Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Private Attributes | List of all members
protocols::simple_filters::ShapeComplementarityFilter Class Reference

#include <ShapeComplementarityFilter.hh>

Inheritance diagram for protocols::simple_filters::ShapeComplementarityFilter:
Inheritance graph
[legend]
Collaboration diagram for protocols::simple_filters::ShapeComplementarityFilter:
Collaboration 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::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::Size > residues1_
 
utility::vector1< core::Size > residues2_
 
bool write_int_area_
 
bool multicomp_
 
std::string sym_dof_name_
 

Additional Inherited Members

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

Detailed Description

Definition at line 45 of file ShapeComplementarityFilter.hh.

Member Typedef Documentation

typedef protocols::moves::DataMap protocols::simple_filters::ShapeComplementarityFilter::DataMap

Definition at line 56 of file ShapeComplementarityFilter.hh.

typedef protocols::filters::Filter protocols::simple_filters::ShapeComplementarityFilter::Filter

Definition at line 49 of file ShapeComplementarityFilter.hh.

typedef protocols::filters::FilterOP protocols::simple_filters::ShapeComplementarityFilter::FilterOP

Definition at line 50 of file ShapeComplementarityFilter.hh.

typedef protocols::filters::Filters_map protocols::simple_filters::ShapeComplementarityFilter::Filters_map

Definition at line 55 of file ShapeComplementarityFilter.hh.

typedef protocols::moves::Movers_map protocols::simple_filters::ShapeComplementarityFilter::Movers_map

Definition at line 57 of file ShapeComplementarityFilter.hh.

typedef core::pose::Pose protocols::simple_filters::ShapeComplementarityFilter::Pose

Definition at line 52 of file ShapeComplementarityFilter.hh.

typedef core::Real protocols::simple_filters::ShapeComplementarityFilter::Real

Definition at line 51 of file ShapeComplementarityFilter.hh.

typedef protocols::filters::Filter protocols::simple_filters::ShapeComplementarityFilter::Super

Definition at line 48 of file ShapeComplementarityFilter.hh.

typedef utility::tag::TagPtr protocols::simple_filters::ShapeComplementarityFilter::TagPtr

Definition at line 54 of file ShapeComplementarityFilter.hh.

Constructor & Destructor Documentation

protocols::simple_filters::ShapeComplementarityFilter::ShapeComplementarityFilter ( )

Definition at line 53 of file ShapeComplementarityFilter.cc.

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 
)

Definition at line 68 of file ShapeComplementarityFilter.cc.

protocols::simple_filters::ShapeComplementarityFilter::ShapeComplementarityFilter ( ShapeComplementarityFilter const &  rval)

Definition at line 82 of file ShapeComplementarityFilter.cc.

virtual protocols::simple_filters::ShapeComplementarityFilter::~ShapeComplementarityFilter ( )
inlinevirtual

Definition at line 73 of file ShapeComplementarityFilter.hh.

Member Function Documentation

bool protocols::simple_filters::ShapeComplementarityFilter::apply ( Pose const &  pose) const
virtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

Definition at line 272 of file ShapeComplementarityFilter.cc.

References core::scoring::sc::_RESULTS::area, compute(), filtered_area_, filtered_sc_, core::scoring::sc::MolecularSurfaceCalculator::GetResults(), core::scoring::sc::MolecularSurfaceCalculator::Reset(), core::scoring::sc::_RESULTS::sc, scc_, and protocols::simple_filters::tr().

virtual filters::FilterOP protocols::simple_filters::ShapeComplementarityFilter::clone ( ) const
inlinevirtual

Implements protocols::filters::Filter.

Definition at line 80 of file ShapeComplementarityFilter.hh.

References ShapeComplementarityFilter().

core::Size protocols::simple_filters::ShapeComplementarityFilter::compute ( Pose const &  pose) const
virtual

calc shape complementarity

Definition at line 105 of file ShapeComplementarityFilter.cc.

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)

Definition at line 95 of file ShapeComplementarityFilter.cc.

References filtered_area_.

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

Definition at line 94 of file ShapeComplementarityFilter.cc.

References filtered_sc_.

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

Implements protocols::filters::Filter.

Definition at line 83 of file ShapeComplementarityFilter.hh.

References ShapeComplementarityFilter().

void protocols::simple_filters::ShapeComplementarityFilter::jump_id ( Size const &  jump_id)

Definition at line 96 of file ShapeComplementarityFilter.cc.

