#include <MutationsFilter.hh>

Inheritance diagram for protocols::simple_filters::MutationsFilter:

Public Member Functions
	MutationsFilter ()
	default ctor More...

bool	apply (core::pose::Pose const &pose) const override
	Constructor with a single target residue. More...

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...

protocols::filters::FilterOP	clone () const override

protocols::filters::FilterOP	fresh_instance () const override

core::Real	compute (core::pose::Pose const &pose, bool const &write) const

void	write_to_pdb (core::pose::Pose const &pose, std::map< core::Size, std::string > const &res_names1, std::map< core::Size, std::string > const &res_names2) const
	Add each mutation to the output pdb if desired. More...

	~MutationsFilter () override

core::pack::task::TaskFactoryOP	task_factory () const

void	task_factory (core::pack::task::TaskFactoryOP task_factory)

core::Real	rate_threshold () const

void	rate_threshold (core::Real const rate)

core::Size	mutation_threshold () const

void	mutation_threshold (core::Size const mut)

bool	mutations () const

void	mutations (bool const muts)

bool	verbose () const

void	verbose (bool const verb)

bool	packable () const

void	packable (bool const pack)

bool	write2pdb () const

void	write2pdb (bool const write)

core::pose::PoseCOP	reference_pose () const

void	reference_pose (core::pose::PoseCOP reference_pose)

void	reference_pose (core::pose::Pose const &pose)

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...

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 Types
typedef protocols::filters::Filter	parent

Private Attributes
core::pack::task::TaskFactoryOP	task_factory_

core::pose::PoseCOP	reference_pose_

core::Real	rate_threshold_

core::Size	mutation_threshold_

bool	mutations_

bool	verbose_

bool	packable_

bool	write2pdb_

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

Member Typedef Documentation

◆ parent

typedef protocols::filters::Filter protocols::simple_filters::MutationsFilter::parent

private

Constructor & Destructor Documentation

◆ MutationsFilter()

protocols::simple_filters::MutationsFilter::MutationsFilter ( )

default ctor

◆ ~MutationsFilter()

protocols::simple_filters::MutationsFilter::~MutationsFilter ( )

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

Constructor with a single target residue.

Implements protocols::filters::Filter.

References compute(), mutation_threshold_, mutations_, rate_threshold_, and protocols::simple_filters::TR().

◆ class_name()

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

static

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

◆ clone()

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

overridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::simple_filters::MutationsFilter::compute	(	core::pose::Pose const &	pose,
		bool const &	write
	)		const

◆ fresh_instance()

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

overridevirtual

Implements protocols::filters::Filter.

◆ mutation_threshold() [1/2]

core::Size protocols::simple_filters::MutationsFilter::mutation_threshold ( ) const

References mutation_threshold_.

Referenced by parse_my_tag().

◆ mutation_threshold() [2/2]

void protocols::simple_filters::MutationsFilter::mutation_threshold ( core::Size const mut )

References mutation_threshold_.

◆ mutations() [1/2]

bool protocols::simple_filters::MutationsFilter::mutations ( ) const

References mutations_.

Referenced by parse_my_tag().

◆ mutations() [2/2]

void protocols::simple_filters::MutationsFilter::mutations ( bool const muts )

References mutations_.

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ packable() [1/2]

bool protocols::simple_filters::MutationsFilter::packable ( ) const

References packable_.

Referenced by parse_my_tag().

◆ packable() [2/2]

void protocols::simple_filters::MutationsFilter::packable ( bool const pack )

References packable_.

◆ parse_my_tag()

void protocols::simple_filters::MutationsFilter::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 class_name(), protocols::rosetta_scripts::legacy_saved_pose_or_input(), mutation_threshold(), mutations(), packable(), core::pack::task::parse_task_operations(), rate_threshold(), reference_pose(), task_factory(), protocols::simple_filters::TR(), verbose(), and write2pdb().

◆ provide_xml_schema()

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

static

References core::pack::task::attributes_for_parse_task_operations(), core::pose::attributes_for_saved_reference_pose(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

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

◆ rate_threshold() [1/2]

core::Real protocols::simple_filters::MutationsFilter::rate_threshold ( ) const

References rate_threshold_.

Referenced by parse_my_tag().

◆ rate_threshold() [2/2]

void protocols::simple_filters::MutationsFilter::rate_threshold ( core::Real const rate )

References rate_threshold_.

