Rosetta
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#include <ContactMolecularSurfaceFilter.hh>
Public Types | |
typedef protocols::filters::Filter | Super |
typedef protocols::filters::Filter | Filter |
typedef protocols::filters::FilterOP | FilterOP |
typedef core::Real | Real |
typedef core::pose::Pose | Pose |
typedef utility::tag::TagCOP | TagCOP |
typedef basic::datacache::DataMap | DataMap |
typedef core::scoring::sc::ContactMolecularSurfaceCalculator | ContactMolecularSurfaceCalculator |
Public Member Functions | |
ContactMolecularSurfaceFilter () | |
ContactMolecularSurfaceFilter (Real const &filtered_area, Real const &distance_weight, bool const quick, bool const verbose, bool const use_rosetta_radii=false) | |
ContactMolecularSurfaceFilter (Real const &filtered_area, Real const &distance_weight, bool const quick, bool const verbose, core::select::residue_selector::ResidueSelectorCOP const selector1, core::select::residue_selector::ResidueSelectorCOP const selector2, bool const use_rosetta_radii=false) | |
~ContactMolecularSurfaceFilter () override=default | |
filters::FilterOP | clone () const override |
filters::FilterOP | fresh_instance () const override |
bool | quick () const |
bool | verbose () const |
bool | use_rosetta_radii () const |
bool | apolar_target () const |
Real | filtered_area () const |
Real | distance_weight () const |
Real | near_squared_size () const |
core::select::residue_selector::ResidueSelectorCOP | selector1 () const |
core::select::residue_selector::ResidueSelectorCOP | selector2 () const |
void | quick (bool const quick) |
void | verbose (bool const verbose) |
void | use_rosetta_radii (bool const use_rosetta_radii) |
void | apolar_target (bool const apolar_target) |
void | filtered_area (Real const filtered_area) |
void | distance_weight (Real const distance_weight) |
void | near_squared_size (Real const near_squared_size) |
void | selector1 (core::select::residue_selector::ResidueSelectorCOP const selector) |
void | selector2 (core::select::residue_selector::ResidueSelectorCOP const selector) |
void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override |
parse xml More... | |
bool | apply (Pose const &pose) const override |
Returns true if the given pose passes the filter, false otherwise. More... | |
Real | report_sm (Pose const &pose) const override |
used to report filter internals through a score or silent file More... | |
core::Real | compute (Pose const &pose) const |
calc contact molecular surface, returns results of the ContactMolecularSurfaceCalculator More... | |
std::string | name () const override |
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Filter () | |
Filter (std::string const &) | |
~Filter () override | |
virtual void | report (std::ostream &, core::pose::Pose const &) const |
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 Member Functions | |
void | setup_from_selectors (Pose const &pose, ContactMolecularSurfaceCalculator &scc) const |
Uses residue selectors to set up the ContactMolecularSurfaceCalculator. More... | |
Private Attributes | |
Real | filtered_area_ |
Real | distance_weight_ |
Real | near_squared_size_ |
bool | apolar_target_ |
bool | quick_ = false |
bool | verbose_ = false |
bool | use_rosetta_radii_ = false |
core::select::residue_selector::ResidueSelectorCOP | selector1_ |
core::select::residue_selector::ResidueSelectorCOP | selector2_ |
Additional Inherited Members | |
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std::string | scorename_ |
typedef core::scoring::sc::ContactMolecularSurfaceCalculator protocols::simple_filters::ContactMolecularSurfaceFilter::ContactMolecularSurfaceCalculator |
typedef protocols::filters::FilterOP protocols::simple_filters::ContactMolecularSurfaceFilter::FilterOP |
typedef utility::tag::TagCOP protocols::simple_filters::ContactMolecularSurfaceFilter::TagCOP |
protocols::simple_filters::ContactMolecularSurfaceFilter::ContactMolecularSurfaceFilter | ( | ) |
protocols::simple_filters::ContactMolecularSurfaceFilter::ContactMolecularSurfaceFilter | ( | Real const & | filtered_area, |
Real const & | distance_weight, | ||
bool const | quick, | ||
bool const | verbose, | ||
bool const | use_rosetta_radii = false |
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protocols::simple_filters::ContactMolecularSurfaceFilter::ContactMolecularSurfaceFilter | ( | Real const & | filtered_area, |
Real const & | distance_weight, | ||
bool const | quick, | ||
bool const | verbose, | ||
core::select::residue_selector::ResidueSelectorCOP const | selector1, | ||
core::select::residue_selector::ResidueSelectorCOP const | selector2, | ||
bool const | use_rosetta_radii = false |
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overridedefault |
bool protocols::simple_filters::ContactMolecularSurfaceFilter::apolar_target | ( | ) | const |
References apolar_target_.
Referenced by apolar_target().
void protocols::simple_filters::ContactMolecularSurfaceFilter::apolar_target | ( | bool const | apolar_target | ) |
References apolar_target(), and apolar_target_.
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overridevirtual |
Returns true if the given pose passes the filter, false otherwise.
Implements protocols::filters::Filter.
References compute(), filtered_area_, and protocols::simple_filters::tr().
