| a_to_i(core::Size const a) const | protocols::normalmode::NormalMode | inline |
| a_to_i_ | protocols::normalmode::NormalMode | private |
| atomID_ | protocols::normalmode::NormalMode | private |
| calc_inertia_tensor(numeric::MathMatrix< core::Real > const Icorr, core::Vector const &Ra, core::Real const Msum) | protocols::normalmode::NormalMode | private |
| calculate_Jacobi_correction(core::Size const a, core::Real const &Ma, core::Vector const &Ra, core::Real const &Msum, numeric::MathMatrix< core::Real > const &Ia, numeric::MathMatrix< core::Real > const &i_Isum, core::Vector &Aa, core::Vector &ta) | protocols::normalmode::NormalMode | private |
| clear_torsions_using() | protocols::normalmode::NormalMode | inline |
| convert_to_torsion_crd(utility::vector1< utility::vector1< core::Real > > const &U) | protocols::normalmode::NormalMode | private |
| dist2_cut() const | protocols::normalmode::NormalMode | inline |
| dist2_cut_ | protocols::normalmode::NormalMode | private |
| e_ | protocols::normalmode::NormalMode | private |
| eckart_correction(bool const bool_in) | protocols::normalmode::NormalMode | inline |
| eckart_correction_ | protocols::normalmode::NormalMode | private |
| eigsrt(utility::vector1< utility::vector1< core::Real > > &eigvec, utility::vector1< core::Real > &eigval) | protocols::normalmode::NormalMode | private |
| eigval_ | protocols::normalmode::NormalMode | private |
| eigvec_cart_ | protocols::normalmode::NormalMode | private |
| eigvec_tor_ | protocols::normalmode::NormalMode | private |
| get_atomID() const | protocols::normalmode::NormalMode | inline |
| get_eigval() const | protocols::normalmode::NormalMode | inline |
| get_eigval(core::Size const imode) const | protocols::normalmode::NormalMode | inline |
| get_eigvec_cart() const | protocols::normalmode::NormalMode | inline |
| get_eigvec_cart(core::Size const imode) const | protocols::normalmode::NormalMode | inline |
| get_eigvec_tor() const | protocols::normalmode::NormalMode | inline |
| get_eigvec_tor(core::Size const imode) const | protocols::normalmode::NormalMode | inline |
| get_importance() const | protocols::normalmode::NormalMode | inline |
| get_importance(core::Size const imode) const | protocols::normalmode::NormalMode | inline |
| get_k(core::Size const i, core::Size const j) const | protocols::normalmode::NormalMode | inline |
| get_torID() const | protocols::normalmode::NormalMode | inline |
| i_to_a(core::Size const i) const | protocols::normalmode::NormalMode | inline |
| i_to_a_ | protocols::normalmode::NormalMode | private |
| importance_ | protocols::normalmode::NormalMode | private |
| k_ | protocols::normalmode::NormalMode | private |
| k_long_ | protocols::normalmode::NormalMode | private |
| k_short_ | protocols::normalmode::NormalMode | private |
| k_SS_ | protocols::normalmode::NormalMode | private |
| k_uniform_ | protocols::normalmode::NormalMode | private |
| make_Hessian_ANM() | protocols::normalmode::NormalMode | private |
| make_Hessian_TNM() | protocols::normalmode::NormalMode | private |
| mode() const | protocols::normalmode::NormalMode | inline |
| mode_ | protocols::normalmode::NormalMode | private |
| natm() const | protocols::normalmode::NormalMode | inline |
| nmode() const | protocols::normalmode::NormalMode | inline |
| NormalMode() | protocols::normalmode::NormalMode | |
| NormalMode(std::string const mode, core::Real distcut) | protocols::normalmode::NormalMode | |
| ntor() const | protocols::normalmode::NormalMode | inline |
| prepare_coord(core::pose::Pose const &pose) | protocols::normalmode::NormalMode | private |
| s_ | protocols::normalmode::NormalMode | private |
| set_harmonic_constant_map(core::pose::Pose const &pose) | protocols::normalmode::NormalMode | private |
| set_harmonic_constants(core::Real const &k_uniform) | protocols::normalmode::NormalMode | |
| set_harmonic_constants(core::Real const &k_short, core::Real const &k_SS, core::Real const &k_long) | protocols::normalmode::NormalMode | |
| set_torsions_using(core::Size const seqpos) | protocols::normalmode::NormalMode | inline |
| solve(core::pose::Pose const &pose) | protocols::normalmode::NormalMode | |
| tau_ | protocols::normalmode::NormalMode | private |
| torID_ | protocols::normalmode::NormalMode | private |
| torsion(bool const bool_in, bool const use_phi=true, bool const use_psi=true, bool const eckart_correction=true) | protocols::normalmode::NormalMode | |
| torsion() const | protocols::normalmode::NormalMode | inline |
| torsion_ | protocols::normalmode::NormalMode | private |
| torsions_using_ | protocols::normalmode::NormalMode | private |
| torsions_using_assigned_ | protocols::normalmode::NormalMode | private |
| update_inertia_tensor(core::Size const a, core::Real &Ma, core::Vector &Ra, numeric::MathMatrix< core::Real > &Icorr, numeric::MathMatrix< core::Real > &Ia, utility::vector1< core::Vector > const xyz_com) | protocols::normalmode::NormalMode | private |
| use_phi_ | protocols::normalmode::NormalMode | private |
| use_psi_ | protocols::normalmode::NormalMode | private |
| use_uniform_k_ | protocols::normalmode::NormalMode | private |
| xyz(core::Size const i) const | protocols::normalmode::NormalMode | inline |
| xyz_ | protocols::normalmode::NormalMode | private |
| ~NormalMode() | protocols::normalmode::NormalMode | |
1.8.7