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Rosetta
2020.50
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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 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 |
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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 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 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
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_ 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.
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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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().
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overridevirtual |
Reimplemented from protocols::filters::Filter.
References compute().
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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().