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core::scoring::atomic_depth::AtomicDepth Class Reference

#include <AtomicDepth.hh>

Inheritance diagram for core::scoring::atomic_depth::AtomicDepth:
Inheritance graph
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Public Member Functions

 AtomicDepth (pose::Pose const &pose, Real probe_radius=1.4, bool poly_leu_depth=false, Real resolution=0.25)
 Constructor for AtomicDepth object If poly_leu_depth is true, mutate pose to poly_leu before depth calculations. The intent is to make this aa independent to avoid surface lysines from adding noise. More...
 
utility::vector1< Realcalcdepth (utility::vector1< conformation::Atom > const &atoms, chemical::AtomTypeSet const &type_set) const
 
Real calcdepth (conformation::Atom const &atom, chemical::AtomTypeSet const &type_set) const
 
void visualize_at_depth (Real depth, std::string const &fname, Real fraction=1.0) const
 

Private Member Functions

void boundbox (pose::Pose const &pose, point3d &minp, point3d &maxp)
 
void boundingatom (pose::Pose const &pose)
 
void initpara (pose::Pose const &pose)
 
void fill_vp ()
 
void fillvoxels (pose::Pose const &pose)
 
void fillatom (conformation::Atom const &atom)
 
void fastoneshell (int innum, int &allocout, std::vector< std::vector< std::vector< voxel2 > > > &boundpoint, int &outnum, int &elimi)
 
void fastdistancemap (int type)
 
void buildboundary ()
 

Private Attributes

point3d ptran_
 
int boxlength_
 
bool flagradius_
 
core::Real proberadius_
 
core::Real fixsf_
 
core::Real scalefactor_
 
point3d pmin_
 
point3d pmax_
 
int pheight_
 
int pwidth_
 
int plength_
 
std::vector< int > widxz_
 
std::vector< std::vector< int > > depty_
 
core::Real cutradis_
 
std::vector< std::vector
< std::vector< volumepixel > > > 
vp_
 
std::shared_ptr< std::vector
< voxel2 > > 
inarray_
 
std::shared_ptr< std::vector
< voxel2 > > 
outarray_
 
int totalsurfacevox_
 
int totalinnervox_
 

Constructor & Destructor Documentation

core::scoring::atomic_depth::AtomicDepth::AtomicDepth ( pose::Pose const &  pose,
Real  probe_radius = 1.4,
bool  poly_leu_depth = false,
Real  resolution = 0.25 
)

Member Function Documentation

void core::scoring::atomic_depth::AtomicDepth::boundbox ( pose::Pose const &  pose,
point3d minp,
point3d maxp 
)
private
void core::scoring::atomic_depth::AtomicDepth::boundingatom ( pose::Pose const &  pose)
private
void core::scoring::atomic_depth::AtomicDepth::buildboundary ( )
private
utility::vector1< Real > core::scoring::atomic_depth::AtomicDepth::calcdepth ( utility::vector1< conformation::Atom > const &  atoms,
chemical::AtomTypeSet const &  type_set 
) const
Real core::scoring::atomic_depth::AtomicDepth::calcdepth ( conformation::Atom const &  atom,
chemical::AtomTypeSet const &  type_set 
) const
void core::scoring::atomic_depth::AtomicDepth::fastdistancemap ( int  type)
private
void core::scoring::atomic_depth::AtomicDepth::fastoneshell ( int  innum,
int &  allocout,
std::vector< std::vector< std::vector< voxel2 > > > &  boundpoint,
int &  outnum,
int &  elimi 
)
private
void core::scoring::atomic_depth::AtomicDepth::fill_vp ( )
private

References pheight_, plength_, pwidth_, and vp_.

Referenced by fillvoxels().

void core::scoring::atomic_depth::AtomicDepth::fillatom ( conformation::Atom const &  atom)
private
void core::scoring::atomic_depth::AtomicDepth::fillvoxels ( pose::Pose const &  pose)
private
void core::scoring::atomic_depth::AtomicDepth::initpara ( pose::Pose const &  pose)
private
void core::scoring::atomic_depth::AtomicDepth::visualize_at_depth ( Real  depth,
std::string const &  fname,
Real  fraction = 1.0 
) const

Member Data Documentation

int core::scoring::atomic_depth::AtomicDepth::boxlength_
private

Referenced by AtomicDepth(), and initpara().

core::Real core::scoring::atomic_depth::AtomicDepth::cutradis_
private

Referenced by fastdistancemap(), and initpara().

std::vector<std::vector<int> > core::scoring::atomic_depth::AtomicDepth::depty_
private

Referenced by AtomicDepth(), boundingatom(), and fillatom().

core::Real core::scoring::atomic_depth::AtomicDepth::fixsf_
private

Referenced by AtomicDepth(), and initpara().

bool core::scoring::atomic_depth::AtomicDepth::flagradius_
private

Referenced by AtomicDepth().

std::shared_ptr<std::vector<voxel2> > core::scoring::atomic_depth::AtomicDepth::inarray_
private

Referenced by fastdistancemap().

std::shared_ptr<std::vector<voxel2> > core::scoring::atomic_depth::AtomicDepth::outarray_
private

Referenced by fastdistancemap(), and fastoneshell().

int core::scoring::atomic_depth::AtomicDepth::pheight_
private
int core::scoring::atomic_depth::AtomicDepth::plength_
private
point3d core::scoring::atomic_depth::AtomicDepth::pmax_
private

Referenced by initpara().

point3d core::scoring::atomic_depth::AtomicDepth::pmin_
private

Referenced by initpara().

core::Real core::scoring::atomic_depth::AtomicDepth::proberadius_
private
point3d core::scoring::atomic_depth::AtomicDepth::ptran_
private
int core::scoring::atomic_depth::AtomicDepth::pwidth_
private
core::Real core::scoring::atomic_depth::AtomicDepth::scalefactor_
private
int core::scoring::atomic_depth::AtomicDepth::totalinnervox_
private

Referenced by fastdistancemap(), and fastoneshell().

int core::scoring::atomic_depth::AtomicDepth::totalsurfacevox_
private

Referenced by fastdistancemap().

std::vector<std::vector<std::vector<volumepixel > > > core::scoring::atomic_depth::AtomicDepth::vp_
private
std::vector<int> core::scoring::atomic_depth::AtomicDepth::widxz_
private

Referenced by AtomicDepth(), boundingatom(), and fillatom().


The documentation for this class was generated from the following files: