#include <ResidueDepthFilter.hh>

Public Member Functions
	ResidueDepthCalculator ()

	~ResidueDepthCalculator ()

utility::vector1< core::Real >	estimate_sidechain_depth (core::pose::Pose const &pose) const

void	report_crd (bool const value)

void	niter (core::Size const value)

void	set_dcut1 (core::Real const value)

void	set_dcut2 (core::Real const value)

core::Real	get_scdepth_avrg (core::Size const ires) const

core::Size	nres () const
	These are only valid after the call to estimate_sidechain_depth() More...

utility::vector1< core::Real >	get_scdepth_avrg () const

utility::vector1< core::Real >	get_scdepth_sdev () const

utility::vector1< core::Real >	get_scdepth_fvar () const

Private Member Functions
void	initialize ()

utility::vector1< core::Vector >	read_unit_waterbox (core::Vector &boxwidth) const

void	get_pose_crd_and_index (core::pose::Pose const &pose, utility::vector1< core::Vector > &protein_crd, utility::vector1< core::Size > &coarse_index, utility::vector1< core::Size > &res_id) const

utility::vector1< core::Vector >	get_coarse_crd (utility::vector1< core::Vector > const &protein_crd, utility::vector1< core::Size > const &coarse_index) const

void	duplicate_waterbox (utility::vector1< core::Vector > const &unit_waterbox_crd, core::Vector const boxwidth, core::Vector const mincrds, core::Vector const maxcrds) const

core::Vector	bring_to_origin (utility::vector1< core::Vector > &protein_crd, core::Vector &maxcrds, core::Vector &mincrds) const

void	append_unitbox (utility::vector1< core::Vector > const &unitbox, utility::vector1< core::Vector > &waterbox_dupl, core::Vector const boxwidth, int const i, int const j, int const k) const

void	pert_protein (utility::vector1< core::Vector > &protein_crd) const

utility::vector1< core::Vector >	quat2U (core::Vector const &quat3, core::Real const &quatw) const

utility::vector1< bool >	get_exclusion_index (utility::vector1< core::Vector > const &protein_crd, utility::vector1< core::Vector > const &protein_coarse_crd) const

utility::vector1< core::Real >	get_scdepth (utility::vector1< bool > const &excluded_wat, utility::vector1< core::Vector > const &protein_crd, utility::vector1< core::Size > const &res_id) const

bool	stack_and_getaverage (utility::vector1< utility::vector1< core::Real > > &sc_depth_stack, utility::vector1< core::Real > const &sc_depth, core::Size const niter) const

Private Attributes
core::Size	niter_

std::string	waterbox_file_

core::Real	dcut1_

core::Real	dcut2_

bool	use_bb_

bool	use_sc_

bool	report_crd_

core::Size	nres_ = 0

utility::vector1< core::Vector >	waterbox_

utility::vector1< core::Real >	sc_depth_avrg_

utility::vector1< core::Real >	sc_depth_sdev_

utility::vector1< core::Real >	sc_depth_fvar_

Constructor & Destructor Documentation

◆ ResidueDepthCalculator()

protocols::simple_filters::ResidueDepthCalculator::ResidueDepthCalculator ( )

◆ ~ResidueDepthCalculator()

protocols::simple_filters::ResidueDepthCalculator::~ResidueDepthCalculator ( )

default

Member Function Documentation

◆ append_unitbox()

void protocols::simple_filters::ResidueDepthCalculator::append_unitbox	(	utility::vector1< core::Vector > const &	unitbox,
		utility::vector1< core::Vector > &	waterbox_dupl,
		core::Vector const	boxwidth,
		int const	i,
		int const	j,
		int const	k
	)		const

private

◆ bring_to_origin()

Vector protocols::simple_filters::ResidueDepthCalculator::bring_to_origin	(	utility::vector1< core::Vector > &	protein_crd,
		core::Vector &	maxcrds,
		core::Vector &	mincrds
	)		const

private

References protocols::membrane::com().

