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protocols::simple_filters::ShapeComplementarityFilter Class Reference

#include <ShapeComplementarityFilter.hh>

Inheritance diagram for protocols::simple_filters::ShapeComplementarityFilter:
Inheritance graph
[legend]

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::ShapeComplementarityCalculator 
ShapeComplementarityCalculator
 
typedef core::scoring::sc::RESULTS ShapeComplementarityCalculatorResults
 

Public Member Functions

 ShapeComplementarityFilter ()
 
 ShapeComplementarityFilter (Real const &filtered_sc, Real const &filtered_area, core::Size const &jump_id, bool const quick, bool const verbose, Real const &filtered_median_distance=1000.0f)
 
 ~ShapeComplementarityFilter () override=default
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
void filtered_sc (Real const &filtered_sc)
 
void filtered_area (Real const &filtered_area)
 
void filtered_median_distance (Real const &filtered_d_median)
 
void jump_id (core::Size const &jump_id)
 
void quick (bool const quick)
 
void verbose (bool const verbose)
 
void residues1 (std::string const &res_string)
 
void residues2 (std::string const &res_string)
 
void sym_dof_name (std::string const &sym_dof_name)
 
std::string sym_dof_name () const
 
void write_int_area (bool write_int_area)
 
bool write_int_area () const
 
void write_median_distance (bool write_median_distance)
 
bool write_median_distance () const
 
void multicomp (bool multicomp)
 
bool multicomp () const
 
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...
 
ShapeComplementarityCalculatorResults compute (Pose const &pose) const
 calc shape complementarity, returns results of the ShapeComplementarityCalculator 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 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 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 Member Functions

void setup_from_selectors (Pose const &pose, ShapeComplementarityCalculator &scc) const
 Uses residue selectors to set up the ShapeComplementarityCalculator. More...
 
void setup_multi_component_symm (Pose const &pose, ShapeComplementarityCalculator &scc, core::Real &nsubs_scalefactor) const
 Uses multi-component symmetric interfaces to set up the ShapeComplementarityCalculator. More...
 
void setup_single_component_symm (Pose const &pose, ShapeComplementarityCalculator &scc, core::Real &nsubs_scalefactor) const
 Uses single-component symmetric interfaces to set up the ShapeComplementarityCalculator. More...
 
void print_sc_results (std::ostream &tr, ShapeComplementarityCalculatorResults const &r, core::Real const nsubs_scalefactor) const
 prints results to given tracer in a human-readable format More...
 
void write_area (Pose const &pose, core::Real const area_val) const
 writes area value to current jd2 job More...
 
void write_median_distance (Pose const &pose, core::Real const d_median) const
 writes median distance value to current jd2 job More...
 

Private Attributes

Real filtered_sc_
 
Real filtered_area_
 
Real filtered_d_median_
 
core::Size jump_id_
 
bool quick_ = false
 
bool verbose_ = false
 
core::select::residue_selector::ResidueSelectorCOP selector1_
 
core::select::residue_selector::ResidueSelectorCOP selector2_
 
bool write_int_area_
 
bool write_d_median_
 
bool multicomp_
 
std::string sym_dof_name_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_filters::ShapeComplementarityFilter::ShapeComplementarityFilter ( )
protocols::simple_filters::ShapeComplementarityFilter::ShapeComplementarityFilter ( Real const &  filtered_sc,
Real const &  filtered_area,
core::Size const &  jump_id,
bool const  quick,
bool const  verbose,
Real const &  filtered_median_distance = 1000.0f 
)
protocols::simple_filters::ShapeComplementarityFilter::~ShapeComplementarityFilter ( )
overridedefault

Member Function Documentation

bool protocols::simple_filters::ShapeComplementarityFilter::apply ( Pose const &  pose) const
overridevirtual
std::string protocols::simple_filters::ShapeComplementarityFilter::class_name ( )
static
filters::FilterOP protocols::simple_filters::ShapeComplementarityFilter::clone ( ) const
inlineoverridevirtual
ShapeComplementarityFilter::ShapeComplementarityCalculatorResults protocols::simple_filters::ShapeComplementarityFilter::compute ( Pose const &  pose) const

calc shape complementarity, returns results of the ShapeComplementarityCalculator

