Rosetta
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#include <ResidueCountFilter.hh>
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 |
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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 | |
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std::string | scorename_ |
protocols::simple_filters::ResidueCountFilter::ResidueCountFilter | ( | ) |
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overridedefault |
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
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 | ||
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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.
References core::chemical::ResidueTypeSet::has_name(), and res_types_.
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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().
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Referenced by protocols::simple_filters::ResidueCountFilterCreator::keyname(), name(), and provide_xml_schema().
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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.
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_.
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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_.
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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_.
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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().
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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().
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overridevirtual |
Reimplemented from protocols::filters::Filter.
References compute(), and core::conformation::membrane::out.
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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_.
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private |
Referenced by compute(), and parse_my_tag().
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Referenced by enable_max_residue_count().
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Referenced by enable_min_residue_count().
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Referenced by max_residue_count().
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Referenced by min_residue_count().
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Referenced by compute(), and packable().
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Referenced by add_residue_property_by_name(), compute(), and res_props().
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Referenced by add_residue_type_by_name(), compute(), and res_types().
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Referenced by compute(), and residue_selector().
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Referenced by task_factory().