Examples with IntVec com.actelion.research.util.datamodel.IntVec used on opensource projects

Example 1 with IntVec

use of com.actelion.research.util.datamodel.IntVec in project openchemlib by Actelion.

the class DescriptorHandlerHashedCFp method createDescriptor.

/**
 * This descriptor requires proper up/down bonds, because it encodes stereo parities.
 * If a passed molecule is generated from idcode parsing, make sure that coordinates
 * and up/down/bonds are available, i.e. that the IDCodeParser was instantiated with
 * the respective option.
 */
public int[] createDescriptor(StereoMolecule mol) {
    if (mol == null)
        return null;
    mol.ensureHelperArrays(Molecule.cHelperRings);
    StereoMolecule fragment = new StereoMolecule(mol.getAtoms(), mol.getBonds());
    // byte[] descriptor = new byte[DESCRIPTOR_SIZE];
    int len = DESCRIPTOR_SIZE / Integer.SIZE;
    IntVec iv = new IntVec(len);
    int[] atomList = new int[mol.getAtoms()];
    boolean[] atomMask = new boolean[mol.getAtoms()];
    for (int rootAtom = 0; rootAtom < mol.getAtoms(); rootAtom++) {
        if (rootAtom != 0)
            Arrays.fill(atomMask, false);
        int min = 0;
        int max = 0;
        for (int sphere = 0; sphere < SPHERE_COUNT && max < mol.getAtoms(); sphere++) {
            if (max == 0) {
                atomList[0] = rootAtom;
                atomMask[rootAtom] = true;
                max = 1;
            } else {
                int newMax = max;
                for (int i = min; i < max; i++) {
                    int atom = atomList[i];
                    for (int j = 0; j < mol.getConnAtoms(atom); j++) {
                        int connAtom = mol.getConnAtom(atom, j);
                        if (!atomMask[connAtom]) {
                            atomMask[connAtom] = true;
                            atomList[newMax++] = connAtom;
                        }
                    }
                }
                min = max;
                max = newMax;
            }
            mol.copyMoleculeByAtoms(fragment, atomMask, true, null);
            // take fragment as it is
            String idcode = new Canonizer(fragment).getIDCode();
            int h = BurtleHasher.hashlittle(idcode, HASH_INIT);
            h = (h & BurtleHasher.hashmask(HASH_BITS));
            iv.setBit(h);
        // System.out.println("atom:"+rootAtom+"\tsphere:"+sphere+"\thash:"+h+"\t"+idcode);
        }
    }
    return iv.get();
}