Parameters
[in]posePose to be analyzed
Exceptions
EXCN_CalcInitFailedThrown if calculator couldn't be initialized
EXCN_ResultsInvalidThrown if computed results are invalid
Returns
ShapeComplementarityCalculator::RESULTS object

References core::scoring::sc::ShapeComplementarityCalculator::Calc(), core::scoring::sc::MolecularSurfaceCalculator::density, core::scoring::sc::MolecularSurfaceCalculator::GetResults(), core::scoring::sc::MolecularSurfaceCalculator::Init(), core::pose::symmetry::is_symmetric(), jump_id_, multicomp_, print_sc_results(), quick_, core::scoring::sc::MolecularSurfaceCalculator::Reset(), selector1_, selector2_, core::scoring::sc::MolecularSurfaceCalculator::settings, setup_from_selectors(), setup_multi_component_symm(), setup_single_component_symm(), protocols::simple_filters::tr(), and verbose_.

Referenced by apply(), and report_sm().

void protocols::simple_filters::ShapeComplementarityFilter::filtered_area ( Real const &  filtered_area)

References filtered_area_.

void protocols::simple_filters::ShapeComplementarityFilter::filtered_median_distance ( Real const &  filtered_d_median)

References filtered_d_median_.

void protocols::simple_filters::ShapeComplementarityFilter::filtered_sc ( Real const &  filtered_sc)

References filtered_sc_.

filters::FilterOP protocols::simple_filters::ShapeComplementarityFilter::fresh_instance ( ) const
inlineoverridevirtual
void protocols::simple_filters::ShapeComplementarityFilter::jump_id ( core::Size const &  jump_id)

References jump_id_.

void protocols::simple_filters::ShapeComplementarityFilter::multicomp ( bool  multicomp)

References multicomp(), and multicomp_.

bool protocols::simple_filters::ShapeComplementarityFilter::multicomp ( ) const

References multicomp_.

Referenced by multicomp(), and parse_my_tag().

std::string protocols::simple_filters::ShapeComplementarityFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::simple_filters::ShapeComplementarityFilter::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::simple_filters::ShapeComplementarityFilter::print_sc_results ( std::ostream &  tr,
ShapeComplementarityCalculatorResults const &  r,
core::Real const  nsubs_scalefactor 
) const
private
void protocols::simple_filters::ShapeComplementarityFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_filters::ShapeComplementarityFilter::quick ( bool const  quick)

References quick_.

core::Real protocols::simple_filters::ShapeComplementarityFilter::report_sm ( Pose const &  ) const
overridevirtual
void protocols::simple_filters::ShapeComplementarityFilter::residues1 ( std::string const &  res_string)

References selector1_.

Referenced by parse_my_tag(), and setup_from_selectors().

void protocols::simple_filters::ShapeComplementarityFilter::residues2 ( std::string const &  res_string)

References selector2_.

Referenced by parse_my_tag(), and setup_from_selectors().

void protocols::simple_filters::ShapeComplementarityFilter::setup_from_selectors ( Pose const &  pose,
ShapeComplementarityCalculator scc 
) const
private

Uses residue selectors to set up the ShapeComplementarityCalculator.

Parameters
[in]posePose to be analyzed
[out]sccInitialized, empty ShapeComplementarityCalculator, to which pose residues are added

References core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::pose::Pose::residue(), residues1(), residues2(), selector1_, selector2_, and protocols::simple_filters::tr().

Referenced by compute().

void protocols::simple_filters::ShapeComplementarityFilter::setup_multi_component_symm ( Pose const &  pose,
ShapeComplementarityCalculator scc,
core::Real nsubs_scalefactor 
) const
private

Uses multi-component symmetric interfaces to set up the ShapeComplementarityCalculator.

