Chimie Théorique » scripts_chimie4psmn » DockOnSurf

    # Check if ctr_coord are the coordinates of an atom and if not creates a

    # dummy one to extract the neighboring atoms.

    ctr_idx = None

    for atom in molec:

        if np.allclose(ctr_coord, atom.position, rtol=1e-2):

            ctr_idx = atom.index

        molec.append(Atom('X', position=ctr_coord))

        cutoffs.append(0.2)

        ctr_idx = len(molec) - 1

    # Builds the neighbors and computes the average vector

    refs, vects = neighbor_list("iD", molec, cutoffs, self_interaction=False)

    neigh_vects = [vects[i] for i, atm in enumerate(refs) if atm == ctr_idx]

        rot_vect = np.cross(ref_vect, axis)

    rot_angle = -get_vect_angle(ref_vect, target_vect, rot_vect)

    molec.rotate(rot_angle, rot_vect, ctr_coord)

    return molec