References jump_id_.

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

Definition at line 101 of file ShapeComplementarityFilter.cc.

References multicomp(), and multicomp_.

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

Definition at line 102 of file ShapeComplementarityFilter.cc.

References multicomp_.

Referenced by multicomp(), and parse_my_tag().

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

Reimplemented from protocols::filters::Filter.

Definition at line 90 of file ShapeComplementarityFilter.hh.

void protocols::simple_filters::ShapeComplementarityFilter::parse_def ( utility::lua::LuaObject const &  def,
utility::lua::LuaObject const &  score_fxns,
utility::lua::LuaObject const &  tasks 
)
virtual

Reimplemented from protocols::filters::Filter.

Definition at line 348 of file ShapeComplementarityFilter.cc.

References core::sequence::end, filtered_area_, filtered_sc_, jump_id_, quick_, residues1_, residues2_, protocols::simple_filters::tr(), verbose_, and write_int_area_.

void protocols::simple_filters::ShapeComplementarityFilter::parse_my_tag ( TagPtr const  tag,
DataMap &  ,
filters::Filters_map const &  ,
Movers_map const &  ,
Pose const &  pose 
)
virtual

parse xml

Reimplemented from protocols::filters::Filter.

Definition at line 298 of file ShapeComplementarityFilter.cc.

References filtered_area_, filtered_sc_, core::pose::get_resnum_list(), jump_id_, multicomp(), quick_, residues1_, residues2_, sym_dof_name(), protocols::simple_filters::tr(), verbose_, and write_int_area_.

void protocols::simple_filters::ShapeComplementarityFilter::quick ( Size const &  quick)

Definition at line 97 of file ShapeComplementarityFilter.cc.

References quick_.

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

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

Definition at line 226 of file ShapeComplementarityFilter.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::sc::_RESULTS::area, compute(), protocols::nonlocal::current_job(), core::pose::Pose::fold_tree(), protocols::jd2::JobDistributor::get_instance(), core::pose::symmetry::get_jump_name_to_subunits(), core::pose::symmetry::get_sym_aware_jump_num(), protocols::filters::Filter::get_user_defined_name(), core::scoring::sc::MolecularSurfaceCalculator::GetResults(), core::pose::symmetry::is_symmetric(), multicomp_, core::pose::symmetry::partition_by_symm_jumps(), core::scoring::sc::MolecularSurfaceCalculator::Reset(), core::pose::Pose::residue(), core::scoring::sc::_RESULTS::sc, scc_, core::pose::symmetry::sym_dof_jump_num(), sym_dof_name(), core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), and write_int_area_.

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

Definition at line 99 of file ShapeComplementarityFilter.cc.

References sym_dof_name(), and sym_dof_name_.

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

Definition at line 100 of file ShapeComplementarityFilter.cc.

References sym_dof_name_.

Referenced by compute(), parse_my_tag(), report_sm(), and sym_dof_name().

void protocols::simple_filters::ShapeComplementarityFilter::verbose ( Size const &  verbose)

Definition at line 98 of file ShapeComplementarityFilter.cc.

References verbose_.

Member Data Documentation

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

Definition at line 137 of file ShapeComplementarityFilter.hh.

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

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

Definition at line 136 of file ShapeComplementarityFilter.hh.

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

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

Definition at line 138 of file ShapeComplementarityFilter.hh.

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

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

Definition at line 146 of file ShapeComplementarityFilter.hh.

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

Size protocols::simple_filters::ShapeComplementarityFilter::quick_
private

Definition at line 139 of file ShapeComplementarityFilter.hh.

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

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

Definition at line 141 of file ShapeComplementarityFilter.hh.

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

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

Definition at line 142 of file ShapeComplementarityFilter.hh.

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

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

Definition at line 134 of file ShapeComplementarityFilter.hh.

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

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

Definition at line 147 of file ShapeComplementarityFilter.hh.

Referenced by sym_dof_name().

Size protocols::simple_filters::ShapeComplementarityFilter::verbose_
private

Definition at line 140 of file ShapeComplementarityFilter.hh.

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

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

Definition at line 143 of file ShapeComplementarityFilter.hh.

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

The documentation for this class was generated from the following files:
Generated on Sat Jun 1 2013 12:53:21 for Rosetta 3.5 by   doxygen 1.8.4