protocols::simple_filters::ShapeComplementarityFilter Class Reference

#include <ShapeComplementarityFilter.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 protocols::filters::Filters_map	Filters_map
typedef basic::datacache::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	residues1 (utility::vector1< core::Size > const &residues)
void	residues2 (utility::vector1< core::Size > const &residues)
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	multicomp (bool multicomp)
bool	multicomp () const
virtual void	parse_my_tag (TagCOP tag, basic::datacache::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_

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::simple_filters::ShapeComplementarityFilter::DataMap

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

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

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

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

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

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

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

typedef utility::tag::TagCOP protocols::simple_filters::ShapeComplementarityFilter::TagCOP

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

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

Implements protocols::filters::Filter.

References compute(), filtered_area_, filtered_sc_, sc, scc_, and protocols::simple_filters::tr.

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

inlinevirtual

Implements protocols::filters::Filter.

References ShapeComplementarityFilter().

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::_RESULTS::area, core::scoring::sc::ShapeComplementarityCalculator::Calc(), core::scoring::sc::_RESULTS::distance, core::pose::Pose::fold_tree(), 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::get_sym_aware_jump_num(), core::pose::symmetry::intracomponent_contact(), core::pose::symmetry::is_symmetric(), jump_id_, multicomp_, core::scoring::sc::_RESULTS::nAtoms, core::pose::symmetry::partition_by_symm_jumps(), quick_, core::pose::Pose::residue(), residues1_, residues2_, runtime_assert, core::scoring::sc::_RESULTS::sc, scc_, utility::string_split(), 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, 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

Implements protocols::filters::Filter.

References ShapeComplementarityFilter().

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

Reimplemented from protocols::filters::Filter.

References begin, end, filtered_area_, filtered_sc_, jump_id_, quick_, residues1_, residues2_, utility::lua::LuaObject::to(), protocols::simple_filters::tr, verbose_, and write_int_area_.

void protocols::simple_filters::ShapeComplementarityFilter::parse_my_tag ( TagCOP  tag, basic::datacache::DataMap &  , filters::Filters_map const &  , Movers_map const &  , Pose const &  pose  )

virtual

parse xml

Reimplemented from protocols::filters::Filter.

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

)

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.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::jd2::Job::add_string_real_pair(), 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::pose::symmetry::is_symmetric(), multicomp_, core::pose::symmetry::partition_by_symm_jumps(), core::pose::Pose::residue(), scc_, core::pose::symmetry::sym_dof_jump_num(), sym_dof_name(), core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), protocols::simple_filters::tr, and write_int_area_.

void protocols::simple_filters::ShapeComplementarityFilter::residues1

(

utility::vector1< core::Size > const &

residues

)

References residues1_.

void protocols::simple_filters::ShapeComplementarityFilter::residues2

(

utility::vector1< core::Size > const &

residues

)

References residues2_.

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

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

)

References verbose_.

void protocols::simple_filters::ShapeComplementarityFilter::write_int_area

(

bool

write_int_area

)

References write_int_area(), and write_int_area_.

bool protocols::simple_filters::ShapeComplementarityFilter::write_int_area

(

)

const

References write_int_area_.

Referenced by write_int_area().

Member Data Documentation

Real protocols::simple_filters::ShapeComplementarityFilter::filtered_area_

private

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

Real protocols::simple_filters::ShapeComplementarityFilter::filtered_sc_

private

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

Size protocols::simple_filters::ShapeComplementarityFilter::jump_id_

private

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

bool protocols::simple_filters::ShapeComplementarityFilter::multicomp_

private

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

Size protocols::simple_filters::ShapeComplementarityFilter::quick_

private

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

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

private

Referenced by compute(), parse_def(), parse_my_tag(), and residues1().

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

private

Referenced by compute(), parse_def(), parse_my_tag(), and residues2().

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

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

bool protocols::simple_filters::ShapeComplementarityFilter::write_int_area_

private

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

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

• src/protocols/simple_filters/ShapeComplementarityFilter.hh
• src/protocols/simple_filters/ShapeComplementarityFilter.cc