| Bicelle(core::Real steepness, Conformation const &conf, core::Size membrane_pos) | core::conformation::membrane::membrane_geometry::Bicelle | |
| Bicelle(core::Real steepness, core::Real thickness, Conformation const &conf, core::Size membrane_pos) | core::conformation::membrane::membrane_geometry::Bicelle | |
| Bicelle(core::Real steepness, core::Real thickness, core::Real bicelle_inner_radius) | core::conformation::membrane::membrane_geometry::Bicelle | |
| Bicelle(core::Real steepness, core::Real thickness, core::Real bicelle_inner_radius, AqueousPoreParametersOP aqueous_pore) | core::conformation::membrane::membrane_geometry::Bicelle | |
| Bicelle() | core::conformation::membrane::membrane_geometry::Bicelle | private |
| bicelle_edge_steepness() const | core::conformation::membrane::membrane_geometry::Bicelle | |
| bicelle_edge_steepness_ | core::conformation::membrane::membrane_geometry::Bicelle | private |
| bicelle_inner_radius() const | core::conformation::membrane::membrane_geometry::Bicelle | |
| bicelle_inner_radius_ | core::conformation::membrane::membrane_geometry::Bicelle | private |
| bicelle_outer_radius() const | core::conformation::membrane::membrane_geometry::Bicelle | |
| bicelle_outer_radius_ | core::conformation::membrane::membrane_geometry::Bicelle | private |
| binormal_vector(Conformation const &conf) const | core::conformation::membrane::MembraneGeometry | protected |
| clone() const override | core::conformation::membrane::membrane_geometry::Bicelle | virtual |
| corrected_coordinate(core::Vector const &xyz, core::Vector const &x_axis) const | core::conformation::membrane::MembraneGeometry | protected |
| corrected_xyz(Conformation const &conf, core::Size resnum, core::Size atomnum) const | core::conformation::membrane::MembraneGeometry | |
| f1(core::Vector const &atom_xyz, core::Vector const &r_alpha, core::Real deriv) const | core::conformation::membrane::MembraneGeometry | |
| f1_pore(core::Real f_thk, numeric::xyzVector< core::Real > const &xyz, Conformation const &conf, core::Size resnum, core::Size atomnum) const | core::conformation::membrane::MembraneGeometry | |
| f2(core::Vector const &atom_xyz, core::Vector const &r_alpha, core::Real deriv) const | core::conformation::membrane::MembraneGeometry | |
| f2_pore(core::Real f_thk, numeric::xyzVector< core::Real > const &xyz, Conformation const &conf, core::Size resnum, core::Size atomnum) const | core::conformation::membrane::MembraneGeometry | |
| f_bicelle(core::Real f_z, core::Vector xyz, const core::Vector mem_cen) const | core::conformation::membrane::membrane_geometry::Bicelle | private |
| f_cavity(numeric::xyzVector< core::Real > const &p) const | core::conformation::membrane::MembraneGeometry | |
| f_cavity_dx(numeric::xyzVector< core::Real > const &p, core::Real f_thk) const | core::conformation::membrane::MembraneGeometry | |
| f_cavity_dy(numeric::xyzVector< core::Real > const &p, core::Real f_thk) const | core::conformation::membrane::MembraneGeometry | |
| f_cavity_dz(numeric::xyzVector< core::Real > const &p, core::Real f_thk) const | core::conformation::membrane::MembraneGeometry | |
| f_cavity_gradient(core::Real const r) const | core::conformation::membrane::MembraneGeometry | |
| f_franklin(core::Real const z, core::Real tau, core::Real kappa) const | core::conformation::membrane::MembraneGeometry | |
| f_franklin_gradient(core::Real const z, core::Real tau, core::Real kappa) const | core::conformation::membrane::MembraneGeometry | |
| f_hydration(core::Real f_thk, numeric::xyzVector< core::Real > const &p) const | core::conformation::membrane::MembraneGeometry | |
| f_hydration_deriv_dz(numeric::xyzVector< core::Real > const &p, core::Real f_thk_deriv_dz) const | core::conformation::membrane::MembraneGeometry | |
| f_imm1(core::Real z_position) const | core::conformation::membrane::MembraneGeometry | |
| f_imm1_deriv(core::Real z_position) const | core::conformation::membrane::MembraneGeometry | |
| f_thickness(Conformation const &conf, core::Real const z) const | core::conformation::membrane::MembraneGeometry | |
| f_thickness_deriv(Conformation const &conf, core::Real const z) const | core::conformation::membrane::MembraneGeometry | |
| f_transition(Conformation const &conf, core::Size resnum, core::Size atomnum) const override | core::conformation::membrane::membrane_geometry::Bicelle | virtual |
| f_transition_deriv(Conformation const &conf, core::Size resnum, core::Size atomnum) const | core::conformation::membrane::membrane_geometry::Bicelle | |
| f_transition_deriv_m(Conformation const &conf, core::Size resnum, core::Size atomnum) const | core::conformation::membrane::membrane_geometry::Bicelle | |
| f_transition_f1(Conformation const &conf, core::Size resnum, core::Size atomnum) const override | core::conformation::membrane::membrane_geometry::Bicelle | virtual |
| f_transition_f2(Conformation const &conf, core::Size resnum, core::Size atomnum) const override | core::conformation::membrane::membrane_geometry::Bicelle | virtual |
