protocols::enzdes::RepackWithoutLigandFilter Class Reference

#include <EnzFilters.hh>

Inheritance diagram for protocols::enzdes::RepackWithoutLigandFilter:

Public Types
typedef protocols::filters::Filter	Filter
typedef protocols::filters::FilterOP	FilterOP

Public Member Functions
	RepackWithoutLigandFilter ()
	RepackWithoutLigandFilter (core::scoring::ScoreFunctionOP scorefxn, core::Real rms_thresh, core::Real energy_thresh, core::select::residue_selector::ResidueSelectorCOP rms_target_res)
bool	apply (core::pose::Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...
FilterOP	clone () const override
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) const
	~RepackWithoutLigandFilter () 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...
void	set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
void	set_cstid_list (std::string setting)
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::scoring::ScoreFunctionOP	scorefxn_
core::Real	rms_threshold_
core::Real	energy_threshold_
bool	calc_dE_
bool	calc_rms_
bool	use_cstids_
bool	rms_all_rpked_
std::string	cstid_list_
core::select::residue_selector::ResidueSelectorCOP	target_res_

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

Member Typedef Documentation

Filter

typedef protocols::filters::Filter protocols::enzdes::RepackWithoutLigandFilter::Filter

FilterOP

typedef protocols::filters::FilterOP protocols::enzdes::RepackWithoutLigandFilter::FilterOP

Constructor & Destructor Documentation

RepackWithoutLigandFilter() [1/2]

protocols::enzdes::RepackWithoutLigandFilter::RepackWithoutLigandFilter ( )

inline

RepackWithoutLigandFilter() [2/2]

protocols::enzdes::RepackWithoutLigandFilter::RepackWithoutLigandFilter	(	core::scoring::ScoreFunctionOP	scorefxn,
		core::Real	rms_thresh,
		core::Real	energy_thresh,
		core::select::residue_selector::ResidueSelectorCOP	rms_target_res
	)

~RepackWithoutLigandFilter()

protocols::enzdes::RepackWithoutLigandFilter::~RepackWithoutLigandFilter ( )

overridedefault

Member Function Documentation

apply()

bool protocols::enzdes::RepackWithoutLigandFilter::apply ( core::pose::Pose const &  pose ) const

overridevirtual

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

Implements protocols::filters::Filter.

References calc_dE_, calc_rms_, compute(), energy_threshold_, and rms_threshold_.

class_name()

std::string protocols::enzdes::RepackWithoutLigandFilter::class_name ( )

static

Referenced by protocols::enzdes::RepackWithoutLigandFilterCreator::keyname().

clone()

FilterOP protocols::enzdes::RepackWithoutLigandFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

core::Real protocols::enzdes::RepackWithoutLigandFilter::compute

(

core::pose::Pose const &

pose

)

const

References protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), calc_dE_, calc_rms_, cstid_list_, protocols::enzdes::enzutil::disable_constraint_scoreterms(), core::pose::Pose::energies(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::get_ptask(), core::select::get_residues_from_subset(), protocols::enzdes::enzutil::get_resnum_from_cstid_list(), core::chemical::ResidueType::is_ligand(), core::conformation::Residue::is_protein(), core::scoring::is_protein_sidechain_heavyatom(), protocols::enzdes::enzutil::remove_all_enzdes_constraints(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), rms_all_rpked_, core::scoring::rmsd_no_super_subset(), scorefxn_, protocols::enzdes::RepackLigandSiteWithoutLigandMover::set_separate_prt_ligand(), core::pose::Pose::size(), target_res_, core::scoring::Energies::total_energies(), core::scoring::total_score, protocols::enzdes::TR(), and use_cstids_.

Referenced by apply(), and report_sm().

fresh_instance()

FilterOP protocols::enzdes::RepackWithoutLigandFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

name()

std::string protocols::enzdes::RepackWithoutLigandFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References protocols::enzdes::DiffAtomSasaFilter::class_name().

parse_my_tag()

void protocols::enzdes::RepackWithoutLigandFilter::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 calc_dE_, calc_rms_, cstid_list_, energy_threshold_, core::pose::get_resnum_selector(), core::scoring::parse_score_function(), rms_all_rpked_, rms_threshold_, scorefxn_, target_res_, protocols::enzdes::TR(), and use_cstids_.

provide_xml_schema()

void protocols::enzdes::RepackWithoutLigandFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References core::scoring::attributes_for_parse_score_function(), protocols::enzdes::DiffAtomSasaFilter::class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::enzdes::RepackWithoutLigandFilterCreator::provide_xml_schema().

report()

void protocols::enzdes::RepackWithoutLigandFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References core::conformation::membrane::out, and core::pose::Pose::size().

report_sm()

core::Real protocols::enzdes::RepackWithoutLigandFilter::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 compute().

set_cstid_list()

void protocols::enzdes::RepackWithoutLigandFilter::set_cstid_list ( std::string  setting )

inline

References cstid_list_.

set_scorefxn()

void protocols::enzdes::RepackWithoutLigandFilter::set_scorefxn ( core::scoring::ScoreFunctionOP  scorefxn )

inline

References scorefxn_.

Member Data Documentation

calc_dE_

bool protocols::enzdes::RepackWithoutLigandFilter::calc_dE_

private

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

calc_rms_

bool protocols::enzdes::RepackWithoutLigandFilter::calc_rms_

private

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

cstid_list_

std::string protocols::enzdes::RepackWithoutLigandFilter::cstid_list_

private

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

energy_threshold_

core::Real protocols::enzdes::RepackWithoutLigandFilter::energy_threshold_

private

Referenced by apply(), and parse_my_tag().

rms_all_rpked_

bool protocols::enzdes::RepackWithoutLigandFilter::rms_all_rpked_

private

Referenced by compute(), and parse_my_tag().

rms_threshold_

core::Real protocols::enzdes::RepackWithoutLigandFilter::rms_threshold_

private

Referenced by apply(), and parse_my_tag().

scorefxn_

core::scoring::ScoreFunctionOP protocols::enzdes::RepackWithoutLigandFilter::scorefxn_

private

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

target_res_

core::select::residue_selector::ResidueSelectorCOP protocols::enzdes::RepackWithoutLigandFilter::target_res_

private

Referenced by compute(), and parse_my_tag().

use_cstids_

bool protocols::enzdes::RepackWithoutLigandFilter::use_cstids_

private

Referenced by compute(), and parse_my_tag().

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

• src/protocols/enzdes/EnzFilters.hh
• src/protocols/enzdes/EnzFilters.cc