#include <PoseBalls.hh>

Inheritance diagram for core::scoring::packing::PoseBalls:

Public Member Functions
	~PoseBalls () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

	PoseBalls (core::pose::Pose const &pose, core::Size Hmode=0, bool ignore_water=true)

	PoseBalls (core::pose::Pose const &pose, core::id::AtomID_Mask const &whichatoms)

core::Size const &	nballs () const

core::Size const &	id_to_index (core::id::AtomID const &aid) const

core::id::AtomID const &	index_to_id (core::Size const &index) const

Ball const &	ball (core::Size const &index) const

Ball const &	ball (core::id::AtomID const &id) const

Ball &	ball (core::Size const &index)

Ball &	ball (core::id::AtomID const &id)

std::string const &	atom_name (core::Size const &index) const

core::Size const &	atom_num (core::Size const &index) const

core::Size const &	atom_type (core::Size const &index) const

std::string const &	res_name (core::Size const &index) const

core::Size const &	res_num (core::Size const &index) const

void	reset_surf ()

void	set_surf (core::Size const &index, core::Size const &ialpha, Real const &val)

Real const &	surf (core::Size const &index, core::Size const &ialpha)

utility::vector1< Ball > const &	balls () const

utility::vector1< core::id::AtomID > const &	atomids () const

char const &	secstruct (core::Size const &i) const

core::Real const &	smooth_nb (core::Size const &i) const

core::Real const &	bfac (core::Size const &i) const

bool	havesurf (core::Size const &i) const

bool	is_heavy (core::Size const &i) const

uint	nbhist (core::Size atype, core::Size bin)

void	output_pdb (std::ostream &out) const

void	compute_smooth_nb ()

Private Attributes
core::Size	nballs_

core::id::AtomID_Map< Size >	id_to_index_

utility::vector1< core::id::AtomID >	index_to_id_

utility::vector1< Ball >	balls_

utility::vector1< std::string >	atom_name_

utility::vector1< core::Size >	atom_num_

utility::vector1< std::string >	res_name_

utility::vector1< core::Size >	res_num_

utility::vector1< core::Size >	atom_type_

utility::vector1< core::Size >	atom_parent_

utility::vector1< core::Real >	smooth_nb_

utility::vector1< core::Real >	bfac_

utility::vector1< bool >	is_heavy_

utility::vector1< char >	secstruct_

utility::vector1< utility::vector1< Real > >	surf_

utility::vector1< utility::vector1< uint > >	nbhist_

Constructor & Destructor Documentation

◆ ~PoseBalls()

core::scoring::packing::PoseBalls::~PoseBalls ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

◆ PoseBalls() [1/2]

core::scoring::packing::PoseBalls::PoseBalls	(	core::pose::Pose const &	pose,
		core::Size	Hmode = `0`,
		bool	ignore_water = `true`
	)

References core::pose::motif::a(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::scoring::dssp::Dssp::dssp_reduced(), core::scoring::packstat::AtomRadiusMap::get_radius(), core::pose::initialize_atomid_map(), core::chemical::AtomType::is_heavyatom(), core::chemical::AtomType::is_hydrogen(), core::chemical::AtomType::is_polar_hydrogen(), core::conformation::Residue::is_virtual(), core::chemical::AtomType::lj_radius(), core::chemical::AtomType::name(), core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::pose::Pose::xyz().

◆ PoseBalls() [2/2]

core::scoring::packing::PoseBalls::PoseBalls	(	core::pose::Pose const &	pose,
		core::id::AtomID_Mask const &	whichatoms
	)

References core::pose::motif::a(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::scoring::dssp::Dssp::dssp_reduced(), core::scoring::packstat::AtomRadiusMap::get_radius(), core::pose::initialize_atomid_map(), core::chemical::AtomType::is_heavyatom(), core::chemical::AtomType::is_hydrogen(), core::chemical::AtomType::lj_radius(), core::chemical::AtomType::name(), core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::pose::Pose::xyz().

Member Function Documentation

◆ atom_name()

std::string const& core::scoring::packing::PoseBalls::atom_name ( core::Size const & index ) const

inline

References atom_name_.

◆ atom_num()

core::Size const& core::scoring::packing::PoseBalls::atom_num ( core::Size const & index ) const

inline

References atom_num_.

Referenced by core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), and core::scoring::packing::initialize_AtomID_Map().

