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protocols::simple_filters::ShapeComplementarityFilter Class Reference

#include <ShapeComplementarityFilter.hh>

Inheritance diagram for protocols::simple_filters::ShapeComplementarityFilter:
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Collaboration diagram for protocols::simple_filters::ShapeComplementarityFilter:
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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::TagPtr TagPtr
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef protocols::moves::DataMap DataMap
 
typedef
protocols::moves::Movers_map 
Movers_map
 

Public Member Functions

 ShapeComplementarityFilter ()
 
 ShapeComplementarityFilter (Real const &filtered_sc, Real const &filtered_area, Size const &jump_id, Size const &quick, Size const &verbose)
 
 ShapeComplementarityFilter (ShapeComplementarityFilter const &rval)
 
virtual ~ShapeComplementarityFilter ()
 
virtual filters::FilterOP clone () const
 
virtual filters::FilterOP fresh_instance () const
 
virtual std::string name () const
 
void filtered_sc (Real const &filtered_sc)
 
void filtered_area (Real const &filtered_area)
 
void jump_id (Size const &jump_id)
 
void quick (Size const &quick)
 
void verbose (Size const &verbose)
 
void multicomp (bool multicomp)
 
void sym_dof_name (std::string const &sym_dof_name)
 
std::string sym_dof_name () const
 
bool multicomp () const
 
virtual void parse_my_tag (TagPtr const tag, DataMap &, filters::Filters_map const &, Movers_map const &, Pose const &)
 parse xml More...
 
void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
 
virtual bool apply (Pose const &pose) const
 Returns true if the given pose passes the filter, false otherwise. More...
 
virtual Real report_sm (Pose const &pose) const
 used to report filter internals through a score or silent file More...
 
virtual Size compute (Pose const &pose) const
 calc shape complementarity More...
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
virtual ~Filter ()
 
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 void apply (core::io::serialization::PipeMap &pmap)
 
virtual void score (core::io::serialization::PipeMap &pmap)
 
virtual core::Real score (core::pose::Pose &pose)
 

Private Attributes

core::scoring::sc::ShapeComplementarityCalculator scc_
 
Real filtered_sc_
 
Real filtered_area_
 
Size jump_id_
 
Size quick_
 
Size verbose_
 
utility::vector1< core::Sizeresidues1_
 
utility::vector1< core::Sizeresidues2_
 
bool write_int_area_
 
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 ( )

Referenced by clone(), and fresh_instance().

protocols::simple_filters::ShapeComplementarityFilter::ShapeComplementarityFilter ( Real const &  filtered_sc,
Real const &  filtered_area,
Size const &  jump_id,
Size const &  quick,
Size const &  verbose 
)
protocols::simple_filters::ShapeComplementarityFilter::ShapeComplementarityFilter ( ShapeComplementarityFilter const &  rval)
virtual protocols::simple_filters::ShapeComplementarityFilter::~ShapeComplementarityFilter ( )
inlinevirtual

Member Function Documentation

bool protocols::simple_filters::ShapeComplementarityFilter::apply ( Pose const &  pose) const
virtual
virtual filters::FilterOP protocols::simple_filters::ShapeComplementarityFilter::clone ( ) const
inlinevirtual
core::Size protocols::simple_filters::ShapeComplementarityFilter::compute ( Pose const &  pose) const
virtual

calc shape complementarity

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::sc::_RESULTS::area, core::scoring::sc::ShapeComplementarityCalculator::Calc(), core::scoring::sc::_RESULTS::d_mean, core::scoring::sc::_RESULTS::d_median, core::scoring::sc::MolecularSurfaceCalculator::density, core::scoring::sc::_RESULTS::distance, core::pose::Pose::fold_tree(), core::pose::symmetry::get_jump_name_to_subunits(), core::pose::symmetry::get_sym_aware_jump_num(), core::scoring::sc::MolecularSurfaceCalculator::GetResults(), core::scoring::sc::MolecularSurfaceCalculator::Init(), core::pose::symmetry::is_symmetric(), jump_id_, multicomp_, core::scoring::sc::_RESULTS::nAllDots, core::scoring::sc::_RESULTS::nAtoms, core::scoring::sc::_RESULTS::nBlockedAtoms, core::scoring::sc::_RESULTS::nBuriedAtoms, core::scoring::sc::_RESULTS::nTrimmedDots, core::pose::symmetry::partition_by_symm_jumps(), quick_, core::scoring::sc::MolecularSurfaceCalculator::Reset(), core::pose::Pose::residue(), residues1_, residues2_, core::scoring::sc::_RESULTS::s_mean, core::scoring::sc::_RESULTS::s_median, core::scoring::sc::_RESULTS::sc, scc_, core::scoring::sc::MolecularSurfaceCalculator::settings, core::scoring::sc::_RESULTS::surface, core::pose::symmetry::sym_dof_jump_num(), sym_dof_name(), core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), protocols::simple_filters::tr(), core::scoring::sc::_RESULTS::trimmedArea, core::scoring::sc::_RESULTS::valid, 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_sc ( Real const &  filtered_sc)

References filtered_sc_.

virtual filters::FilterOP protocols::simple_filters::ShapeComplementarityFilter::fresh_instance ( ) const
inlinevirtual
void protocols::simple_filters::ShapeComplementarityFilter::jump_id ( 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().

virtual std::string protocols::simple_filters::ShapeComplementarityFilter::name ( ) const
inlinevirtual

Reimplemented from protocols::filters::Filter.

void protocols::simple_filters::ShapeComplementarityFilter::parse_def ( utility::lua::LuaObject const &  def,
utility::lua::LuaObject const &  score_fxns,
utility::lua::LuaObject const &  tasks 
)
virtual
void protocols::simple_filters::ShapeComplementarityFilter::parse_my_tag ( TagPtr const  tag,
DataMap ,
filters::Filters_map const &  ,
Movers_map const &  ,
Pose const &  pose 
)
virtual
void protocols::simple_filters::ShapeComplementarityFilter::quick ( Size const &  quick)

References quick_.

core::Real protocols::simple_filters::ShapeComplementarityFilter::report_sm ( Pose const &  ) const
virtual
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 ( Size const &  verbose)

References verbose_.

Member Data Documentation

Real protocols::simple_filters::ShapeComplementarityFilter::filtered_area_
private
Real protocols::simple_filters::ShapeComplementarityFilter::filtered_sc_
private
Size protocols::simple_filters::ShapeComplementarityFilter::jump_id_
private
bool protocols::simple_filters::ShapeComplementarityFilter::multicomp_
private

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

Size protocols::simple_filters::ShapeComplementarityFilter::quick_
private
utility::vector1<core::Size> protocols::simple_filters::ShapeComplementarityFilter::residues1_
private

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

utility::vector1<core::Size> protocols::simple_filters::ShapeComplementarityFilter::residues2_
private

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

core::scoring::sc::ShapeComplementarityCalculator protocols::simple_filters::ShapeComplementarityFilter::scc_
mutableprivate

Referenced by apply(), compute(), and report_sm().

std::string protocols::simple_filters::ShapeComplementarityFilter::sym_dof_name_
private

Referenced by sym_dof_name().

Size protocols::simple_filters::ShapeComplementarityFilter::verbose_
private
bool protocols::simple_filters::ShapeComplementarityFilter::write_int_area_
private

Referenced by parse_def(), parse_my_tag(), and report_sm().


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