Gemmi C++ API
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Public Member Functions | Public Attributes | List of all members
gemmi::SolventMasker Struct Reference

#include <solmask.hpp>

Public Member Functions

 SolventMasker (AtomicRadiiSet choice, double constant_r_=0.)
 
void set_radii (AtomicRadiiSet choice, double constant_r_=0.)
 
template<typename T >
void clear (Grid< T > &grid) const
 fill whole grid with 1
 
template<typename T >
void mask_points (Grid< T > &grid, const Model &model) const
 set grid points around atoms to 0
 
void mask_points (Grid< float > &grid, const Model &model) const
 
template<typename T >
void symmetrize (Grid< T > &grid) const
 Apply symmetry to grid (to fill whole grid).
 
template<typename T >
void shrink (Grid< T > &grid) const
 
template<typename T >
void invert (Grid< T > &grid) const
 
template<typename T >
int remove_islands (Grid< T > &grid) const
 
template<typename T >
void put_mask_on_grid (Grid< T > &grid, const Model &model) const
 
void set_to_zero (Grid< float > &grid, const Model &model) const
 

Public Attributes

AtomicRadiiSet atomic_radii_set
 
bool ignore_hydrogen
 
bool ignore_zero_occupancy_atoms
 
bool use_atom_occupancy = false
 
double rprobe
 
double rshrink
 
double island_min_volume
 
double constant_r
 
double requested_spacing = 0.
 

Detailed Description

Definition at line 284 of file solmask.hpp.

Constructor & Destructor Documentation

◆ SolventMasker()

gemmi::SolventMasker::SolventMasker ( AtomicRadiiSet  choice,
double  constant_r_ = 0. 
)
inline

Definition at line 295 of file solmask.hpp.

Member Function Documentation

◆ set_radii()

void gemmi::SolventMasker::set_radii ( AtomicRadiiSet  choice,
double  constant_r_ = 0. 
)
inline

Definition at line 300 of file solmask.hpp.

◆ clear()

template<typename T >
void gemmi::SolventMasker::clear ( Grid< T > &  grid) const
inline

fill whole grid with 1

Definition at line 330 of file solmask.hpp.

◆ mask_points() [1/2]

template<typename T >
void gemmi::SolventMasker::mask_points ( Grid< T > &  grid,
const Model &  model 
) const
inline

set grid points around atoms to 0

Definition at line 333 of file solmask.hpp.

◆ mask_points() [2/2]

void gemmi::SolventMasker::mask_points ( Grid< float > &  grid,
const Model &  model 
) const
inline

Definition at line 338 of file solmask.hpp.

◆ symmetrize()

template<typename T >
void gemmi::SolventMasker::symmetrize ( Grid< T > &  grid) const
inline

Apply symmetry to grid (to fill whole grid).

If we are using an integer/binary mask this is done by distributing all 0-value grid points - while for a float map/mask we are setting each grid point to the minimum value.

Definition at line 350 of file solmask.hpp.

◆ shrink()

template<typename T >
void gemmi::SolventMasker::shrink ( Grid< T > &  grid) const
inline

Definition at line 359 of file solmask.hpp.

◆ invert()

template<typename T >
void gemmi::SolventMasker::invert ( Grid< T > &  grid) const
inline

Definition at line 366 of file solmask.hpp.

◆ remove_islands()

template<typename T >
int gemmi::SolventMasker::remove_islands ( Grid< T > &  grid) const
inline

Definition at line 375 of file solmask.hpp.

◆ put_mask_on_grid()

template<typename T >
void gemmi::SolventMasker::put_mask_on_grid ( Grid< T > &  grid,
const Model &  model 
) const
inline

Definition at line 393 of file solmask.hpp.

◆ set_to_zero()

void gemmi::SolventMasker::set_to_zero ( Grid< float > &  grid,
const Model &  model 
) const
inline

Definition at line 402 of file solmask.hpp.

Member Data Documentation

◆ atomic_radii_set

AtomicRadiiSet gemmi::SolventMasker::atomic_radii_set

Definition at line 285 of file solmask.hpp.

◆ ignore_hydrogen

bool gemmi::SolventMasker::ignore_hydrogen

Definition at line 286 of file solmask.hpp.

◆ ignore_zero_occupancy_atoms

bool gemmi::SolventMasker::ignore_zero_occupancy_atoms

Definition at line 287 of file solmask.hpp.

◆ use_atom_occupancy

bool gemmi::SolventMasker::use_atom_occupancy = false

Definition at line 288 of file solmask.hpp.

◆ rprobe

double gemmi::SolventMasker::rprobe

Definition at line 289 of file solmask.hpp.

◆ rshrink

double gemmi::SolventMasker::rshrink

Definition at line 290 of file solmask.hpp.

◆ island_min_volume

double gemmi::SolventMasker::island_min_volume

Definition at line 291 of file solmask.hpp.

◆ constant_r

double gemmi::SolventMasker::constant_r

Definition at line 292 of file solmask.hpp.

◆ requested_spacing

double gemmi::SolventMasker::requested_spacing = 0.

Definition at line 293 of file solmask.hpp.

The documentation for this struct was generated from the following file:
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