◆ atom_type()

core::Size const& core::scoring::packing::PoseBalls::atom_type ( core::Size const & index ) const

inline

References atom_type_.

Referenced by core::scoring::packing::compute_dec15_score(), core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_score(), core::scoring::packing::compute_rosettaholes_score(), and core::scoring::packing::compute_smooth_nb_deriv().

◆ atomids()

utility::vector1<core::id::AtomID> const& core::scoring::packing::PoseBalls::atomids ( ) const

inline

References index_to_id_.

◆ ball() [1/4]

Ball& core::scoring::packing::PoseBalls::ball ( core::id::AtomID const & id )

inline

References balls_, and id_to_index_.

◆ ball() [2/4]

Ball const& core::scoring::packing::PoseBalls::ball ( core::id::AtomID const & id ) const

inline

References balls_, and id_to_index_.

◆ ball() [3/4]

Ball& core::scoring::packing::PoseBalls::ball ( core::Size const & index )

inline

References balls_.

◆ ball() [4/4]

Ball const& core::scoring::packing::PoseBalls::ball ( core::Size const & index ) const

inline

References balls_.

Referenced by core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), core::scoring::packing::compute_holes_surfs(), core::scoring::packing::compute_smooth_nb_deriv(), and core::scoring::packing::get_surf_vol_deriv().

◆ balls()

utility::vector1<Ball> const& core::scoring::packing::PoseBalls::balls ( ) const

inline

References balls_.

◆ bfac()

core::Real const& core::scoring::packing::PoseBalls::bfac ( core::Size const & i ) const

inline

References bfac_.

◆ compute_smooth_nb()

void core::scoring::packing::PoseBalls::compute_smooth_nb ( )

References core::scoring::packing::sigmoidish_neighbor(), and protocols::kinmatch::xyz().

◆ havesurf()

bool core::scoring::packing::PoseBalls::havesurf ( core::Size const & i ) const

inline

References atom_parent_.

◆ id_to_index()

core::Size const& core::scoring::packing::PoseBalls::id_to_index ( core::id::AtomID const & aid ) const

inline

References id_to_index_.

◆ index_to_id()

core::id::AtomID const& core::scoring::packing::PoseBalls::index_to_id ( core::Size const & index ) const

inline

References index_to_id_.

Referenced by core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_score(), core::scoring::packing::compute_rosettaholes_score(), core::scoring::packing::compute_smooth_nb_deriv(), and core::scoring::packing::get_surf_vol_deriv().

◆ is_heavy()

bool core::scoring::packing::PoseBalls::is_heavy ( core::Size const & i ) const

inline

References is_heavy_.

Referenced by core::scoring::packing::compute_smooth_nb_deriv().

◆ nballs()

core::Size const& core::scoring::packing::PoseBalls::nballs ( ) const

inline

References nballs_.

◆ nbhist()

uint core::scoring::packing::PoseBalls::nbhist	(	core::Size	atype,
		core::Size	bin
	)

inline

References nbhist_.

◆ output_pdb()

void core::scoring::packing::PoseBalls::output_pdb ( std::ostream & out ) const

References core::chemical::element::F, core::chemical::element::I, core::scoring::sasa::LJ, and core::conformation::membrane::out.

◆ res_name()

std::string const& core::scoring::packing::PoseBalls::res_name ( core::Size const & index ) const

inline

References res_name_.

Referenced by core::scoring::packing::compute_holes_deriv_res(), and core::scoring::packing::compute_holes_score_res().

◆ res_num()

core::Size const& core::scoring::packing::PoseBalls::res_num ( core::Size const & index ) const

inline

References res_num_.

Referenced by core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), and core::scoring::packing::initialize_AtomID_Map().

◆ reset_surf()

void core::scoring::packing::PoseBalls::reset_surf ( )

inline

References nballs_, and surf_.

Referenced by core::scoring::packing::compute_holes_surfs().

◆ secstruct()

char const& core::scoring::packing::PoseBalls::secstruct ( core::Size const & i ) const

inline

References secstruct_.

Referenced by core::scoring::packing::compute_dec15_score(), core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_score(), core::scoring::packing::compute_rosettaholes_score(), and core::scoring::packing::compute_smooth_nb_deriv().

◆ set_surf()

void core::scoring::packing::PoseBalls::set_surf	(	core::Size const &	index,
		core::Size const &	ialpha,
		Real const &	val
	)

inline

References atom_parent_, surf_, and protocols::hybridization::val.

