Chimie Théorique » scripts_chimie4psmn » DockOnSurf

def correct_coll(molec, slab, ctr_coord, site_coord, num_pts,

                 min_coll_height, norm_vect, slab_nghbs, molec_nghbs,

    # TODO Rethink this function

    """Tries to adsorb a molecule on a slab trying to avoid collisions by doing

    small rotations.

    @param coll_coeff: The coefficient that multiplies the covalent radius of

        atoms resulting in a distance that two atoms being closer to that is

        considered as atomic collision.

    @return collision: bool, whether the structure generated has collisions

        between slab and adsorbate.

    """

        slab_molec = deepcopy(slab)

        molec.euler_rotate(k * d_angle, k * d_angle / 2, k * d_angle,

                           center=ctr_coord)

                      norm_vect=norm_vect)

        collision = check_collision(slab_molec, slab_num_atoms, min_coll_height,

                                    norm_vect, slab_nghbs, molec_nghbs,