| fa_elec_lipid(Conformation const &conf, core::Size resnum, core::Size atomnum) const override | core::conformation::membrane::membrane_geometry::Bicelle | virtual |
| fa_elec_lipid_deriv(Conformation const &conf, core::Size resnum, core::Size atomnum) const override | core::conformation::membrane::membrane_geometry::Bicelle | virtual |
| g_radius(numeric::xyzVector< core::Real > const &p) const | core::conformation::membrane::MembraneGeometry | |
| g_radius_gradient_dx(numeric::xyzVector< core::Real > const &p) const | core::conformation::membrane::MembraneGeometry | |
| g_radius_gradient_dy(numeric::xyzVector< core::Real > const &p) const | core::conformation::membrane::MembraneGeometry | |
| g_radius_gradient_dz(numeric::xyzVector< core::Real > const &p) const | core::conformation::membrane::MembraneGeometry | |
| geometry_enum() const override | core::conformation::membrane::membrane_geometry::Bicelle | virtual |
| geometry_string() const override | core::conformation::membrane::membrane_geometry::Bicelle | virtual |
| h_bicelle(core::Vector xyz, const core::Vector mem_cen) const | core::conformation::membrane::membrane_geometry::Bicelle | private |
| h_bicelle_deriv_wrt_r(core::Vector xyz, const core::Vector mem_cen) const | core::conformation::membrane::membrane_geometry::Bicelle | private |
| has_pore() const | core::conformation::membrane::MembraneGeometry | |
| membrane_steepness() const | core::conformation::membrane::MembraneGeometry | virtual |
| membrane_thickness() const | core::conformation::membrane::MembraneGeometry | virtual |
| MembraneGeometry()=delete | core::conformation::membrane::MembraneGeometry | |
| MembraneGeometry(core::Real steepness) | core::conformation::membrane::MembraneGeometry | |
| MembraneGeometry(core::Real steepness, core::Real thickness) | core::conformation::membrane::MembraneGeometry | |
| MembraneGeometry(core::Real steepness, core::Real thickness, AqueousPoreParametersOP aqueous_pore) | core::conformation::membrane::MembraneGeometry | |
| normal_vector(Conformation const &conf) const | core::conformation::membrane::MembraneGeometry | protected |
| pore_params_ | core::conformation::membrane::MembraneGeometry | private |
| pore_transition_steepness_ | core::conformation::membrane::MembraneGeometry | private |
| protein_slice_diameter() const | core::conformation::membrane::membrane_geometry::Bicelle | |
| protein_slice_diameter_ | core::conformation::membrane::membrane_geometry::Bicelle | private |
| protein_slice_diameter_at_mem_cen(Conformation const &conf, core::Size membrane_pos) const | core::conformation::membrane::membrane_geometry::Bicelle | private |
| r_alpha(Conformation const &conf, core::Size resnum, core::Size atomnum) const | core::conformation::membrane::membrane_geometry::Bicelle | |
| r_alpha_m(Conformation const &conf, core::Size resnum, core::Size atomnum) const | core::conformation::membrane::membrane_geometry::Bicelle | |
| r_alpha_p_x(numeric::xyzVector< core::Real > const &xyz) const | core::conformation::membrane::MembraneGeometry | |
| r_alpha_p_y(numeric::xyzVector< core::Real > const &xyz) const | core::conformation::membrane::MembraneGeometry | |
| r_alpha_p_z(Conformation const &conf, core::Size resnum, core::Size atomnum) const | core::conformation::membrane::MembraneGeometry | |
| set_aqueous_pore_parameters(AqueousPoreParametersOP aqueous_pore) | core::conformation::membrane::MembraneGeometry | |
| set_bicelle_edge_steepness(core::Real edge_steepness) | core::conformation::membrane::membrane_geometry::Bicelle | |
| set_inner_radius(core::Real inner_r) | core::conformation::membrane::membrane_geometry::Bicelle | |
| set_outer_radius(core::Real outer_r) | core::conformation::membrane::membrane_geometry::Bicelle | |
| set_protein_slice_diameter(core::Real diameter) | core::conformation::membrane::membrane_geometry::Bicelle | |
| show() const override | core::conformation::membrane::membrane_geometry::Bicelle | virtual |
| show(std::ostream &output) const override | core::conformation::membrane::membrane_geometry::Bicelle | virtual |
| steepness_ | core::conformation::membrane::MembraneGeometry | private |
| thickness_ | core::conformation::membrane::MembraneGeometry | private |
| thickness_vector(Conformation const &conf) const | core::conformation::membrane::MembraneGeometry | protected |
| update_edge_steepness() | core::conformation::membrane::membrane_geometry::Bicelle | private |
| update_inner_radius() | core::conformation::membrane::membrane_geometry::Bicelle | private |
| update_outer_radius() | core::conformation::membrane::membrane_geometry::Bicelle | private |
| update_radii() | core::conformation::membrane::membrane_geometry::Bicelle | |
| ~Bicelle() override | core::conformation::membrane::membrane_geometry::Bicelle | |
| ~MembraneGeometry() override | core::conformation::membrane::MembraneGeometry | |
