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IMP Reference Guide
2.18.0
The Integrative Modeling Platform
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This is the complete list of members for IMP::em::SurfaceShellDensityMap, including all inherited members.
| add(const DensityMap *other) | IMP::em::DensityMap | |
| add(Float d) | IMP::em::DensityMap | |
| add_to_map(DensityMap *dm, const Particles &pis) | IMP::em::DensityMap | related |
| allocated_data() (defined in IMP::em::DensityMap) | IMP::em::DensityMap | protected |
| binarize(float scene_val) | IMP::em::SurfaceShellDensityMap | |
| calc_all_voxel2loc() | IMP::em::DensityMap | |
| calcRMS() | IMP::em::DensityMap | |
| calculate_particles_bounding_box(const Particles &ps) | IMP::em::SampledDensityMap | protected |
| clear_caches() | IMP::Object | virtual |
| copy_map(const DensityMap *other) | IMP::em::DensityMap | |
| create_density_map(algebra::DenseGrid3D< float > &grid) | IMP::em::DensityMap | related |
| create_density_map(algebra::DenseGrid3D< double > &grid) | IMP::em::DensityMap | related |
| data_ (defined in IMP::em::DensityMap) | IMP::em::DensityMap | protected |
| data_allocated_ (defined in IMP::em::DensityMap) | IMP::em::DensityMap | protected |
| DensityMap(std::string name="DensityMap%1%") (defined in IMP::em::DensityMap) | IMP::em::DensityMap | |
| DensityMap(const DensityHeader &header, std::string name="DensityMap%1%") | IMP::em::DensityMap | |
| determine_grid_size(double resolution, double voxel_size, int sig_cutoff) | IMP::em::SampledDensityMap | protected |
| do_destroy() | IMP::Object | protectedvirtual |
| float2real(float *f_data, boost::scoped_array< double > &r_data) (defined in IMP::em::DensityMap) | IMP::em::DensityMap | protected |
| get_binarized_interior(DensityMap *dmap) | IMP::em::DensityMap | related |
| get_centroid(double threshold=0.0) const | IMP::em::DensityMap | |
| get_check_level() const (defined in IMP::Object) | IMP::Object | |
| get_cropped(float threshold) | IMP::em::DensityMap | |
| get_cropped(Particles ps, double distance, bool inverse=false, bool keep_map_dimensions=false) | IMP::em::DensityMap | |
| get_cropped(const algebra::BoundingBox3D &bb) | IMP::em::DensityMap | |
| get_density(const DensityMap *m, const algebra::Vector3D &v) | IMP::em::DensityMap | related |
| get_dim_index_by_location(const algebra::Vector3D &v, int ind) const | IMP::em::DensityMap | |
| get_dim_index_by_location(float loc_val, int ind) const (defined in IMP::em::DensityMap) | IMP::em::DensityMap | |
| get_header() const | IMP::em::DensityMap | |
| get_header_writable() | IMP::em::DensityMap | |
| get_kernel_params() (defined in IMP::em::SampledDensityMap) | IMP::em::SampledDensityMap | |
| get_location_by_voxel(long index) const | IMP::em::DensityMap | |
| get_location_in_dim_by_voxel(long index, int dim) const | IMP::em::DensityMap | |
| get_locations_string(float t) | IMP::em::DensityMap | |
| get_log_level() const (defined in IMP::Object) | IMP::Object | |
| get_max_value() const | IMP::em::DensityMap | |
| get_maximum_value_in_xy_plane(int z_ind) | IMP::em::DensityMap | |
| get_maximum_value_in_xz_plane(int y_ind) | IMP::em::DensityMap | |
| get_maximum_value_in_yz_plane(int x_ind) | IMP::em::DensityMap | |
| get_min_value() const | IMP::em::DensityMap | |
| get_minimum_resampled_value() | IMP::em::SampledDensityMap | |
| get_name() const (defined in IMP::Object) | IMP::Object | |
| get_number_of_voxels() const | IMP::em::DensityMap | |
| get_origin() const (defined in IMP::em::DensityMap) | IMP::em::DensityMap | |
| get_resampled(DensityMap *input, double scaling) | IMP::em::DensityMap | related |
| get_rms_calculated() const (defined in IMP::em::DensityMap) | IMP::em::DensityMap | |
| get_sampled_particles() const (defined in IMP::em::SampledDensityMap) | IMP::em::SampledDensityMap | |
| get_spacing() const | IMP::em::DensityMap | |