◆ duplicate_waterbox()

void protocols::simple_filters::ResidueDepthCalculator::duplicate_waterbox	(	utility::vector1< core::Vector > const &	unit_waterbox_crd,
		core::Vector const	boxwidth,
		core::Vector const	mincrds,
		core::Vector const	maxcrds
	)		const

private

References protocols::simple_filters::TR().

◆ estimate_sidechain_depth()

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::estimate_sidechain_depth ( core::pose::Pose const & pose ) const

References core::pose::Pose::size(), and protocols::simple_filters::TR().

Referenced by protocols::simple_filters::ResidueDepthFilter::get_residue_depth(), and protocols::simple_filters::ResidueDepthFilter::get_SDE_score().

◆ get_coarse_crd()

utility::vector1< Vector > protocols::simple_filters::ResidueDepthCalculator::get_coarse_crd	(	utility::vector1< core::Vector > const &	protein_crd,
		utility::vector1< core::Size > const &	coarse_index
	)		const

private

◆ get_exclusion_index()

utility::vector1< bool > protocols::simple_filters::ResidueDepthCalculator::get_exclusion_index	(	utility::vector1< core::Vector > const &	protein_crd,
		utility::vector1< core::Vector > const &	protein_coarse_crd
	)		const

private

References core::kinematics::tree::distance_squared(), and protocols::simple_filters::TR().

◆ get_pose_crd_and_index()

void protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index	(	core::pose::Pose const &	pose,
		utility::vector1< core::Vector > &	protein_crd,
		utility::vector1< core::Size > &	coarse_index,
		utility::vector1< core::Size > &	res_id
	)		const

private

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::conformation::Residue::atom_name(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

◆ get_scdepth()

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::get_scdepth	(	utility::vector1< bool > const &	excluded_wat,
		utility::vector1< core::Vector > const &	protein_crd,
		utility::vector1< core::Size > const &	res_id
	)		const

private

◆ get_scdepth_avrg() [1/2]

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::get_scdepth_avrg ( ) const

inline

References sc_depth_avrg_.

◆ get_scdepth_avrg() [2/2]

core::Real protocols::simple_filters::ResidueDepthCalculator::get_scdepth_avrg ( core::Size const ires ) const

inline

References sc_depth_avrg_.

Referenced by protocols::simple_filters::ResidueDepthFilter::get_scdepth_avrg(), and protocols::simple_filters::ResidueDepthFilter::make_context().

◆ get_scdepth_fvar()

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::get_scdepth_fvar ( ) const

inline

References sc_depth_fvar_.

Referenced by protocols::simple_filters::ResidueDepthFilter::get_scdepth_fvar().

◆ get_scdepth_sdev()

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::get_scdepth_sdev ( ) const

inline

References sc_depth_sdev_.

Referenced by protocols::simple_filters::ResidueDepthFilter::get_scdepth_sdev().

◆ initialize()

void protocols::simple_filters::ResidueDepthCalculator::initialize ( )

private

◆ niter()

void protocols::simple_filters::ResidueDepthCalculator::niter ( core::Size const value )

inline

References niter_.

Referenced by protocols::simple_filters::ResidueDepthFilter::set_niter().

◆ nres()

core::Size protocols::simple_filters::ResidueDepthCalculator::nres ( ) const

inline

These are only valid after the call to estimate_sidechain_depth()

References nres_.

◆ pert_protein()

void protocols::simple_filters::ResidueDepthCalculator::pert_protein ( utility::vector1< core::Vector > & protein_crd ) const

private

References core::scoring::rg, protocols::simple_filters::TR(), core::chemical::element::U, and protocols::hybridization::val.

◆ quat2U()

utility::vector1< Vector > protocols::simple_filters::ResidueDepthCalculator::quat2U	(	core::Vector const &	quat3,
		core::Real const &	quatw
	)		const

private

References core::chemical::element::U.

◆ read_unit_waterbox()

utility::vector1< Vector > protocols::simple_filters::ResidueDepthCalculator::read_unit_waterbox ( core::Vector & boxwidth ) const

private

References core::conformation::Residue::aa(), core::chemical::aa_h2o, core::conformation::Residue::is_virtual_residue(), core::import_pose::PDB_file, core::pose::Pose::pdb_info(), core::import_pose::pose_from_file(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::simple_filters::TR(), and core::conformation::Residue::xyz().

