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IMP Reference Guide  2.8.0
The Integrative Modeling Platform
IMP::em::SurfaceShellDensityMap Member List

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::DensityMaprelated
allocated_data() (defined in IMP::em::DensityMap)IMP::em::DensityMapprotected
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::SampledDensityMapprotected
clear_caches()IMP::Objectvirtual
copy_map(const DensityMap *other)IMP::em::DensityMap
create_density_map(algebra::DenseGrid3D< float > &grid)IMP::em::DensityMaprelated
create_density_map(algebra::DenseGrid3D< double > &grid)IMP::em::DensityMaprelated
data_ (defined in IMP::em::DensityMap)IMP::em::DensityMapprotected
data_allocated_ (defined in IMP::em::DensityMap)IMP::em::DensityMapprotected
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(emreal resolution, emreal voxel_size, int sig_cutoff)IMP::em::SampledDensityMapprotected
do_destroy()IMP::Objectprotectedvirtual
float2real(float *f_data, boost::scoped_array< emreal > &r_data) (defined in IMP::em::DensityMap)IMP::em::DensityMapprotected
get_binarized_interior(DensityMap *dmap)IMP::em::DensityMaprelated
get_centroid(emreal 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(const algebra::BoundingBox3D &bb)IMP::em::DensityMap
get_density(const DensityMap *m, const algebra::Vector3D &v)IMP::em::DensityMaprelated
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::DensityMaprelated
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::DensityMaprelated
get_transformed(DensityMap *input, const algebra::Transformation3D &tr)IMP::em::DensityMaprelated
get_transformed_into(const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true)IMP::em::DensityMaprelated
get_type_name() const (defined in IMP::em::DensityMap)IMP::em::DensityMapvirtual
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 IMP::em::DensityMapvirtual
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::DensityMapprotected
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::SampledDensityMapprotected
kt_ (defined in IMP::em::SampledDensityMap)IMP::em::SampledDensityMapprotected
loc_calculated_IMP::em::DensityMapprotected
lower_voxel_shift(emreal loc, emreal kdist, emreal 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::SurfaceShellDensityMapprotected
neighbor_shift_ (defined in IMP::em::SurfaceShellDensityMap)IMP::em::SurfaceShellDensityMapprotected
NonCopyable() (defined in IMP::NonCopyable)IMP::NonCopyableprotected
normalized_ (defined in IMP::em::DensityMap)IMP::em::DensityMapprotected
num_shells_ (defined in IMP::em::SurfaceShellDensityMap)IMP::em::SurfaceShellDensityMapprotected
Object(std::string name)IMP::Objectprotected
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::SampledDensityMapprotected
read_map(std::string filename, MapReaderWriter *reader)IMP::em::DensityMaprelated
read_map(std::string filename)IMP::em::DensityMaprelated
real2float(emreal *r_data, boost::scoped_array< float > &f_data) (defined in IMP::em::DensityMap)IMP::em::DensityMapprotected
resample()IMP::em::SurfaceShellDensityMapvirtual
reset_all_voxel2loc() (defined in IMP::em::DensityMap)IMP::em::DensityMapprotected
reset_data(float value=0.0)IMP::em::DensityMap
rms_calculated_ (defined in IMP::em::DensityMap)IMP::em::DensityMapprotected
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, emreal resolution, emreal 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, emreal maxradius, emreal resolution, emreal voxel_size, int sig_offset) (defined in IMP::em::SampledDensityMap)IMP::em::SampledDensityMapprotected
set_kernel() (defined in IMP::em::SurfaceShellDensityMap)IMP::em::SurfaceShellDensityMapprotected
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::SurfaceShellDensityMapprotected
set_neighbor_mask(float radius) (defined in IMP::em::SampledDensityMap)IMP::em::SampledDensityMapprotected
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::SurfaceShellDensityMapprotected
set_value(long index, emreal value)IMP::em::DensityMap
set_value(float x, float y, float z, emreal 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::SurfaceShellDensityMapprotected
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::DensityMapprotected
update_resolution(Float res)IMP::em::SampledDensityMap
update_voxel_size(float new_apix)IMP::em::DensityMap
upper_voxel_shift(emreal loc, emreal kdist, emreal orig, int ndim) const (defined in IMP::em::DensityMap)IMP::em::DensityMap
weight_key_ (defined in IMP::em::SampledDensityMap)IMP::em::SampledDensityMapprotected
write_map(DensityMap *m, std::string filename, MapReaderWriter *writer)IMP::em::DensityMaprelated
write_map(DensityMap *m, std::string filename)IMP::em::DensityMaprelated
x_key_ (defined in IMP::em::SampledDensityMap)IMP::em::SampledDensityMapprotected
x_loc_IMP::em::DensityMapprotected
xyz_ind2voxel(int x, int y, int z) const IMP::em::DensityMap
xyzr_ (defined in IMP::em::SampledDensityMap)IMP::em::SampledDensityMapprotected
y_key_ (defined in IMP::em::SampledDensityMap)IMP::em::SampledDensityMapprotected
y_loc_ (defined in IMP::em::DensityMap)IMP::em::DensityMapprotected
z_key_ (defined in IMP::em::SampledDensityMap)IMP::em::SampledDensityMapprotected
z_loc_ (defined in IMP::em::DensityMap)IMP::em::DensityMapprotected
~DensityMap() (defined in IMP::em::DensityMap)IMP::em::DensityMapprotectedvirtual
~Object() (defined in IMP::Object)IMP::Objectvirtual