The class represents a molecule as shells of distance from the surface.
Definition at line 27 of file SurfaceShellDensityMap.h.
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| | SurfaceShellDensityMap () |
| | Creates a new density map. More...
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| | SurfaceShellDensityMap (const DensityHeader &header) |
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| | SurfaceShellDensityMap (const ParticlesTemp &ps, float voxel_size, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int num_shells=5) |
| | Generate a surface shell density map from the input particles. More...
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| void | binarize (float scene_val) |
| | Set the value of the map voxels as either scene or background. More...
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| bool | has_background_neighbor (long voxel_ind) const |
| | Checks if the one of the neighbors of the voxel is a background voxel. More...
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| void | resample () |
| | Resample the grid to consist of density shells of a model. More...
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| | SampledDensityMap (KernelType kt=GAUSSIAN) |
| | Creates a new density map for sampled map. More...
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| | SampledDensityMap (const DensityHeader &header, KernelType kt=GAUSSIAN) |
| | The size of the map is determined by the header and the data is allocated. More...
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| | SampledDensityMap (const ParticlesTemp &ps, emreal resolution, emreal voxel_size, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int sig_cutoff=3, KernelType kt=GAUSSIAN) |
| | Generate a sampled density map from the particles. More...
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KernelParameters * | get_kernel_params () |
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| float | get_minimum_resampled_value () |
| | Get minimum density value between voxels that correspond to particles. More...
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const Particles & | get_sampled_particles () const |
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FloatKey | get_weight_key () const |
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const core::XYZRs & | get_xyzr_particles () const |
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| void | 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()) |
| | Project particles on the grid by their mass value. More...
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| void | set_particles (const ParticlesTemp &ps, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key()) |
| | setting particles in case they were not set by the constructor More...
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| void | update_resolution (Float res) |
| | Update the simulation resolution. More...
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| DensityMap (std::string name="DensityMap%1%") |
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| | DensityMap (const DensityHeader &header, std::string name="DensityMap%1%") |
| | Construct a density map as instructed in the input header. More...
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| void | add (const DensityMap *other) |
| | Sums two grids; the result is kept in the map. More...
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| void | add (Float d) |
| | Add a number to every voxel in the map. More...
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| void | calc_all_voxel2loc () |
| | Calculates the coordinates that correspond to all voxels. More...
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| emreal | calcRMS () |
| | Calculates RMSD and mean of a map values as stored in the header. More...
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| void | copy_map (const DensityMap *other) |
| | Copy map into this map. More...
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| algebra::Vector3D | get_centroid (emreal threshold=0.0) const |
| | Get the centroid of all voxels with density above a given threshold. More...
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| DensityMap * | get_cropped (float threshold) |
| | Create and return a new cropped map. More...
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| DensityMap * | get_cropped (const algebra::BoundingBox3D &bb) |
| | Create and return a new cropped map with the given bounding box extent. More...
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| int | get_dim_index_by_location (const algebra::Vector3D &v, int ind) const |
| | Calculate dimension index of a given location. More...
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int | get_dim_index_by_location (float loc_val, int ind) const |
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| const DensityHeader * | get_header () const |
| | Returns a read-only pointer to the header of the map. More...
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| DensityHeader * | get_header_writable () |
| | Returns a pointer to the header of the map in a writable version. More...
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| algebra::Vector3D | get_location_by_voxel (long index) const |
| | Calculate the location of a given voxel. More...
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| float | get_location_in_dim_by_voxel (long index, int dim) const |
| | Calculate the location of a given voxel in a given dimension. More...
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| std::string | get_locations_string (float t) |
| | Print the locations of all voxels with value above a given threshold. More...
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| emreal | get_max_value () const |
| | Returns the value of the voxel with the highest density. More...
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| float | get_maximum_value_in_xy_plane (int z_ind) |
| | Get the maximum value in a XY plane indicated by a Z index. More...
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| float | get_maximum_value_in_xz_plane (int y_ind) |
| | Get the maximum value in a XZ plane indicated by a Y index. More...
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| float | get_maximum_value_in_yz_plane (int x_ind) |
| | Get the maximum value in a YZ plane indicated by a X index. More...
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| emreal | get_min_value () const |
| | Returns the value of the voxel with the lowest density. More...
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| long | get_number_of_voxels () const |
| | Get the number of map voxels. More...
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algebra::Vector3D | get_origin () const |
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bool | get_rms_calculated () const |
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| Float | get_spacing () const |
| | Get the voxel size of the map. More...
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algebra::Vector3D | get_top () const |
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virtual std::string | get_type_name () const |
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| emreal | get_value (float x, float y, float z) const |
| | Gets the value of the voxel located at (x,y,z) More...
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emreal | get_value (const algebra::Vector3D &point) const |
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| emreal | get_value (long index) const |
| | Gets the value of the voxel at a given index. More...