◆ reference_pose() [1/3]

core::pose::PoseCOP protocols::simple_filters::MutationsFilter::reference_pose ( ) const

References reference_pose_.

Referenced by compute(), and parse_my_tag().

◆ reference_pose() [2/3]

void protocols::simple_filters::MutationsFilter::reference_pose ( core::pose::Pose const & pose )

References reference_pose_.

◆ reference_pose() [3/3]

void protocols::simple_filters::MutationsFilter::reference_pose ( core::pose::PoseCOP reference_pose )

References reference_pose_.

◆ report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), core::conformation::membrane::out, and write2pdb().

◆ report_sm()

core::Real protocols::simple_filters::MutationsFilter::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().

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::simple_filters::MutationsFilter::task_factory ( ) const

References task_factory_.

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

◆ task_factory() [2/2]

void protocols::simple_filters::MutationsFilter::task_factory ( core::pack::task::TaskFactoryOP task_factory )

References task_factory(), and task_factory_.

◆ verbose() [1/2]

bool protocols::simple_filters::MutationsFilter::verbose ( ) const

References verbose_.

Referenced by parse_my_tag().

◆ verbose() [2/2]

void protocols::simple_filters::MutationsFilter::verbose ( bool const verb )

References verbose_.

◆ write2pdb() [1/2]

bool protocols::simple_filters::MutationsFilter::write2pdb ( ) const

References write2pdb_.

Referenced by parse_my_tag(), and report().

◆ write2pdb() [2/2]

void protocols::simple_filters::MutationsFilter::write2pdb ( bool const write )

References write2pdb_.

◆ write_to_pdb()

void protocols::simple_filters::MutationsFilter::write_to_pdb	(	core::pose::Pose const &	pose,
		std::map< core::Size, std::string > const &	res_names1,
		std::map< core::Size, std::string > const &	res_names2
	)		const

Add each mutation to the output pdb if desired.

References protocols::jd2::add_string_to_current_job(), protocols::filters::Filter::get_user_defined_name(), and core::pose::Pose::pdb_info().

Referenced by compute().

Member Data Documentation

◆ mutation_threshold_

core::Size protocols::simple_filters::MutationsFilter::mutation_threshold_

private

Referenced by apply(), and mutation_threshold().

◆ mutations_

bool protocols::simple_filters::MutationsFilter::mutations_

private

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

◆ packable_

bool protocols::simple_filters::MutationsFilter::packable_

private

Referenced by compute(), and packable().

◆ rate_threshold_

core::Real protocols::simple_filters::MutationsFilter::rate_threshold_

private

Referenced by apply(), and rate_threshold().

◆ reference_pose_

core::pose::PoseCOP protocols::simple_filters::MutationsFilter::reference_pose_

private

Referenced by reference_pose().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::simple_filters::MutationsFilter::task_factory_

private

Referenced by compute(), and task_factory().

◆ verbose_

bool protocols::simple_filters::MutationsFilter::verbose_

private

Referenced by compute(), and verbose().

◆ write2pdb_

bool protocols::simple_filters::MutationsFilter::write2pdb_

private

Referenced by write2pdb().

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

src/protocols/simple_filters/MutationsFilter.hh
src/protocols/simple_filters/MutationsFilter.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ MutationsFilter()

◆ ~MutationsFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ fresh_instance()

◆ mutation_threshold() [1/2]

◆ mutation_threshold() [2/2]

◆ mutations() [1/2]

◆ mutations() [2/2]

◆ name()

◆ packable() [1/2]

◆ packable() [2/2]

◆ parse_my_tag()

◆ provide_xml_schema()

◆ rate_threshold() [1/2]

◆ rate_threshold() [2/2]

◆ reference_pose() [1/3]

◆ reference_pose() [2/3]

◆ reference_pose() [3/3]

◆ report()

◆ report_sm()

◆ task_factory() [1/2]

◆ task_factory() [2/2]

◆ verbose() [1/2]

◆ verbose() [2/2]

◆ write2pdb() [1/2]

◆ write2pdb() [2/2]

◆ write_to_pdb()

Member Data Documentation

◆ mutation_threshold_

◆ mutations_

◆ packable_

◆ rate_threshold_

◆ reference_pose_

◆ task_factory_

◆ verbose_

◆ write2pdb_