#include <ResidueCountFilter.hh>

Inheritance diagram for protocols::simple_filters::ResidueCountFilter:

Public Member Functions
	ResidueCountFilter ()

	~ResidueCountFilter () override

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) const

core::Real	round_to_Real (core::Real x) const

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::Size	max_residue_count () const

void	max_residue_count (core::Size value)

bool	enable_max_residue_count () const

void	enable_max_residue_count (bool value)

core::Size	min_residue_count () const

void	min_residue_count (core::Size value)

utility::vector1< std::string >	res_types () const

void	res_types (utility::vector1< std::string > const &res_type)

utility::vector1< core::chemical::ResidueProperty > const &	res_props () const

void	res_props (utility::vector1< core::chemical::ResidueProperty > const &res_prop)

bool	enable_min_residue_count () const

void	enable_min_residue_count (bool value)

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

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

void	residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)

bool	packable () const

void	packable (bool const pack)

bool	add_residue_type_by_name (core::chemical::ResidueTypeSet const &res_type_set, std::string const &res_type_input)
	Checks whether a residue type is present in the provided residue type set, and if so, adds it to res_types_. More...

bool	add_residue_property_by_name (std::string const &prop_input)
	add proeprties to peroperty vector @detail given user specified properties, adds them to the property vector to count. I still need to add a way to check the sanity @input res_type_set, the residue type set of the input structure @input res_type_input, the user specified residue type name 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 Attributes
core::Size	max_residue_count_

bool	enable_max_residue_count_

core::Size	min_residue_count_

bool	enable_min_residue_count_

bool	count_as_percentage_

utility::vector1< std::string >	res_types_

utility::vector1< core::chemical::ResidueProperty >	res_props_

bool	packable_

core::pack::task::TaskFactoryOP	task_factory_

core::select::residue_selector::ResidueSelectorCOP	selector_

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

Constructor & Destructor Documentation

◆ ResidueCountFilter()

protocols::simple_filters::ResidueCountFilter::ResidueCountFilter ( )

◆ ~ResidueCountFilter()

protocols::simple_filters::ResidueCountFilter::~ResidueCountFilter ( )

overridedefault

Member Function Documentation

◆ add_residue_property_by_name()

bool protocols::simple_filters::ResidueCountFilter::add_residue_property_by_name ( std::string const & prop_input )

add proeprties to peroperty vector @detail given user specified properties, adds them to the property vector to count. I still need to add a way to check the sanity @input res_type_set, the residue type set of the input structure @input res_type_input, the user specified residue type name

Returns: false if res_type_input doesn't match any residue type names, true otherwise

Author: Parisa Hosseinzadeh (paris.nosp@m.ah@u.nosp@m.w.edu), Baker laboratory.

References core::chemical::ResidueProperties::get_property_from_string(), core::chemical::NO_PROPERTY, res_props_, and protocols::simple_filters::TR().

Referenced by parse_my_tag().

◆ add_residue_type_by_name()

bool protocols::simple_filters::ResidueCountFilter::add_residue_type_by_name	(	core::chemical::ResidueTypeSet const &	res_type_set,
		std::string const &	res_type_input
	)

Checks whether a residue type is present in the provided residue type set, and if so, adds it to res_types_.

Checks whether a residue type is present in the provided residue type set, and if so, adds it to res_types_ @detail given user specified residue type string, look for residue type name and add it to the list of types to count if it is present in the specified ResidueTypeSet. @input res_type_set, the residue type set of the input structure @input res_type_input, the user specified residue type name.

Returns: false if res_type_input doesn't match any residue type names, true otherwise

References core::chemical::ResidueTypeSet::has_name(), and res_types_.

◆ apply()

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

overridevirtual

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

Implements protocols::filters::Filter.

References compute(), enable_max_residue_count(), enable_min_residue_count(), max_residue_count(), min_residue_count(), core::conformation::Residue::name(), core::conformation::Residue::name3(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::simple_filters::TR().

◆ class_name()

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

static

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

◆ clone()

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

overridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::simple_filters::ResidueCountFilter::compute ( core::pose::Pose const & pose ) const

The logic here ensures that any residue that is selected by type OR by properties is counted once and only once. So, for example, if I say, "count THR and beta-branched and polar", each threonine residue is still only counted once.

Author: Original author unknown.; Updated by Parisa Hosseinzadeh (paris.nosp@m.ah@u.nosp@m.w.edu) to add property counting.; Logic updated by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu) to avoid double-counting if names and multiple properties are specified.

References count_as_percentage_, core::chemical::ResidueTypeBase::has_property(), core::conformation::Residue::name(), core::conformation::Residue::name3(), packable_, res_props_, res_types_, core::pose::Pose::residue(), protocols::rosetta_scripts::residue_packer_states(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), round_to_Real(), selector_, core::pose::Pose::size(), and task_factory().

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

◆ enable_max_residue_count() [1/2]

bool protocols::simple_filters::ResidueCountFilter::enable_max_residue_count ( ) const

References enable_max_residue_count_.

Referenced by apply(), and parse_my_tag().

◆ enable_max_residue_count() [2/2]

void protocols::simple_filters::ResidueCountFilter::enable_max_residue_count ( bool value )

References enable_max_residue_count_.

◆ enable_min_residue_count() [1/2]

bool protocols::simple_filters::ResidueCountFilter::enable_min_residue_count ( ) const

References enable_min_residue_count_.

Referenced by apply(), and parse_my_tag().

◆ enable_min_residue_count() [2/2]

void protocols::simple_filters::ResidueCountFilter::enable_min_residue_count ( bool value )

References enable_min_residue_count_.

◆ fresh_instance()

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

overridevirtual

Implements protocols::filters::Filter.

◆ max_residue_count() [1/2]

core::Size protocols::simple_filters::ResidueCountFilter::max_residue_count ( ) const

References max_residue_count_.

Referenced by apply(), and parse_my_tag().

◆ max_residue_count() [2/2]

void protocols::simple_filters::ResidueCountFilter::max_residue_count ( core::Size value )

References max_residue_count_.

◆ min_residue_count() [1/2]

core::Size protocols::simple_filters::ResidueCountFilter::min_residue_count ( ) const

References min_residue_count_.

Referenced by apply(), and parse_my_tag().

◆ min_residue_count() [2/2]

void protocols::simple_filters::ResidueCountFilter::min_residue_count ( core::Size value )

References min_residue_count_.

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ packable() [1/2]

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

References packable_.

Referenced by parse_my_tag().

◆ packable() [2/2]

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

References packable_.

◆ parse_my_tag()

void protocols::simple_filters::ResidueCountFilter::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 add_residue_property_by_name(), count_as_percentage_, enable_max_residue_count(), enable_min_residue_count(), max_residue_count(), min_residue_count(), packable(), core::select::residue_selector::parse_residue_selector(), core::pack::task::parse_task_operations(), res_types(), residue_selector(), task_factory(), and protocols::simple_filters::TR().

◆ provide_xml_schema()

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

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), core::pack::task::attributes_for_parse_task_operations(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

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

◆ report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

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

◆ report_sm()

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

◆ res_props() [1/2]

utility::vector1< core::chemical::ResidueProperty > const & protocols::simple_filters::ResidueCountFilter::res_props ( ) const

References res_props_.

Referenced by res_props().

◆ res_props() [2/2]

void protocols::simple_filters::ResidueCountFilter::res_props ( utility::vector1< core::chemical::ResidueProperty > const & res_prop )

References res_props(), and res_props_.

◆ res_types() [1/2]

utility::vector1< std::string > protocols::simple_filters::ResidueCountFilter::res_types ( ) const

References res_types_.

Referenced by parse_my_tag(), and res_types().

◆ res_types() [2/2]

void protocols::simple_filters::ResidueCountFilter::res_types ( utility::vector1< std::string > const & res_type )

References res_types(), and res_types_.

◆ residue_selector()

void protocols::simple_filters::ResidueCountFilter::residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

References selector_.

Referenced by parse_my_tag().

◆ round_to_Real()

Real protocols::simple_filters::ResidueCountFilter::round_to_Real ( core::Real x ) const

Referenced by compute().

◆ task_factory() [1/2]

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

References task_factory_.

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

◆ task_factory() [2/2]

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

References task_factory(), and task_factory_.

Member Data Documentation

◆ count_as_percentage_

bool protocols::simple_filters::ResidueCountFilter::count_as_percentage_

private

Referenced by compute(), and parse_my_tag().

◆ enable_max_residue_count_

bool protocols::simple_filters::ResidueCountFilter::enable_max_residue_count_

private

Referenced by enable_max_residue_count().

◆ enable_min_residue_count_

bool protocols::simple_filters::ResidueCountFilter::enable_min_residue_count_

private

Referenced by enable_min_residue_count().

◆ max_residue_count_

core::Size protocols::simple_filters::ResidueCountFilter::max_residue_count_

private

Referenced by max_residue_count().

◆ min_residue_count_

core::Size protocols::simple_filters::ResidueCountFilter::min_residue_count_

private

Referenced by min_residue_count().

◆ packable_

bool protocols::simple_filters::ResidueCountFilter::packable_

private

Referenced by compute(), and packable().

◆ res_props_

utility::vector1< core::chemical::ResidueProperty > protocols::simple_filters::ResidueCountFilter::res_props_

private

Referenced by add_residue_property_by_name(), compute(), and res_props().

◆ res_types_

utility::vector1< std::string > protocols::simple_filters::ResidueCountFilter::res_types_

private

Referenced by add_residue_type_by_name(), compute(), and res_types().

◆ selector_

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ResidueCountFilter::selector_

private

Referenced by compute(), and residue_selector().

◆ task_factory_

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

private

Referenced by task_factory().

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

src/protocols/simple_filters/ResidueCountFilter.hh
src/protocols/simple_filters/ResidueCountFilter.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ ResidueCountFilter()

◆ ~ResidueCountFilter()

Member Function Documentation

◆ add_residue_property_by_name()

◆ add_residue_type_by_name()

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ enable_max_residue_count() [1/2]

◆ enable_max_residue_count() [2/2]

◆ enable_min_residue_count() [1/2]

◆ enable_min_residue_count() [2/2]

◆ fresh_instance()

◆ max_residue_count() [1/2]

◆ max_residue_count() [2/2]

◆ min_residue_count() [1/2]

◆ min_residue_count() [2/2]

◆ name()

◆ packable() [1/2]

◆ packable() [2/2]

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ res_props() [1/2]

◆ res_props() [2/2]

◆ res_types() [1/2]

◆ res_types() [2/2]

◆ residue_selector()

◆ round_to_Real()

◆ task_factory() [1/2]

◆ task_factory() [2/2]

Member Data Documentation

◆ count_as_percentage_

◆ enable_max_residue_count_

◆ enable_min_residue_count_

◆ max_residue_count_

◆ min_residue_count_

◆ packable_

◆ res_props_

◆ res_types_

◆ selector_

◆ task_factory_