protocols::simple_filters::EnergyPerResidueFilter Class Reference

#include <EnergyPerResidueFilter.hh>

Inheritance diagram for protocols::simple_filters::EnergyPerResidueFilter:

Public Member Functions
	EnergyPerResidueFilter ()
	EnergyPerResidueFilter (core::Size const resnum, core::scoring::ScoreFunctionCOP scorefxn, core::scoring::ScoreType const score_type, core::Real const threshold, bool const whole_interface=false, bool const whole_protein=false, bool const select_resnums=false, bool const select_around_resnums=false, core::Real aournd_shell=8.0, std::string string_resnums="", std::string string_around_resnums="", core::Size const rb_jump=1, core::Real const interface_distance_cutoff=8.0, bool const bb_bb=false)
	EnergyPerResidueFilter (EnergyPerResidueFilter const &init)
void	apply_helper (std::string name, core::pose::Pose const &pose, utility::vector1< bool > &use_all_residues) const
bool	apply (core::pose::Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...
filters::FilterOP	clone () const override
filters::FilterOP	fresh_instance () const override
void	report (std::ostream &out, core::pose::Pose const &pose) const override
core::Real	report_sm (core::pose::Pose const &pose) const override
	used to report filter internals through a score or silent file More...
core::Real	compute (core::pose::Pose const &pose, core::Size const resid) const
core::Real	compute (core::pose::Pose const &pose) const
	~EnergyPerResidueFilter () override
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
core::scoring::ScoreFunctionOP	scorefxn () const
core::scoring::ScoreType	score_type () const
core::Real	threshold () const
bool	bb_bb () const
void	resnum (core::Size rn)
void	resnum (std::string const &rn)
void	scorefxn (core::scoring::ScoreFunctionOP scorefxn)
void	score_type (core::scoring::ScoreType score_type)
void	threshold (core::Real const th)
void	bb_bb (bool const b_b)
std::string	name () const override
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string const &)
	~Filter () override
virtual std::string	get_type () const
std::string	get_user_defined_name () const
void	set_user_defined_name (std::string const &name)
virtual void	clear ()
	used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
virtual core::Real	score (core::pose::Pose &pose)
virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	class_name ()
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Attributes
core::Size	resnum_
std::string	resnum_string_
core::scoring::ScoreFunctionOP	scorefxn_
core::scoring::ScoreType	score_type_
core::Real	threshold_
bool	whole_interface_
bool	whole_protein_
bool	select_resnums_
bool	select_around_resnums_
std::string	string_resnums_
std::string	string_around_resnums_
core::Real	around_shell_
core::Size	rb_jump_
core::Real	interface_distance_cutoff_
bool	bb_bb_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Constructor & Destructor Documentation

EnergyPerResidueFilter() [1/3]

protocols::simple_filters::EnergyPerResidueFilter::EnergyPerResidueFilter ( )

inline

EnergyPerResidueFilter() [2/3]

protocols::simple_filters::EnergyPerResidueFilter::EnergyPerResidueFilter	(	core::Size const	resnum,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::scoring::ScoreType const	score_type,
		core::Real const	threshold,
		bool const	whole_interface = false,
		bool const	whole_protein = false,
		bool const	select_resnums = false,
		bool const	select_around_resnums = false,
		core::Real	aournd_shell = 8.0,
		std::string	string_resnums = "",
		std::string	string_around_resnums = "",
		core::Size const	rb_jump = 1,
		core::Real const	interface_distance_cutoff = 8.0,
		bool const	bb_bb = false
	)

References score_type_, scorefxn(), scorefxn_, and core::scoring::total_score.

EnergyPerResidueFilter() [3/3]

protocols::simple_filters::EnergyPerResidueFilter::EnergyPerResidueFilter

(

EnergyPerResidueFilter const &

init

)

References core::init::init(), and scorefxn_.

~EnergyPerResidueFilter()

protocols::simple_filters::EnergyPerResidueFilter::~EnergyPerResidueFilter ( )

overridedefault

Member Function Documentation

apply()

bool protocols::simple_filters::EnergyPerResidueFilter::apply ( core::pose::Pose const &  pose ) const

overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References apply_helper(), compute(), protocols::buns::energy, protocols::simple_filters::energy_per_residue_filter_tracer(), core::conformation::Residue::is_protein(), core::conformation::Residue::name3(), core::scoring::name_from_score_type(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), resnum(), score_type_, core::pose::Pose::size(), and threshold_.

