Method to extract substructures from atom containers

Extract.java

 public static IAtomContainer extractSubstructure(
            IAtomContainer atomContainer, int... atomIndices) throws CloneNotSupportedException {
        IAtomContainer substructure = (IAtomContainer) atomContainer.clone();
        int numberOfAtoms = substructure.getAtomCount();
        IAtom[] atoms = new IAtom[numberOfAtoms];
        for (int atomIndex = 0; atomIndex < numberOfAtoms; atomIndex++) {
            atoms[atomIndex] = substructure.getAtom(atomIndex);
        }
        
        Arrays.sort(atomIndices);
        for (int index = 0; index < numberOfAtoms; index++) {
            if (Arrays.binarySearch(atomIndices, index) < 0) {
                IAtom atom = atoms[index];
                substructure.removeAtomAndConnectedElectronContainers(atom);
            }
        }
        
        return substructure;
    }