Parameters
[in]posePose to be analyzed
[out]sccInitialized, empty ShapeComplementarityCalculator, to which pose residues are added
[out]nsubs_scalefactorWrites number of subunits, to be used as scaling factor for sc calculations

References core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::pose::symmetry::get_full_intracomponent_neighbor_resis(), core::pose::symmetry::get_full_intracomponent_resis(), core::pose::symmetry::get_jump_name_to_subunits(), core::pose::symmetry::intracomponent_contact(), core::pose::Pose::residue(), sym_dof_name(), and protocols::simple_filters::tr().

Referenced by compute().

void protocols::simple_filters::ShapeComplementarityFilter::setup_single_component_symm ( Pose const &  pose,
ShapeComplementarityCalculator scc,
core::Real nsubs_scalefactor 
) const
private

Uses single-component symmetric interfaces to set up the ShapeComplementarityCalculator.

Parameters
[in]posePose to be analyzed
[out]sccInitialized, empty ShapeComplementarityCalculator, to which pose residues are added
[out]nsubs_scalefactorWrites number of subunits, to be used as scaling factor for sc calculations

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::pose::Pose::fold_tree(), core::pose::symmetry::get_sym_aware_jump_num(), core::pose::symmetry::partition_by_symm_jumps(), core::pose::Pose::residue(), core::pose::Pose::size(), core::pose::symmetry::sym_dof_jump_num(), sym_dof_name(), and core::pose::symmetry::symmetry_info().

Referenced by compute().

void protocols::simple_filters::ShapeComplementarityFilter::sym_dof_name ( std::string const &  sym_dof_name)

References sym_dof_name(), and sym_dof_name_.

std::string protocols::simple_filters::ShapeComplementarityFilter::sym_dof_name ( ) const
void protocols::simple_filters::ShapeComplementarityFilter::verbose ( bool const  verbose)

References verbose_.

void protocols::simple_filters::ShapeComplementarityFilter::write_area ( Pose const &  pose,
core::Real const  area_val 
) const
private
void protocols::simple_filters::ShapeComplementarityFilter::write_int_area ( bool  write_int_area)
bool protocols::simple_filters::ShapeComplementarityFilter::write_int_area ( ) const

References write_int_area_.

Referenced by write_int_area().

void protocols::simple_filters::ShapeComplementarityFilter::write_median_distance ( bool  write_median_distance)
bool protocols::simple_filters::ShapeComplementarityFilter::write_median_distance ( ) const

References write_d_median_.

Referenced by report_sm(), and write_median_distance().

void protocols::simple_filters::ShapeComplementarityFilter::write_median_distance ( Pose const &  pose,
core::Real const  d_median 
) const
private

writes median distance value to current jd2 job

Parameters
[in]posePose being analyzed
[in]d_medianMedian distance to be reported

References protocols::jd2::add_string_real_pair_to_current_job(), and protocols::filters::Filter::get_user_defined_name().

Member Data Documentation

Real protocols::simple_filters::ShapeComplementarityFilter::filtered_area_
private

Referenced by apply(), filtered_area(), and parse_my_tag().

Real protocols::simple_filters::ShapeComplementarityFilter::filtered_d_median_
private
Real protocols::simple_filters::ShapeComplementarityFilter::filtered_sc_
private

Referenced by apply(), filtered_sc(), and parse_my_tag().

core::Size protocols::simple_filters::ShapeComplementarityFilter::jump_id_
private

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

bool protocols::simple_filters::ShapeComplementarityFilter::multicomp_
private

Referenced by compute(), multicomp(), and write_area().

bool protocols::simple_filters::ShapeComplementarityFilter::quick_ = false
private

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

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ShapeComplementarityFilter::selector1_
private
core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ShapeComplementarityFilter::selector2_
private
std::string protocols::simple_filters::ShapeComplementarityFilter::sym_dof_name_
private

Referenced by sym_dof_name().

bool protocols::simple_filters::ShapeComplementarityFilter::verbose_ = false
private

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

bool protocols::simple_filters::ShapeComplementarityFilter::write_d_median_
private
bool protocols::simple_filters::ShapeComplementarityFilter::write_int_area_
private

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