◆ report_crd()

void protocols::simple_filters::ResidueDepthCalculator::report_crd ( bool const value )

inline

References report_crd_.

Referenced by protocols::simple_filters::ResidueDepthFilter::set_report_crd().

◆ set_dcut1()

void protocols::simple_filters::ResidueDepthCalculator::set_dcut1 ( core::Real const value )

inline

References dcut1_.

Referenced by protocols::simple_filters::ResidueDepthFilter::parse_my_tag().

◆ set_dcut2()

void protocols::simple_filters::ResidueDepthCalculator::set_dcut2 ( core::Real const value )

inline

References dcut2_.

Referenced by protocols::simple_filters::ResidueDepthFilter::parse_my_tag().

◆ stack_and_getaverage()

bool protocols::simple_filters::ResidueDepthCalculator::stack_and_getaverage	(	utility::vector1< utility::vector1< core::Real > > &	sc_depth_stack,
		utility::vector1< core::Real > const &	sc_depth,
		core::Size const	niter
	)		const

private

References protocols::simple_filters::TR().

Member Data Documentation

◆ dcut1_

core::Real protocols::simple_filters::ResidueDepthCalculator::dcut1_

private

Referenced by set_dcut1().

◆ dcut2_

core::Real protocols::simple_filters::ResidueDepthCalculator::dcut2_

private

Referenced by set_dcut2().

◆ niter_

core::Size protocols::simple_filters::ResidueDepthCalculator::niter_

private

Referenced by niter().

◆ nres_

core::Size protocols::simple_filters::ResidueDepthCalculator::nres_ = 0

mutableprivate

Referenced by nres().

◆ report_crd_

bool protocols::simple_filters::ResidueDepthCalculator::report_crd_

private

Referenced by report_crd().

◆ sc_depth_avrg_

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::sc_depth_avrg_

mutableprivate

Referenced by get_scdepth_avrg().

◆ sc_depth_fvar_

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::sc_depth_fvar_

mutableprivate

Referenced by get_scdepth_fvar().

◆ sc_depth_sdev_

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::sc_depth_sdev_

mutableprivate

Referenced by get_scdepth_sdev().

◆ use_bb_

bool protocols::simple_filters::ResidueDepthCalculator::use_bb_

private

◆ use_sc_

bool protocols::simple_filters::ResidueDepthCalculator::use_sc_

private

◆ waterbox_

utility::vector1< core::Vector > protocols::simple_filters::ResidueDepthCalculator::waterbox_

mutableprivate

◆ waterbox_file_

std::string protocols::simple_filters::ResidueDepthCalculator::waterbox_file_

private

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

src/protocols/simple_filters/ResidueDepthFilter.hh
src/protocols/simple_filters/ResidueDepthFilter.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ ResidueDepthCalculator()

◆ ~ResidueDepthCalculator()

Member Function Documentation

◆ append_unitbox()

◆ bring_to_origin()

◆ duplicate_waterbox()

◆ estimate_sidechain_depth()

◆ get_coarse_crd()

◆ get_exclusion_index()

◆ get_pose_crd_and_index()

◆ get_scdepth()

◆ get_scdepth_avrg() [1/2]

◆ get_scdepth_avrg() [2/2]

◆ get_scdepth_fvar()

◆ get_scdepth_sdev()

◆ initialize()

◆ niter()

◆ nres()

◆ pert_protein()

◆ quat2U()

◆ read_unit_waterbox()

◆ report_crd()

◆ set_dcut1()

◆ set_dcut2()

◆ stack_and_getaverage()

Member Data Documentation

◆ dcut1_

◆ dcut2_

◆ niter_

◆ nres_

◆ report_crd_

◆ sc_depth_avrg_

◆ sc_depth_fvar_

◆ sc_depth_sdev_

◆ use_bb_

◆ use_sc_

◆ waterbox_

◆ waterbox_file_