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protocols::simple_filters::ResidueCountFilter Class Reference

#include <ResidueCountFilter.hh>

Inheritance diagram for protocols::simple_filters::ResidueCountFilter:
Inheritance graph

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)
< 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_
< core::chemical::ResidueProperty
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 ( )

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

false if res_type_input doesn't match any residue type names, true otherwise
Parisa Hosseinzadeh (, 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.

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
std::string protocols::simple_filters::ResidueCountFilter::class_name ( )
filters::FilterOP protocols::simple_filters::ResidueCountFilter::clone ( ) const
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.

Original author unknown.
Updated by Parisa Hosseinzadeh ( to add property counting.
Logic updated by Vikram K. Mulligan ( 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)
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)
filters::FilterOP protocols::simple_filters::ResidueCountFilter::fresh_instance ( ) const
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

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 &   
void protocols::simple_filters::ResidueCountFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
void protocols::simple_filters::ResidueCountFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const

Reimplemented from protocols::filters::Filter.

References compute().

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

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_

Referenced by compute(), and parse_my_tag().

bool protocols::simple_filters::ResidueCountFilter::enable_max_residue_count_
bool protocols::simple_filters::ResidueCountFilter::enable_min_residue_count_
core::Size protocols::simple_filters::ResidueCountFilter::max_residue_count_

Referenced by max_residue_count().

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

Referenced by min_residue_count().

bool protocols::simple_filters::ResidueCountFilter::packable_

Referenced by compute(), and packable().

utility::vector1< core::chemical::ResidueProperty > protocols::simple_filters::ResidueCountFilter::res_props_
utility::vector1< std::string > protocols::simple_filters::ResidueCountFilter::res_types_
core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ResidueCountFilter::selector_

Referenced by compute(), and residue_selector().

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

Referenced by task_factory().

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