| get_top() const (defined in IMP::em::DensityMap) | IMP::em::DensityMap | |
| get_transformed(const DensityMap *input, const algebra::Transformation3D &tr, double threshold) | IMP::em::DensityMap | related |
| get_transformed(DensityMap *input, const algebra::Transformation3D &tr) | IMP::em::DensityMap | related |
| get_transformed_into(const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true) | IMP::em::DensityMap | related |
| get_type_name() const override (defined in IMP::em::DensityMap) | IMP::em::DensityMap | virtual |
| get_value(float x, float y, float z) const | IMP::em::DensityMap | |
| get_value(const algebra::Vector3D &point) const (defined in IMP::em::DensityMap) | IMP::em::DensityMap | |
| get_value(long index) const | IMP::em::DensityMap | |
| get_version_info() const override | IMP::em::DensityMap | virtual |
| get_voxel_by_location(float x, float y, float z) const | IMP::em::DensityMap | |
| get_voxel_by_location(const algebra::Vector3D &v) const | IMP::em::DensityMap | |
| get_weight_key() const (defined in IMP::em::SampledDensityMap) | IMP::em::SampledDensityMap | |
| get_xyzr_particles() const (defined in IMP::em::SampledDensityMap) | IMP::em::SampledDensityMap | |
| has_background_neighbor(long voxel_ind) const | IMP::em::SurfaceShellDensityMap | |
| header_ (defined in IMP::em::DensityMap) | IMP::em::DensityMap | protected |
| is_normalized() const (defined in IMP::em::DensityMap) | IMP::em::DensityMap | |
| is_part_of_volume(float x, float y, float z) const | IMP::em::DensityMap | |
| is_part_of_volume(const algebra::Vector3D &v) const | IMP::em::DensityMap | |
| is_xyz_ind_part_of_volume(int ix, int iy, int iz) const (defined in IMP::em::DensityMap) | IMP::em::DensityMap | |
| kernel_params_ | IMP::em::SampledDensityMap | protected |
| kt_ (defined in IMP::em::SampledDensityMap) | IMP::em::SampledDensityMap | protected |
| loc_calculated_ | IMP::em::DensityMap | protected |
| lower_voxel_shift(double loc, double kdist, double orig, int ndim) const (defined in IMP::em::DensityMap) | IMP::em::DensityMap | |
| multiply(float factor) | IMP::em::DensityMap | |
| neighbor_dist_ (defined in IMP::em::SurfaceShellDensityMap) | IMP::em::SurfaceShellDensityMap | protected |
| neighbor_shift_ (defined in IMP::em::SurfaceShellDensityMap) | IMP::em::SurfaceShellDensityMap | protected |
| NonCopyable() (defined in IMP::NonCopyable) | IMP::NonCopyable | protected |
| normalized_ (defined in IMP::em::DensityMap) | IMP::em::DensityMap | protected |
| num_shells_ (defined in IMP::em::SurfaceShellDensityMap) | IMP::em::SurfaceShellDensityMap | protected |
| Object(std::string name) | IMP::Object | protected |
| pad(int nx, int ny, int nz, float val=0.0) | IMP::em::DensityMap | |
| pad_margin(int mrg_x, int mrg_y, int mrg_z, float val=0.0) | IMP::em::DensityMap | |
| pick_max(const DensityMap *other) | IMP::em::DensityMap | |
| project(const ParticlesTemp &ps, int x_margin, int y_margin, int z_margin, algebra::Vector3D shift=algebra::Vector3D(0., 0., 0.), FloatKey mass_key=atom::Mass::get_mass_key()) | IMP::em::SampledDensityMap | |
| ps_ (defined in IMP::em::SampledDensityMap) | IMP::em::SampledDensityMap | protected |
| read_map(std::string filename, MapReaderWriter *reader) | IMP::em::DensityMap | related |
| read_map(std::string filename) | IMP::em::DensityMap | related |
| real2float(double *r_data, boost::scoped_array< float > &f_data) (defined in IMP::em::DensityMap) | IMP::em::DensityMap | protected |
| resample() override | IMP::em::SurfaceShellDensityMap | virtual |
| reset_all_voxel2loc() (defined in IMP::em::DensityMap) | IMP::em::DensityMap | protected |
| reset_data(float value=0.0) | IMP::em::DensityMap | |
| rms_calculated_ (defined in IMP::em::DensityMap) | IMP::em::DensityMap | protected |
| same_dimensions(const DensityMap *other) const | IMP::em::DensityMap | |