Referenced by core::scoring::packing::compute_holes_surfs().

◆ smooth_nb()

core::Real const& core::scoring::packing::PoseBalls::smooth_nb ( core::Size const & i ) const

inline

References smooth_nb_.

Referenced by core::scoring::packing::compute_dec15_score(), core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_score(), and core::scoring::packing::compute_rosettaholes_score().

◆ surf()

Real const& core::scoring::packing::PoseBalls::surf	(	core::Size const &	index,
		core::Size const &	ialpha
	)

inline

References surf_.

Referenced by core::scoring::packing::compute_dec15_score(), core::scoring::packing::compute_holes_score(), and core::scoring::packing::compute_rosettaholes_score().

Member Data Documentation

◆ atom_name_

utility::vector1<std::string> core::scoring::packing::PoseBalls::atom_name_

private

Referenced by atom_name().

◆ atom_num_

utility::vector1<core::Size> core::scoring::packing::PoseBalls::atom_num_

private

Referenced by atom_num().

◆ atom_parent_

utility::vector1<core::Size> core::scoring::packing::PoseBalls::atom_parent_

private

Referenced by havesurf(), and set_surf().

◆ atom_type_

utility::vector1<core::Size> core::scoring::packing::PoseBalls::atom_type_

private

Referenced by atom_type().

◆ balls_

utility::vector1<Ball> core::scoring::packing::PoseBalls::balls_

private

Referenced by ball(), and balls().

◆ bfac_

utility::vector1<core::Real> core::scoring::packing::PoseBalls::bfac_

private

Referenced by bfac().

◆ id_to_index_

core::id::AtomID_Map<Size> core::scoring::packing::PoseBalls::id_to_index_

private

Referenced by ball(), and id_to_index().

◆ index_to_id_

utility::vector1<core::id::AtomID> core::scoring::packing::PoseBalls::index_to_id_

private

Referenced by atomids(), and index_to_id().

◆ is_heavy_

utility::vector1<bool> core::scoring::packing::PoseBalls::is_heavy_

private

Referenced by is_heavy().

◆ nballs_

core::Size core::scoring::packing::PoseBalls::nballs_

private

Referenced by nballs(), and reset_surf().

◆ nbhist_

utility::vector1<utility::vector1<uint> > core::scoring::packing::PoseBalls::nbhist_

private

Referenced by nbhist().

◆ res_name_

utility::vector1<std::string> core::scoring::packing::PoseBalls::res_name_

private

Referenced by res_name().

◆ res_num_

utility::vector1<core::Size> core::scoring::packing::PoseBalls::res_num_

private

Referenced by res_num().

◆ secstruct_

utility::vector1<char> core::scoring::packing::PoseBalls::secstruct_

private

Referenced by secstruct().

◆ smooth_nb_

utility::vector1<core::Real> core::scoring::packing::PoseBalls::smooth_nb_

private

Referenced by smooth_nb().

◆ surf_

utility::vector1<utility::vector1<Real> > core::scoring::packing::PoseBalls::surf_

private

Referenced by reset_surf(), set_surf(), and surf().

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

src/core/scoring/packing/PoseBalls.hh
src/core/scoring/packing/PoseBalls.cc

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ ~PoseBalls()

◆ PoseBalls() [1/2]

◆ PoseBalls() [2/2]

Member Function Documentation

◆ atom_name()

◆ atom_num()

◆ atom_type()

◆ atomids()

◆ ball() [1/4]

◆ ball() [2/4]

◆ ball() [3/4]

◆ ball() [4/4]

◆ balls()

◆ bfac()

◆ compute_smooth_nb()

◆ havesurf()

◆ id_to_index()

◆ index_to_id()

◆ is_heavy()

◆ nballs()

◆ nbhist()

◆ output_pdb()

◆ res_name()

◆ res_num()

◆ reset_surf()

◆ secstruct()

◆ set_surf()

◆ smooth_nb()

◆ surf()

Member Data Documentation

◆ atom_name_

◆ atom_num_

◆ atom_parent_

◆ atom_type_

◆ balls_

◆ bfac_

◆ id_to_index_

◆ index_to_id_

◆ is_heavy_

◆ nballs_

◆ nbhist_

◆ res_name_

◆ res_num_

◆ secstruct_

◆ smooth_nb_

◆ surf_