| approximate_scaffolding_cap_radius(bool use_default) | Mesh | |
| assign_mesh2surface() | DynamicMesh | |
| calculate_element_area_volume() | Mesh | |
| calculate_gag_scaffolding_forces_fd() const | Mesh | |
| calculate_gag_scaffolding_internal_energy() const | Mesh | |
| calculate_gag_scaffolding_internal_energy(const std::vector< Matrix > &scaffoldingPoints) const | Mesh | |
| calculate_gag_scaffolding_internal_energy(const std::vector< Matrix > &scaffoldingPoints, const std::vector< GagSubunit > &subunits) const | Mesh | |
| calculate_gag_subunit_rotation_torques_fd() | Mesh | |
| calculate_gag_subunit_translation_forces_fd() | Mesh | |
| calculate_mean_force() | Mesh | |
| calculate_scaffolding_energy_force(bool doLocalSearch) | Mesh | |
| centerScaffoldingSphere | Mesh | |
| clear_force_on_vertices_and_energy_on_faces() | Mesh | |
| Compute_Energy_And_Force() | Mesh | |
| determine_boundary_vertices_faces() | Mesh | |
| determine_ghost_vertices_faces() | Mesh | |
| DynamicMesh(Param &srcParam) | DynamicMesh | |
| element_energy_force_patch(const std::vector< Matrix > &sampleRows, const std::vector< Matrix > &coordOneRingVertices, Face &face, const double spontCurv, double &meanCurv, Matrix &normVector, double &eBend, Matrix &fBend, Matrix &fArea, Matrix &fVolume) | Mesh | |
| energy_force_regularization() | Mesh | |
| enumerate_gauss_quadrature_point_area_volume(const std::vector< Matrix > &sampleRows, const Matrix &dots, double &area, double &volume) | Mesh | protected |
| enumerate_legacy_x_only_volume(const Matrix &matOneRingVertex) | Mesh | protected |
| faces | Mesh | |
| faces_share_edge(const Face &face1, const Face &face2) | Mesh | |
| faces_share_edge(const Face &face1, const Face &face2, std::vector< int > &commonElements) | Mesh | |
| find_center_of_scaffolding_sphere(bool use_default) | Mesh | |
| find_opposite_node_index(const int &node1, const int &node2, const int &node3) | Mesh | |
| findClosestRcap(double membraneCapRadius) | Mesh | |
| forceOnScaffoldingPoints | Mesh | |
| forceTotalOnScaffolding | Mesh | |
| gagAngles | Mesh | |
| gagBonds | Mesh | |
| gagInitialAlignmentRotation | Mesh | |
| gagInteractions | Mesh | |
| gagScaffoldingTopologyInitialized | Mesh | |
| gagSubunits | Mesh | |
| gagTorsions | Mesh | |
| get_max_force_magnitude() | Mesh | |
| get_one_ring_vertex_matrix(const Face &face) | Mesh | protected |
| get_relative_pt_periodic(int i, int n, int m) | DynamicMesh | protected |
| get_squared_distance_sp_and_v(const Matrix &scaffoldingPoint, const Vertex &vertex) | Mesh | protected |
| initialize_gag_scaffolding_topology() | Mesh | |
| interpolateHeight(double r, const std::vector< double > &r_vals, const std::vector< double > &h_vals) | Mesh | |
| irregularRows | Mesh | |
| is_interior_vertex(int iVertex) const | Mesh | |
| loadMembraneShapeProfile(double membraneCapRadius, std::vector< double > &r_vals, std::vector< double > &h_vals) | Mesh | |
| manage_force_for_boundary_ghost_vertex() | Mesh | |
| matMesh | DynamicMesh | |
| matSurface | DynamicMesh | |
| Mesh(Param &srcParam) | Mesh | |
| Mesh(const std::vector< Vertex > &srcVertices, const std::vector< Face > &srcFaces, Param &srcParam) __attribute__((deprecated("Initialize with Mesh(Param &srcParam) and setup with setup_from_vertices_faces instead."))) | Mesh | |
| mesh2surface | DynamicMesh | |
| move_vertices_based_on_scaffolding(bool fixDir=true) | Mesh | |
| orient_scaffolding_plane_to_membrane() | Mesh | |
| param | Mesh | |
| postprocess_ghost_periodic() | DynamicMesh | |
| pre_relax_gag_scaffolding() | Mesh | |
| propagate_scaffolding() | Mesh | |
| refine_loop_once() | Mesh | |
| report_valence_histogram() const | Mesh | |
| report_volume_rebaseline() | Mesh | |
| scaffoldingMovementVector | Mesh | |
| set_adjacent_faces_of_faces() | Mesh | |
| set_adjacent_faces_of_vertices_sorted() | Mesh | |
| set_adjacent_vertices_of_vertices_sorted() | Mesh | |
| set_axes_division_flat() | Mesh | |
| set_insertion_patch(const vector< vector< int > > &insertionPatch) | Mesh | |
| set_one_ring_vertices_sorted() | Mesh | |
| set_scaffolding_insertion_curvature() | Mesh | |
| set_scaffolding_vertices_correspondence() | Mesh | |
| set_spontaneous_curvature_for_face(const double &insertCurv, const double &spontCurv) | Mesh | |
| set_vertices_faces_flat() | Mesh | |
| setup_flat() | DynamicMesh | |
| setup_from_vertices_faces(const std::vector< std::vector< double > > &verticesData, const std::vector< std::vector< int > > &facesData) | Mesh | |
| sort_vertices_on_faces() | Mesh | |
| sum_legacy_x_only_volume() | Mesh | |
| sum_membrane_area_and_volume(double &area, double &volume) | Mesh | |
| surface2mesh | DynamicMesh | |
| update_previous_coord_for_vertex() | Mesh | |
| update_previous_energy_for_face() | Mesh | |
| update_previous_force_for_vertex() | Mesh | |
| update_reference_coord_from_previous_coord() | Mesh | |
| update_vertices_mat_with_vector() | DynamicMesh | |
| update_vertices_vector_with_mat() | DynamicMesh | |
| validate_volume_constraint_topology() const | Mesh | |
| vertices | Mesh | |
| write_faces_csv(const std::string &outfile_name) | Mesh | |
| write_gag_scaffolding_state_dat(const std::string &outfile_name) const | Mesh | |
| write_vertices_csv(const std::string &outfile_name) | Mesh | |
| write_vertices_csv_with_type(const std::string &outfile_name) | Mesh | |