| same_origin(const DensityMap *other) const | IMP::em::DensityMap | |
| same_voxel_size(const DensityMap *other) const | IMP::em::DensityMap | |
| SampledDensityMap(KernelType kt=GAUSSIAN) | IMP::em::SampledDensityMap | |
| SampledDensityMap(const DensityHeader &header, KernelType kt=GAUSSIAN) | IMP::em::SampledDensityMap | |
| SampledDensityMap(const ParticlesTemp &ps, double resolution, double voxel_size, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int sig_cutoff=3, KernelType kt=GAUSSIAN) | IMP::em::SampledDensityMap | |
| set_check_level(CheckLevel l) | IMP::Object | |
| set_header(const algebra::Vector3D &lower_bound, const algebra::Vector3D &upper_bound, double maxradius, double resolution, double voxel_size, int sig_offset) (defined in IMP::em::SampledDensityMap) | IMP::em::SampledDensityMap | protected |
| set_kernel() (defined in IMP::em::SurfaceShellDensityMap) | IMP::em::SurfaceShellDensityMap | protected |
| set_log_level(LogLevel l) | IMP::Object | |
| set_name(std::string name) (defined in IMP::Object) | IMP::Object | |
| set_neighbor_mask() (defined in IMP::em::SurfaceShellDensityMap) | IMP::em::SurfaceShellDensityMap | protected |
| set_neighbor_mask(float radius) (defined in IMP::em::SampledDensityMap) | IMP::em::SampledDensityMap | protected |
| set_origin(float x, float y, float z) | IMP::em::DensityMap | |
| set_origin(const IMP::algebra::Vector3D &v) (defined in IMP::em::DensityMap) | IMP::em::DensityMap | |
| set_particles(const ParticlesTemp &ps, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key()) | IMP::em::SampledDensityMap | |
| set_surface_shell(std::vector< long > *shell) | IMP::em::SurfaceShellDensityMap | protected |
| set_value(long index, double value) | IMP::em::DensityMap | |
| set_value(float x, float y, float z, double value) | IMP::em::DensityMap | |
| set_void_map(int nx, int ny, int nz) | IMP::em::DensityMap | |
| set_was_used(bool tf) const | IMP::Object | |
| show(std::ostream &out=std::cout) const (defined in IMP::Object) | IMP::Object | |
| std_normalize() | IMP::em::DensityMap | |
| surface_val_ (defined in IMP::em::SurfaceShellDensityMap) | IMP::em::SurfaceShellDensityMap | protected |
| SurfaceShellDensityMap() | IMP::em::SurfaceShellDensityMap | |
| SurfaceShellDensityMap(const DensityHeader &header) | IMP::em::SurfaceShellDensityMap | |
| SurfaceShellDensityMap(const ParticlesTemp &ps, float voxel_size, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int num_shells=5) | IMP::em::SurfaceShellDensityMap | |
| update_header() | IMP::em::DensityMap | protected |
| update_resolution(Float res) | IMP::em::SampledDensityMap | |
| update_voxel_size(float new_apix) | IMP::em::DensityMap | |
| upper_voxel_shift(double loc, double kdist, double orig, int ndim) const (defined in IMP::em::DensityMap) | IMP::em::DensityMap | |
| weight_key_ (defined in IMP::em::SampledDensityMap) | IMP::em::SampledDensityMap | protected |
| write_map(DensityMap *m, std::string filename, MapReaderWriter *writer) | IMP::em::DensityMap | related |
| write_map(DensityMap *m, std::string filename) | IMP::em::DensityMap | related |
| x_key_ (defined in IMP::em::SampledDensityMap) | IMP::em::SampledDensityMap | protected |
| x_loc_ | IMP::em::DensityMap | protected |
| xyz_ind2voxel(int x, int y, int z) const | IMP::em::DensityMap | |
| xyzr_ (defined in IMP::em::SampledDensityMap) | IMP::em::SampledDensityMap | protected |
| y_key_ (defined in IMP::em::SampledDensityMap) | IMP::em::SampledDensityMap | protected |
| y_loc_ (defined in IMP::em::DensityMap) | IMP::em::DensityMap | protected |
| z_key_ (defined in IMP::em::SampledDensityMap) | IMP::em::SampledDensityMap | protected |
| z_loc_ (defined in IMP::em::DensityMap) | IMP::em::DensityMap | protected |
| ~DensityMap() (defined in IMP::em::DensityMap) | IMP::em::DensityMap | protectedvirtual |
| ~Object() (defined in IMP::Object) | IMP::Object | virtual |