#include <ResidueBurialFilter.hh>

Inheritance diagram for protocols::simple_filters::ResidueBurialFilter:

Collaboration diagram for protocols::simple_filters::ResidueBurialFilter:

Public Member Functions
	ResidueBurialFilter ()

	ResidueBurialFilter (core::Size const target_residue, core::Size const neighbors, core::Real const distance_threshold)

bool	apply (core::pose::Pose const &pose) const
	Returns true if the given pose passes the filter, false otherwise. More...

void	report (std::ostream &out, core::pose::Pose const &pose) const

core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...

core::Size	compute (core::pose::Pose const &pose) const

filters::FilterOP	clone () const

filters::FilterOP	fresh_instance () const

core::pack::task::TaskFactoryOP	task_factory () const

void	task_factory (core::pack::task::TaskFactoryOP tf)

virtual	~ResidueBurialFilter ()

void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)

core::Real	residue_fraction_buried () const

void	residue_fraction_buried (core::Real const r)

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string const &)

	Filter (Filter const &)

virtual	~Filter ()

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)

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

virtual std::string	name () const

Private Attributes
core::Size	target_residue_

core::Size	neighbors_

core::Real	distance_threshold_

core::pack::task::TaskFactoryOP	task_factory_

core::Real	residue_fraction_buried_
	used to determine which residues to check for burial dynamically. All designable residues will be checked, and if any of them is buried, returns true More...

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Constructor & Destructor Documentation

protocols::simple_filters::ResidueBurialFilter::ResidueBurialFilter ( )

Referenced by clone(), and fresh_instance().

protocols::simple_filters::ResidueBurialFilter::ResidueBurialFilter	(	core::Size const	target_residue,
		core::Size const	neighbors,
		core::Real const	distance_threshold
	)

protocols::simple_filters::ResidueBurialFilter::~ResidueBurialFilter ( )

virtual

Member Function Documentation

bool protocols::simple_filters::ResidueBurialFilter::apply ( core::pose::Pose const & pose) const

virtual

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

Implements protocols::filters::Filter.

References apply(), compute(), distance_threshold_, core::conformation::Residue::name3(), neighbors_, core::pose::Pose::residue(), residue_fraction_buried(), protocols::rosetta_scripts::residue_packer_states(), target_residue_, and task_factory().

Referenced by apply().

filters::FilterOP protocols::simple_filters::ResidueBurialFilter::clone ( ) const

virtual

Implements protocols::filters::Filter.

References ResidueBurialFilter().

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

counts the number of residues to target_residue_ across all chains in the pose, other than the one containing target_residue_

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::kinematics::distance(), distance_threshold_, core::conformation::Conformation::num_chains(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), target_residue_, and core::pose::Pose::total_residue().

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

filters::FilterOP protocols::simple_filters::ResidueBurialFilter::fresh_instance ( ) const

virtual

Implements protocols::filters::Filter.

References ResidueBurialFilter().

void protocols::simple_filters::ResidueBurialFilter::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &	pose
	)

virtual

Reimplemented from protocols::filters::Filter.

References core::pose::get_resnum(), and core::TR().

void protocols::simple_filters::ResidueBurialFilter::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

virtual

Reimplemented from protocols::filters::Filter.

References compute(), core::conformation::Residue::name3(), core::pose::Pose::residue(), target_residue_, and task_factory().

core::Real protocols::simple_filters::ResidueBurialFilter::report_sm ( core::pose::Pose const & ) const

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute(), and task_factory().

core::Real protocols::simple_filters::ResidueBurialFilter::residue_fraction_buried ( ) const

inline

References residue_fraction_buried_.

Referenced by apply().

void protocols::simple_filters::ResidueBurialFilter::residue_fraction_buried ( core::Real const r)

inline

References residue_fraction_buried_.

core::pack::task::TaskFactoryOP protocols::simple_filters::ResidueBurialFilter::task_factory ( ) const

References task_factory_.

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

void protocols::simple_filters::ResidueBurialFilter::task_factory ( core::pack::task::TaskFactoryOP tf)

References task_factory_.

Member Data Documentation

core::Real protocols::simple_filters::ResidueBurialFilter::distance_threshold_

private

Referenced by apply(), and compute().

core::Size protocols::simple_filters::ResidueBurialFilter::neighbors_

private

Referenced by apply().

core::Real protocols::simple_filters::ResidueBurialFilter::residue_fraction_buried_

private

used to determine which residues to check for burial dynamically. All designable residues will be checked, and if any of them is buried, returns true

Referenced by residue_fraction_buried().

core::Size protocols::simple_filters::ResidueBurialFilter::target_residue_

private

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

core::pack::task::TaskFactoryOP protocols::simple_filters::ResidueBurialFilter::task_factory_

private

Referenced by task_factory().

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

src/protocols/simple_filters/ResidueBurialFilter.hh
src/protocols/protein_interface_design/parse_filters.cc
src/protocols/simple_filters/ResidueBurialFilter.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation