protocols::simple_filters::ResidueCountFilter Class Reference

#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 given user specified properties, adds them to the property vector to count. I still need to add a way to check the sanity res_type_set, the residue type set of the input structure 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 (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 bool	filter_provides_citation_info () const
	Does this filter provide information about how to cite it? More...
virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...
virtual bool	filter_is_unpublished () const
	Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. 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

protocols::simple_filters::ResidueCountFilter::ResidueCountFilter

(

)

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

overridedefault

Member Function Documentation

bool protocols::simple_filters::ResidueCountFilter::add_residue_property_by_name

(

std::string const &

prop_input

)

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

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_ 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. res_type_set, the residue type set of the input structure 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_.

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().

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

static

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

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

overridevirtual

Implements protocols::filters::Filter.

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().

bool protocols::simple_filters::ResidueCountFilter::enable_max_residue_count

(

)

const

References enable_max_residue_count_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::ResidueCountFilter::enable_max_residue_count

(

bool

value

)

References enable_max_residue_count_.

bool protocols::simple_filters::ResidueCountFilter::enable_min_residue_count

(

)

const

References enable_min_residue_count_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::ResidueCountFilter::enable_min_residue_count

(

bool

value

)

References enable_min_residue_count_.

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

overridevirtual

Implements protocols::filters::Filter.

core::Size protocols::simple_filters::ResidueCountFilter::max_residue_count

(

)

const

References max_residue_count_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::ResidueCountFilter::max_residue_count

(

core::Size

value

)

References max_residue_count_.

core::Size protocols::simple_filters::ResidueCountFilter::min_residue_count

(

)

const

References min_residue_count_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::ResidueCountFilter::min_residue_count

(

core::Size

value

)

References min_residue_count_.

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

bool protocols::simple_filters::ResidueCountFilter::packable

(

)

const

References packable_.

Referenced by parse_my_tag().

void protocols::simple_filters::ResidueCountFilter::packable

(

bool const

pack

)

References packable_.

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().

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().

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute().

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().

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

(

)

const

References res_props_.

Referenced by res_props().

void protocols::simple_filters::ResidueCountFilter::res_props

(

utility::vector1< core::chemical::ResidueProperty > const &

res_prop

)

References res_props(), and res_props_.

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

(

)

const

References res_types_.

Referenced by parse_my_tag(), and res_types().

void protocols::simple_filters::ResidueCountFilter::res_types

(

utility::vector1< std::string > const &

res_type

)

References res_types(), and res_types_.

void protocols::simple_filters::ResidueCountFilter::residue_selector

(

core::select::residue_selector::ResidueSelectorCOP

selector

)

References selector_.

Referenced by parse_my_tag().

Real protocols::simple_filters::ResidueCountFilter::round_to_Real

(

core::Real

x

)

const

Referenced by compute().

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

(

)

const

References task_factory_.

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

void protocols::simple_filters::ResidueCountFilter::task_factory

(

core::pack::task::TaskFactoryOP

task_factory

)

References task_factory(), and task_factory_.

Member Data Documentation

bool protocols::simple_filters::ResidueCountFilter::count_as_percentage_

private

Referenced by compute(), and parse_my_tag().

bool protocols::simple_filters::ResidueCountFilter::enable_max_residue_count_

private

Referenced by enable_max_residue_count().

bool protocols::simple_filters::ResidueCountFilter::enable_min_residue_count_

private

Referenced by enable_min_residue_count().

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

private

Referenced by max_residue_count().

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

private

Referenced by min_residue_count().

bool protocols::simple_filters::ResidueCountFilter::packable_

private

Referenced by compute(), and packable().

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

private

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

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

private

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

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

private

Referenced by compute(), and residue_selector().

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