Referenced by protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions().

apply_helper()

void protocols::simple_filters::EnergyPerResidueFilter::apply_helper	(	std::string	name,
		core::pose::Pose const &	pose,
		utility::vector1< bool > &	use_all_residues
	)		const

References around_shell_, protocols::scoring::Interface::calculate(), core::kinematics::distance(), protocols::scoring::Interface::distance(), protocols::simple_filters::energy_per_residue_filter_tracer(), core::pose::Pose::fold_tree(), core::pose::get_resnum_list(), interface_distance_cutoff_, protocols::scoring::Interface::is_interface(), name(), core::scoring::name_from_score_type(), core::conformation::Residue::nbr_atom(), core::pose::Pose::num_jump(), core::pose::parse_resnum(), core::kinematics::FoldTree::partition_by_jump(), rb_jump_, core::pose::Pose::residue(), resnum_, resnum_string_, score_type_, select_around_resnums_, select_resnums_, core::pose::Pose::size(), string_around_resnums_, string_resnums_, core::pose::Pose::update_residue_neighbors(), whole_interface_, and core::conformation::Residue::xyz().

Referenced by apply(), report(), and report_sm().

bb_bb() [1/2]

bool protocols::simple_filters::EnergyPerResidueFilter::bb_bb

(

)

const

References bb_bb_.

bb_bb() [2/2]

void protocols::simple_filters::EnergyPerResidueFilter::bb_bb

(

bool const

b_b

)

References bb_bb_.

class_name()

std::string protocols::simple_filters::EnergyPerResidueFilter::class_name ( )

static

Referenced by protocols::simple_filters::EnergyPerResidueFilterCreator::keyname(), name(), and provide_xml_schema().

clone()

filters::FilterOP protocols::simple_filters::EnergyPerResidueFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

compute() [1/2]

core::Real protocols::simple_filters::EnergyPerResidueFilter::compute

(

core::pose::Pose const &

pose

)

const

References bb_bb_, core::chemical::CENTROID_t, core::pose::Pose::energies(), protocols::simple_filters::energy_per_residue_filter_tracer(), core::scoring::fa_atr, core::scoring::fa_rep, core::chemical::FULL_ATOM_t, core::scoring::interchain_env, core::scoring::interchain_vdw, core::pose::Pose::is_centroid(), core::pose::Pose::is_fullatom(), core::pose::parse_resnum(), core::scoring::Energies::residue_total_energies(), resnum(), resnum_, resnum_string_, protocols::filters::Filter::score(), score_type_, scorefxn_, core::util::switch_to_residue_type_set(), core::scoring::total_score, and core::pose::Pose::update_residue_neighbors().

compute() [2/2]

core::Real protocols::simple_filters::EnergyPerResidueFilter::compute	(	core::pose::Pose const &	pose,
		core::Size const	resid
	)		const

References bb_bb_, core::chemical::CENTROID_t, core::pose::Pose::energies(), protocols::simple_filters::energy_per_residue_filter_tracer(), core::scoring::fa_atr, core::scoring::fa_rep, core::chemical::FULL_ATOM_t, core::scoring::interchain_env, core::scoring::interchain_vdw, core::pose::Pose::is_centroid(), core::pose::Pose::is_fullatom(), core::scoring::Energies::residue_total_energies(), protocols::filters::Filter::score(), score_type_, scorefxn_, core::util::switch_to_residue_type_set(), core::scoring::total_score, and core::pose::Pose::update_residue_neighbors().

Referenced by apply(), protocols::simple_filters::ResidueIEFilter::compute(), protocols::protein_interface_design::find_lowest_constraint_energy_residue(), report(), and report_sm().

fresh_instance()

filters::FilterOP protocols::simple_filters::EnergyPerResidueFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

name()

std::string protocols::simple_filters::EnergyPerResidueFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by apply_helper().

parse_my_tag()

void protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag ( utility::tag::TagCOP  , basic::datacache::DataMap &    )

overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References around_shell_, bb_bb_, protocols::simple_filters::energy_per_residue_filter_tracer(), core::pose::get_resnum_string(), core::scoring::get_score_function_name(), interface_distance_cutoff_, core::scoring::parse_score_function(), rb_jump_, resnum_, resnum_string_, score_type_, core::scoring::score_type_from_name(), scorefxn_, select_around_resnums_, select_resnums_, string_around_resnums_, string_resnums_, threshold_, whole_interface_, and whole_protein_.

provide_xml_schema()

void protocols::simple_filters::EnergyPerResidueFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References core::pose::attributes_for_get_resnum_string(), core::scoring::attributes_for_parse_score_function(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::simple_filters::EnergyPerResidueFilterCreator::provide_xml_schema().

report()

void protocols::simple_filters::EnergyPerResidueFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References apply_helper(), compute(), protocols::buns::energy, core::conformation::Residue::is_protein(), core::conformation::Residue::name3(), core::scoring::name_from_score_type(), core::conformation::membrane::out, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), resnum(), score_type_, and core::pose::Pose::size().

report_sm()

core::Real protocols::simple_filters::EnergyPerResidueFilter::report_sm ( core::pose::Pose const &  ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References apply_helper(), compute(), protocols::buns::energy, core::conformation::Residue::is_protein(), core::pose::Pose::residue(), and core::pose::Pose::size().

resnum() [1/2]

void protocols::simple_filters::EnergyPerResidueFilter::resnum

(

core::Size

rn

)

References resnum_.

