protocols::simple_filters::MutationsFilter Class Reference

#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 (Filter 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

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

private

Constructor & Destructor Documentation

protocols::simple_filters::MutationsFilter::MutationsFilter

(

)

default ctor

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

overridedefault

Member Function Documentation

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().

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

static

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

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

overridevirtual

Implements protocols::filters::Filter.

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

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::is_symmetric(), mutations_, core::chemical::ResidueTypeBase::name(), core::conformation::Residue::name3(), packable_, core::pose::Pose::pdb_info(), reference_pose(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), task_factory(), task_factory_, protocols::simple_filters::TR(), verbose_, and write_to_pdb().

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

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

overridevirtual

Implements protocols::filters::Filter.

core::Size protocols::simple_filters::MutationsFilter::mutation_threshold

(

)

const

References mutation_threshold_.

Referenced by parse_my_tag().

void protocols::simple_filters::MutationsFilter::mutation_threshold

(

core::Size const

mut

)

References mutation_threshold_.

bool protocols::simple_filters::MutationsFilter::mutations

(

)

const

References mutations_.

Referenced by parse_my_tag().

void protocols::simple_filters::MutationsFilter::mutations

(

bool const

muts

)

References mutations_.

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

bool protocols::simple_filters::MutationsFilter::packable

(

)

const

References packable_.

Referenced by parse_my_tag().

void protocols::simple_filters::MutationsFilter::packable

(

bool const

pack

)

References packable_.

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().

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().

core::Real protocols::simple_filters::MutationsFilter::rate_threshold

(

)

const

References rate_threshold_.

Referenced by parse_my_tag().

void protocols::simple_filters::MutationsFilter::rate_threshold

(

core::Real const

rate

)

References rate_threshold_.

core::pose::PoseCOP protocols::simple_filters::MutationsFilter::reference_pose

(

)

const

References reference_pose_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_filters::MutationsFilter::reference_pose

(

core::pose::PoseCOP

reference_pose

)

References reference_pose_.

void protocols::simple_filters::MutationsFilter::reference_pose

(

core::pose::Pose const &

pose

)

References reference_pose_.

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and write2pdb().

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().

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

(

)

const

References task_factory_.

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

void protocols::simple_filters::MutationsFilter::task_factory

(

core::pack::task::TaskFactoryOP

task_factory

)

References task_factory(), and task_factory_.

bool protocols::simple_filters::MutationsFilter::verbose

(

)

const

References verbose_.

Referenced by parse_my_tag().

void protocols::simple_filters::MutationsFilter::verbose

(

bool const

verb

)

References verbose_.

bool protocols::simple_filters::MutationsFilter::write2pdb

(

)

const

References write2pdb_.

Referenced by parse_my_tag(), and report().

void protocols::simple_filters::MutationsFilter::write2pdb

(

bool const

write

)

References write2pdb_.

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

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

private

Referenced by apply(), and mutation_threshold().

bool protocols::simple_filters::MutationsFilter::mutations_

private

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

bool protocols::simple_filters::MutationsFilter::packable_

private

Referenced by compute(), and packable().

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

private

Referenced by apply(), and rate_threshold().

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

private

Referenced by reference_pose().

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

private

Referenced by compute(), and task_factory().

bool protocols::simple_filters::MutationsFilter::verbose_

private

Referenced by compute(), and verbose().

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