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def alignmol(mol):
    coordinates = []
    masses = []
    coords = OEFloatArray(mol.GetMaxAtomIdx() * 3)
    mol.GetCoords(coords)
    totalMass = 0
    for atom in mol.GetAtoms():
        idx = atom.GetIdx()
        coordinates.append((coords[idx * 3], coords[idx * 3 + 1], coords[idx * 3 + 2]))
        m = 1
        if options.usevolumes:
            r = OEGetBondiVdWRadius(atom.GetAtomicNum())
            v = 4.0 * r * r * r * math.pi / 3.0
            m *= v
        if options.useweights:
            m *= OEGetAverageWeight(atom.GetAtomicNum())
        masses.append(m)
        totalMass += m

    coordinates = numpy.array(coordinates)
    masses = numpy.array(masses)
    trans = -numpy.sum(coordinates * masses[:, numpy.newaxis], axis=0) / totalMass
    OETranslate(mol, OEFloatArray(trans))
    coordinates += trans
    #this is shamelessly stolen from the mdanalysis package
    values = zip(masses, coordinates)
    # Create the inertia tensor
    # m_i = mass of atom i
    # (x_i, y_i, z_i) = pos of atom i
    # Ixx = sum(m_i*(y_i^2+z_i^2)); Iyy = sum(m_i*(x_i^2+z_i^2)); Izz = sum(m_i*(x_i^2+y_i^2))
    # Ixy = Iyx = -1*sum(m_i*x_i*y_i)
    # Ixz = Izx = -1*sum(m_i*x_i*z_i)
    # Iyz = Izy = -1*sum(m_i*y_i*z_i)
    Ixx = reduce(lambda t, a: t + a[0] * (a[1][1] * a[1][1] + a[1][2] * a[1][2]), values, 0.)
    Iyy = reduce(lambda t, a: t + a[0] * (a[1][0] * a[1][0] + a[1][2] * a[1][2]), values, 0.)
    Izz = reduce(lambda t, a: t + a[0] * (a[1][0] * a[1][0] + a[1][1] * a[1][1]), values, 0.)
    Ixy = Iyx = -1 * reduce(lambda t, a: t + a[0] * a[1][0] * a[1][1], values, 0.)
    Ixz = Izx = -1 * reduce(lambda t, a: t + a[0] * a[1][0] * a[1][2], values, 0.)
    Iyz = Izy = -1 * reduce(lambda t, a: t + a[0] * a[1][1] * a[1][2], values, 0.)
    inertia = numpy.array([[Ixx, Ixy, Ixz], [Iyx, Iyy, Iyz], [Izx, Izy, Izz]])

    eigenval, eigenvec = eig(inertia)
        # Sort
    indices = numpy.argsort(eigenval)
        # Return transposed in more logical form. See Issue 33.
    principalAxes = eigenvec[:,indices].T
    if det(principalAxes) < 0:
        principalAxes = -principalAxes #remove reflection

    rotmat = OEFloatArray(principalAxes.flatten())
    OERotate(mol, rotmat)
    return