Referenced by apply(), compute(), and report().

resnum() [2/2]

void protocols::simple_filters::EnergyPerResidueFilter::resnum

(

std::string const &

rn

)

References resnum_string_.

score_type() [1/2]

core::scoring::ScoreType protocols::simple_filters::EnergyPerResidueFilter::score_type

(

)

const

References score_type_.

Referenced by score_type().

score_type() [2/2]

void protocols::simple_filters::EnergyPerResidueFilter::score_type

(

core::scoring::ScoreType

score_type

)

References score_type(), and score_type_.

scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::simple_filters::EnergyPerResidueFilter::scorefxn

(

)

const

References scorefxn_.

Referenced by EnergyPerResidueFilter(), and scorefxn().

scorefxn() [2/2]

void protocols::simple_filters::EnergyPerResidueFilter::scorefxn

(

core::scoring::ScoreFunctionOP

scorefxn

)

References scorefxn(), and scorefxn_.

threshold() [1/2]

core::Real protocols::simple_filters::EnergyPerResidueFilter::threshold

(

)

const

References threshold_.

threshold() [2/2]

void protocols::simple_filters::EnergyPerResidueFilter::threshold

(

core::Real const

th

)

References threshold_.

Member Data Documentation

around_shell_

core::Real protocols::simple_filters::EnergyPerResidueFilter::around_shell_

private

Referenced by apply_helper(), and parse_my_tag().

bb_bb_

bool protocols::simple_filters::EnergyPerResidueFilter::bb_bb_

private

Referenced by bb_bb(), compute(), and parse_my_tag().

interface_distance_cutoff_

core::Real protocols::simple_filters::EnergyPerResidueFilter::interface_distance_cutoff_

private

Referenced by apply_helper(), and parse_my_tag().

rb_jump_

core::Size protocols::simple_filters::EnergyPerResidueFilter::rb_jump_

private

Referenced by apply_helper(), and parse_my_tag().

resnum_

core::Size protocols::simple_filters::EnergyPerResidueFilter::resnum_

private

Referenced by apply_helper(), compute(), parse_my_tag(), and resnum().

resnum_string_

std::string protocols::simple_filters::EnergyPerResidueFilter::resnum_string_

private

Referenced by apply_helper(), compute(), parse_my_tag(), and resnum().

score_type_

core::scoring::ScoreType protocols::simple_filters::EnergyPerResidueFilter::score_type_

private

Referenced by apply(), apply_helper(), compute(), EnergyPerResidueFilter(), parse_my_tag(), report(), and score_type().

scorefxn_

core::scoring::ScoreFunctionOP protocols::simple_filters::EnergyPerResidueFilter::scorefxn_

private

Referenced by compute(), EnergyPerResidueFilter(), parse_my_tag(), and scorefxn().

select_around_resnums_

bool protocols::simple_filters::EnergyPerResidueFilter::select_around_resnums_

private

Referenced by apply_helper(), and parse_my_tag().

select_resnums_

bool protocols::simple_filters::EnergyPerResidueFilter::select_resnums_

private

Referenced by apply_helper(), and parse_my_tag().

string_around_resnums_

std::string protocols::simple_filters::EnergyPerResidueFilter::string_around_resnums_

private

Referenced by apply_helper(), and parse_my_tag().

string_resnums_

std::string protocols::simple_filters::EnergyPerResidueFilter::string_resnums_

private

Referenced by apply_helper(), and parse_my_tag().

threshold_

core::Real protocols::simple_filters::EnergyPerResidueFilter::threshold_

private

Referenced by apply(), parse_my_tag(), and threshold().

whole_interface_

bool protocols::simple_filters::EnergyPerResidueFilter::whole_interface_

private

Referenced by apply_helper(), and parse_my_tag().

whole_protein_

bool protocols::simple_filters::EnergyPerResidueFilter::whole_protein_

private

Referenced by parse_my_tag().

---

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

• src/protocols/simple_filters/EnergyPerResidueFilter.hh
• src/protocols/simple_filters/EnergyPerResidueFilter.cc