#include <AtomicDepth.hh>

Inheritance diagram for core::scoring::atomic_depth::AtomicDepth:

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< Real >	calcdepth (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`
	)

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.

References boxlength_, buildboundary(), depty_, fastdistancemap(), fillvoxels(), fixsf_, flagradius_, core::conformation::get_residue_from_name1(), initpara(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::n_non_polymeric_residue_connections(), pheight_, plength_, proberadius_, pwidth_, core::pose::Pose::replace_residue(), core::pose::Pose::residue_type(), scalefactor_, core::conformation::Residue::set_chi(), core::pose::Pose::size(), protocols::kinmatch::str(), core::scoring::TR(), vp_, and widxz_.

Member Function Documentation

void core::scoring::atomic_depth::AtomicDepth::boundbox	(	pose::Pose const &	pose,
		point3d &	minp,
		point3d &	maxp
	)

private

References core::conformation::Residue::atom_type(), core::chemical::AtomType::is_virtual(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::atomic_depth::point3d::x, protocols::kinmatch::xyz(), core::conformation::Residue::xyz(), core::scoring::atomic_depth::point3d::y, and core::scoring::atomic_depth::point3d::z.

Referenced by initpara().

void core::scoring::atomic_depth::AtomicDepth::boundingatom ( pose::Pose const & pose )

private

References core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::chemical::ResidueTypeBase::atom_type_set(), depty_, core::chemical::AtomType::is_virtual(), core::chemical::AtomTypeSet::n_atomtypes(), core::conformation::Residue::nheavyatoms(), proberadius_, core::pose::Pose::residue(), scalefactor_, core::pose::Pose::size(), core::conformation::Residue::type(), and widxz_.

Referenced by initpara().

void core::scoring::atomic_depth::AtomicDepth::buildboundary ( )

private

References core::scoring::atomic_depth::nb, pheight_, plength_, pwidth_, and vp_.

Referenced by AtomicDepth().

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

References pheight_, plength_, proberadius_, ptran_, pwidth_, scalefactor_, core::conformation::Atom::type(), vp_, core::scoring::atomic_depth::point3d::x, core::conformation::Atom::xyz(), core::scoring::atomic_depth::point3d::y, and core::scoring::atomic_depth::point3d::z.

void core::scoring::atomic_depth::AtomicDepth::fastdistancemap ( int type )

private

References cutradis_, core::kinematics::distance(), fastoneshell(), inarray_, outarray_, pheight_, plength_, pwidth_, scalefactor_, totalinnervox_, totalsurfacevox_, and vp_.

Referenced by AtomicDepth().

void core::scoring::atomic_depth::AtomicDepth::fastoneshell	(	int	innum,
		int &	allocout,
		std::vector< std::vector< std::vector< voxel2 > > > &	boundpoint,
		int &	outnum,
		int &	elimi
	)