeToString.

String nodeToString(IAtom atom) {
    // System.out.println("-->nodeToString for atom: " + curSLNContainer.getAtomNumber(atom));
    StringBuffer sb = new StringBuffer();
    TopLayer afs = firstSphere.get(atom);
    AtomSLNNode curNode = nodes.get(atom);
    List<String> branches = new ArrayList<String>();
    List<String> closureStrings = new ArrayList<String>();
    for (int i = 0; i < afs.atoms.size(); i++) {
        IAtom neighborAt = afs.atoms.get(i);
        if (neighborAt == curNode.parent)
            continue;
        AtomSLNNode neighborNode = nodes.get(neighborAt);
        if (// This node has not been registered yet
        neighborNode == null) {
            // Registering a new Node and a new branch
            AtomSLNNode newNode = new AtomSLNNode();
            newNode.atom = neighborAt;
            newNode.parent = atom;
            nodes.put(newNode.atom, newNode);
            String bond_str = afs.bonds.get(i).toString();
            String newBranch = bond_str + nodeToString(neighborAt);
            branches.add(newBranch);
        } else {
            IBond neighborBo = afs.bonds.get(i);
            // This check is needed. Otherwise the ring closure will be described twice (for both atoms of the bond)
            if (ringClosures.contains(neighborBo))
                continue;
            ringClosures.add(neighborBo);
            // Handle a new ring closure
            // Set the ID of the first atom from the ring closure
            // Because of the recursion approach the atoms are not yet added converted to strings
            int neighID = ((SLNAtom) neighborAt).atomID;
            if (// The neighbor atom does not have ID
            neighID == -1) {
                // A new atom ID is generated
                maxAtomID++;
                neighID = maxAtomID;
                setAtomID((SLNAtom) neighborAt, neighID);
            }
            String newClosure = afs.bonds.get(i).toString() + "@" + neighID;
            closureStrings.add(newClosure);
        // System.out.println("  #add ring closure: atom " + curSLNContainer.getAtomNumber(atom) + " to atom "
        // + curSLNContainer.getAtomNumber(neighborAt) + " with ID " + neighID);
        }
    }
    // Add atom from the current node
    sb.append(atom.toString());
    // Add ring closures
    for (int i = 0; i < closureStrings.size(); i++) sb.append(closureStrings.get(i));
    // Add branches
    if (branches.size() > 0) {
        for (int i = 0; i < branches.size() - 1; i++) sb.append("(" + branches.get(i).toString() + ")");
        sb.append(branches.get(branches.size() - 1).toString());
    }
    return (sb.toString());
}

Example 5 with TopLayer

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

the class SmartsIsomorphismTester method setQueryAtomSequence.

void setQueryAtomSequence(IQueryAtom firstAt) {
    IQueryAtom firstAtom;
    QuerySequenceElement seqEl;
    TopLayer topLayer;
    int n;
    if (firstAt == null)
        firstAtom = (IQueryAtom) query.getFirstAtom();
    else
        firstAtom = firstAt;
    sequence.clear();
    sequencedAtoms.clear();
    sequencedBondAt1.clear();
    sequencedBondAt2.clear();
    // Set first sequence atom
    sequencedAtoms.add(firstAtom);
    seqEl = new QuerySequenceElement();
    seqEl.center = firstAtom;
    topLayer = (TopLayer) firstAtom.getProperty(TopLayer.TLProp);
    n = topLayer.atoms.size();
    seqEl.atoms = new IQueryAtom[n];
    seqEl.bonds = new IQueryBond[n];
    for (int i = 0; i < n; i++) {
        sequencedAtoms.add((IQueryAtom) topLayer.atoms.get(i));
        seqEl.atoms[i] = (IQueryAtom) topLayer.atoms.get(i);
        seqEl.bonds[i] = (IQueryBond) topLayer.bonds.get(i);
        addSeqBond(seqEl.center, seqEl.atoms[i]);
    }
    sequence.add(seqEl);
    // Sequencing the entire query structure
    Stack<QuerySequenceElement> stack = new Stack<QuerySequenceElement>();
    stack.push(seqEl);
    while (!stack.empty()) {
        // curAddedAtoms.clear();
        QuerySequenceElement curSeqAt = stack.pop();
        for (int i = 0; i < curSeqAt.atoms.length; i++) {
            topLayer = (TopLayer) curSeqAt.atoms[i].getProperty(TopLayer.TLProp);
            if (topLayer.atoms.size() == 1)
                // it is terminal atom and no further sequencing should be done
                continue;
            int[] a = getSeqAtomsInLayer(topLayer);
            n = 0;
            for (int k = 0; k < a.length; k++) if (a[k] == 0)
                n++;
            if (n > 0) {
                seqEl = new QuerySequenceElement();
                seqEl.center = curSeqAt.atoms[i];
                seqEl.atoms = new IQueryAtom[n];
                seqEl.bonds = new IQueryBond[n];
                sequence.add(seqEl);
                stack.add(seqEl);
            }
            int j = 0;
            for (int k = 0; k < a.length; k++) {
                if (a[k] == 0) {
                    seqEl.atoms[j] = (IQueryAtom) topLayer.atoms.get(k);
                    seqEl.bonds[j] = (IQueryBond) topLayer.bonds.get(k);
                    addSeqBond(seqEl.center, seqEl.atoms[j]);
                    sequencedAtoms.add(seqEl.atoms[j]);
                    // curAddedAtoms.add(seqEl.atoms[j]);
                    j++;
                } else {
                    if (curSeqAt.center == topLayer.atoms.get(k))
                        continue;
                    // is already sequenced
                    if (getSeqBond(curSeqAt.atoms[i], topLayer.atoms.get(k)) != -1)
                        continue;
                    // topLayer.atoms.get(k) atom is already sequenced.
                    // Therefore sequnce element of 'bond' type is registered.
                    // newSeqEl is not added in the stack (this is not needed for this bond)
                    QuerySequenceElement newSeqEl = new QuerySequenceElement();
                    newSeqEl.center = null;
                    newSeqEl.atoms = new IQueryAtom[2];
                    newSeqEl.bonds = new IQueryBond[1];
                    newSeqEl.atoms[0] = curSeqAt.atoms[i];
                    newSeqEl.atoms[1] = (IQueryAtom) topLayer.atoms.get(k);
                    addSeqBond(newSeqEl.atoms[0], newSeqEl.atoms[1]);
                    newSeqEl.bonds[0] = (IQueryBond) topLayer.bonds.get(k);
                    sequence.add(newSeqEl);
                }
            }
        }
    }
    for (int i = 0; i < sequence.size(); i++) sequence.get(i).setAtomNums(query);
}