protocols::simple_filters::EnergyPerResidueFilter Class Reference

#include <EnergyPerResidueFilter.hh>

Inheritance diagram for protocols::simple_filters::EnergyPerResidueFilter:

Collaboration 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, core::Size const rb_jump=1, core::Real const interface_distance_cutoff=8.0, bool const bb_bb=false)
	EnergyPerResidueFilter (EnergyPerResidueFilter const &init)
bool	apply (core::pose::Pose const &pose) const
	Returns true if the given pose passes the filter, false otherwise. More...
filters::FilterOP	clone () const
filters::FilterOP	fresh_instance () const
void	report (std::ostream &out, core::pose::Pose const &pose) const
core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...
core::Real	compute (core::pose::Pose const &pose) const
virtual	~EnergyPerResidueFilter ()
void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
core::Size	resnum () const
core::scoring::ScoreFunctionOP	scorefxn () const
core::scoring::ScoreType	score_type () const
core::Real	threshold () const
bool	bb_bb () const
void	resnum (core::Size 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)
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string const &)
	Filter (Filter const &)
virtual	~Filter ()
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 void	apply (core::io::serialization::PipeMap &pmap)
virtual void	score (core::io::serialization::PipeMap &pmap)
virtual core::Real	score (core::pose::Pose &pose)
virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
virtual std::string	name () const

Private Attributes
core::Size	resnum_
core::scoring::ScoreFunctionOP	scorefxn_
core::scoring::ScoreType	score_type_
core::Real	threshold_
bool	whole_interface_
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

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

inline

Referenced by clone(), and fresh_instance().

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,
		core::Size const	rb_jump = 1,
		core::Real const	interface_distance_cutoff = 8.0,
		bool const	bb_bb = false
	)

References score_type_, scorefxn_, and core::scoring::total_score.

protocols::simple_filters::EnergyPerResidueFilter::EnergyPerResidueFilter

(

EnergyPerResidueFilter const &

init)

References scorefxn_.

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

virtual

Member Function Documentation

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

virtual

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

Implements protocols::filters::Filter.

References compute(), core::pose::Pose::conformation(), protocols::simple_filters::energy_per_residue_filter_tracer(), core::conformation::Residue::name3(), core::scoring::name_from_score_type(), core::conformation::Conformation::num_chains(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), resnum_, score_type_, threshold_, and whole_interface_.

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

bool protocols::simple_filters::EnergyPerResidueFilter::bb_bb

(

)

const

References bb_bb_.

void protocols::simple_filters::EnergyPerResidueFilter::bb_bb

(

bool const

b_b)

References bb_bb_.

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

inlinevirtual

Implements protocols::filters::Filter.

References EnergyPerResidueFilter().

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

(

core::pose::Pose const &

pose)

const

References bb_bb_, core::chemical::CENTROID, protocols::simple_filters::energy_per_residue_filter_tracer(), core::scoring::fa_atr, core::scoring::fa_rep, core::chemical::FA_STANDARD, core::scoring::interchain_env, core::scoring::interchain_vdw, resnum_, protocols::filters::Filter::score(), score_type_, scorefxn_, core::util::switch_to_residue_type_set(), and core::scoring::total_score.

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

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

inlinevirtual

Implements protocols::filters::Filter.

References EnergyPerResidueFilter().

void protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag ( utility::tag::TagPtr const  tag, protocols::moves::DataMap &  data, filters::Filters_map const &  , protocols::moves::Movers_map const &  , core::pose::Pose const &  pose  )

virtual

Reimplemented from protocols::filters::Filter.

References protocols::moves::DataMap::get(), core::pose::get_resnum(), core::scoring::score_type_from_name(), and core::TR().

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

virtual

Reimplemented from protocols::filters::Filter.

References protocols::comparative_modeling::features::A, protocols::scoring::Interface::calculate(), compute(), protocols::scoring::Interface::distance(), core::pose::Pose::energies(), core::scoring::fa_atr, core::scoring::fa_dun, core::scoring::fa_pair, core::scoring::fa_rep, core::scoring::fa_sol, core::pose::Pose::fold_tree(), core::scoring::hbond_bb_sc, core::scoring::hbond_sc, interface_distance_cutoff_, protocols::scoring::Interface::is_interface(), core::conformation::Residue::is_protein(), core::conformation::Residue::name3(), core::scoring::name_from_score_type(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::pdb_info(), rb_jump_, core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), resnum_, score_type_, threshold_, core::pose::Pose::total_residue(), core::scoring::total_score, core::pose::Pose::update_residue_neighbors(), and whole_interface_.

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

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

core::Size protocols::simple_filters::EnergyPerResidueFilter::resnum

(

)

const

References resnum_.

void protocols::simple_filters::EnergyPerResidueFilter::resnum

(

core::Size const

rn)

References resnum_.

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

(

)

const

References score_type_.

Referenced by score_type().

void protocols::simple_filters::EnergyPerResidueFilter::score_type

(

core::scoring::ScoreType

score_type)

References score_type(), and score_type_.

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

(

)

const

References scorefxn_.

Referenced by scorefxn().

void protocols::simple_filters::EnergyPerResidueFilter::scorefxn

(

core::scoring::ScoreFunctionOP

scorefxn)

References scorefxn(), and scorefxn_.

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

(

)

const

References threshold_.

void protocols::simple_filters::EnergyPerResidueFilter::threshold

(

core::Real const

th)

References threshold_.

Member Data Documentation

bool protocols::simple_filters::EnergyPerResidueFilter::bb_bb_

private

Referenced by bb_bb(), and compute().

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

private

Referenced by report().

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

private

Referenced by report().

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

private

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

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

private

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

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

private

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

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

private

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

bool protocols::simple_filters::EnergyPerResidueFilter::whole_interface_

private

Referenced by apply(), and report().

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

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