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static |
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overridevirtual |
Implements protocols::filters::Filter.
core::Real protocols::simple_filters::ContactMolecularSurfaceFilter::compute | ( | Pose const & | pose | ) | const |
calc contact molecular surface, returns results of the ContactMolecularSurfaceCalculator
[in] | pose | Pose to be analyzed |
EXCN_CalcInitFailed | Thrown if calculator couldn't be initialized |
EXCN_ResultsInvalid | Thrown if computed results are invalid |
References core::scoring::sc::ContactMolecularSurfaceCalculator::CalcContactArea(), core::scoring::sc::MolecularSurfaceCalculator::density, distance_weight_, core::scoring::sc::MolecularSurfaceCalculator::Init(), core::scoring::sc::MolecularSurfaceCalculator::near_squared_size, near_squared_size_, quick_, core::scoring::sc::MolecularSurfaceCalculator::Reset(), selector1_, selector2_, core::scoring::sc::MolecularSurfaceCalculator::settings, setup_from_selectors(), protocols::simple_filters::tr(), core::scoring::sc::MolecularSurfaceCalculator::use_rosetta_radii, use_rosetta_radii_, verbose_, and core::scoring::sc::MolecularSurfaceCalculator::weight.
Referenced by apply(), and report_sm().
core::Real protocols::simple_filters::ContactMolecularSurfaceFilter::distance_weight | ( | ) | const |
References distance_weight_.
Referenced by distance_weight().
void protocols::simple_filters::ContactMolecularSurfaceFilter::distance_weight | ( | core::Real const | distance_weight | ) |
References distance_weight(), and distance_weight_.
core::Real protocols::simple_filters::ContactMolecularSurfaceFilter::filtered_area | ( | ) | const |
References filtered_area_.
Referenced by filtered_area().
void protocols::simple_filters::ContactMolecularSurfaceFilter::filtered_area | ( | core::Real const | filtered_area | ) |
References filtered_area(), and filtered_area_.
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overridevirtual |
Implements protocols::filters::Filter.
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overridevirtual |
Reimplemented from protocols::filters::Filter.
References class_name().
core::Real protocols::simple_filters::ContactMolecularSurfaceFilter::near_squared_size | ( | ) | const |
References near_squared_size_.
Referenced by near_squared_size().
void protocols::simple_filters::ContactMolecularSurfaceFilter::near_squared_size | ( | core::Real const | near_squared_size | ) |
References near_squared_size(), and near_squared_size_.
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overridevirtual |
parse xml
Reimplemented from protocols::filters::Filter.
References apolar_target_, distance_weight_, filtered_area_, core::select::residue_selector::get_residue_selector(), near_squared_size_, quick_, selector1_, selector2_, protocols::simple_filters::tr(), use_rosetta_radii_, and verbose_.
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static |
bool protocols::simple_filters::ContactMolecularSurfaceFilter::quick | ( | ) | const |
void protocols::simple_filters::ContactMolecularSurfaceFilter::quick | ( | bool const | quick | ) |
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overridevirtual |
used to report filter internals through a score or silent file
Reimplemented from protocols::filters::Filter.
References compute(), and protocols::simple_filters::tr().
core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ContactMolecularSurfaceFilter::selector1 | ( | ) | const |
References selector1_.
void protocols::simple_filters::ContactMolecularSurfaceFilter::selector1 | ( | core::select::residue_selector::ResidueSelectorCOP const | selector | ) |
References selector1_.
core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ContactMolecularSurfaceFilter::selector2 | ( | ) | const |
References selector2_.
void protocols::simple_filters::ContactMolecularSurfaceFilter::selector2 | ( | core::select::residue_selector::ResidueSelectorCOP const | selector | ) |
References selector2_.
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private |
Uses residue selectors to set up the ContactMolecularSurfaceCalculator.
[in] | pose | Pose to be analyzed |
[out] | scc | Initialized, empty ContactMolecularSurfaceCalculator, to which pose residues are added |
References core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), apolar_target_, core::pose::Pose::residue(), selector1_, selector2_, and protocols::simple_filters::tr().
Referenced by compute().
bool protocols::simple_filters::ContactMolecularSurfaceFilter::use_rosetta_radii | ( | ) | const |
References use_rosetta_radii_.
Referenced by use_rosetta_radii().
void protocols::simple_filters::ContactMolecularSurfaceFilter::use_rosetta_radii | ( | bool const | use_rosetta_radii | ) |
References use_rosetta_radii(), and use_rosetta_radii_.
bool protocols::simple_filters::ContactMolecularSurfaceFilter::verbose | ( | ) | const |
void protocols::simple_filters::ContactMolecularSurfaceFilter::verbose | ( | bool const | verbose | ) |
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Referenced by apolar_target(), parse_my_tag(), and setup_from_selectors().
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Referenced by compute(), distance_weight(), and parse_my_tag().
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Referenced by apply(), filtered_area(), and parse_my_tag().
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Referenced by compute(), near_squared_size(), and parse_my_tag().
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Referenced by compute(), parse_my_tag(), and quick().
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Referenced by compute(), parse_my_tag(), selector1(), and setup_from_selectors().
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Referenced by compute(), parse_my_tag(), selector2(), and setup_from_selectors().
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Referenced by compute(), parse_my_tag(), and use_rosetta_radii().
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Referenced by compute(), parse_my_tag(), and verbose().