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| virtual ::IMP::VersionInfo | get_version_info () const |
| | Get information about the module and version of the object. More...
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| long | get_voxel_by_location (float x, float y, float z) const |
| | Calculate the voxel of a given location. More...
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| long | get_voxel_by_location (const algebra::Vector3D &v) const |
| | Calculate the voxel of a given location. More...
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bool | is_normalized () const |
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| bool | is_part_of_volume (float x, float y, float z) const |
| | Checks whether a given point is in the grid. More...
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| bool | is_part_of_volume (const algebra::Vector3D &v) const |
| | Checks whether a given point is in the grid. More...
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bool | is_xyz_ind_part_of_volume (int ix, int iy, int iz) const |
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int | lower_voxel_shift (emreal loc, emreal kdist, emreal orig, int ndim) const |
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| void | multiply (float factor) |
| | Multiply in place each voxel in the map by the input factor. More...
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| void | pad (int nx, int ny, int nz, float val=0.0) |
| | Increase the dimension of the map. More...
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| DensityMap * | pad_margin (int mrg_x, int mrg_y, int mrg_z, float val=0.0) |
| | Create a new padded map. More...
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| void | pick_max (const DensityMap *other) |
| | Pick the max value between two corresponding voxels between two maps. More...
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| void | reset_data (float value=0.0) |
| | Set the density voxels to some value and reset the management flags. More...
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| bool | same_dimensions (const DensityMap *other) const |
| | Checks if two maps have the same dimensions. More...
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| bool | same_origin (const DensityMap *other) const |
| | Checks if two maps have the same origin. More...
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| bool | same_voxel_size (const DensityMap *other) const |
| | Checks if two maps have the same voxel size. More...
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| void | set_origin (float x, float y, float z) |
| | Sets the origin of the header. More...
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void | set_origin (const IMP::algebra::Vector3D &v) |
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| void | set_value (long index, emreal value) |
| | Set the value of the voxel at a given index. More...
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| void | set_value (float x, float y, float z, emreal value) |
| | Set the value of the voxel at given coordinates. More...
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| void | set_void_map (int nx, int ny, int nz) |
| | Set the map dimension and reset all voxels to 0. More...
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| void | std_normalize () |
| | Normalize the density voxels according to standard deviation (stdv). More...
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| void | update_voxel_size (float new_apix) |
| | Update the voxel size of the map. More...
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int | upper_voxel_shift (emreal loc, emreal kdist, emreal orig, int ndim) const |
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| long | xyz_ind2voxel (int x, int y, int z) const |
| | Calculate the voxel of a given xyz index. More...
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| virtual void | clear_caches () |
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CheckLevel | get_check_level () const |
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LogLevel | get_log_level () const |
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| void | set_check_level (CheckLevel l) |
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| void | set_log_level (LogLevel l) |
| | Set the logging level used in this object. More...
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| void | set_was_used (bool tf) const |
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void | show (std::ostream &out=std::cout) const |
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const std::string & | get_name () const |
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void | set_name (std::string name) |
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| void | add_to_map (DensityMap *dm, const Particles &pis) |
| | Rasterize the particles into an existing density map. More...
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| DensityMap * | create_density_map (algebra::DenseGrid3D< float > &grid) |
| | Return a density map with the values taken from the grid. More...
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| DensityMap * | create_density_map (algebra::DenseGrid3D< double > &grid) |
| | Return a density map with the values taken from the grid. More...
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| DensityMap * | get_binarized_interior (DensityMap *dmap) |
| | Return a binarized map with 1 for voxels that are internal in the input map. More...
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| double | get_density (const DensityMap *m, const algebra::Vector3D &v) |
| | Get density value at point v, interpolating linearly from the sample values. More...
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| DensityMap * | get_resampled (DensityMap *input, double scaling) |
| | Get a resampled version of the map. More...
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| DensityMap * | get_transformed (const DensityMap *input, const algebra::Transformation3D &tr, double threshold) |
| | Return a new density map containing a rotated version of the old one. More...
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| DensityMap * | get_transformed (DensityMap *input, const algebra::Transformation3D &tr) |
| | Return a new density map containing a rotated version of the old one. More...
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| void | get_transformed_into (const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true) |
| | Rotate a density map into another map. More...
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| DensityMap * | read_map (std::string filename, MapReaderWriter *reader) |
| | Read a density map from a file (using the given reader) and return it. More...
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| DensityMap * | read_map (std::string filename) |
| | Read a density map from a file and return it. More...
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| void | write_map (DensityMap *m, std::string filename, MapReaderWriter *writer) |
| | Write a density map to a file using the given writer. More...
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| void | write_map (DensityMap *m, std::string filename) |
| | Write a density map to a file. More...
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Inheritance diagram for IMP::em::SurfaceShellDensityMap: