#include <SSMotifFinderFilter.hh>

Public Member Functions
	SSMotifFinder ()

virtual	~SSMotifFinder ()

filters::FilterOP	clone () const

filters::FilterOP	fresh_instance () const

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

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

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, filters::Filters_map const &filters, moves::Movers_map const &, core::pose::Pose const &)

core::Size	from_res () const

void	from_res (core::Size const r)

core::Size	to_res () const

void	to_res (core::Size const r)

core::Size	template_stem1 () const

void	template_stem1 (core::Size const r)

core::Size	template_stem2 () const

void	template_stem2 (core::Size const r)

core::Real	rmsd () const

void	rmsd (core::Real const c)

core::kinematics::Jump	jump () const

core::kinematics::Jump	compute_jump (core::pose::Pose const &pose, core::Size const start, core::Size const end) const

std::string	filename () const

void	filename (std::string const s)

std::string	pdbname () const

void	pdbname (std::string const s)

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 Member Functions
void	superimpose_pose_on_template (core::pose::Pose const &, core::pose::Pose &, core::Size const, core::Size const ) const

Private Attributes
core::Size	from_res_

core::Size	to_res_

core::pose::PoseOP	template_pose_

core::Size	template_stem1_

core::Size	template_stem2_

core::kinematics::Jump	jump_

core::Real	rmsd_

std::string	filename_

std::string	pdbname_

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

Constructor & Destructor Documentation

protocols::simple_filters::SSMotifFinder::SSMotifFinder ( )

References filters.

Referenced by clone(), and fresh_instance().

protocols::simple_filters::SSMotifFinder::~SSMotifFinder ( )

virtual

Member Function Documentation

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

virtual

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

Implements protocols::filters::Filter.

References core::pose::Pose::conformation(), core::scoring::dssp::Dssp::dssp_reduced(), filename_, from_res(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::conformation::Residue::is_protein(), pair, pdbname_, protocols::simple_filters::res_rmsd(), core::conformation::Conformation::residue(), rmsd(), superimpose_pose_on_template(), template_pose_, template_stem1(), template_stem2(), to_res(), core::pose::Pose::total_residue(), protocols::simple_filters::TR, and protocols::simple_filters::write_to_file().

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

inlinevirtual

Implements protocols::filters::Filter.

References SSMotifFinder().

core::kinematics::Jump protocols::simple_filters::SSMotifFinder::compute_jump	(	core::pose::Pose const &	pose,
		core::Size const	start,
		core::Size const	end
	)		const

References core::pose::Pose::conformation(), core::conformation::Conformation::num_chains(), core::conformation::Conformation::residue(), runtime_assert, and protocols::simple_filters::TR.

Referenced by parse_my_tag().

std::string protocols::simple_filters::SSMotifFinder::filename ( ) const

inline

References filename_.

Referenced by parse_my_tag().

void protocols::simple_filters::SSMotifFinder::filename ( std::string const s )

inline

References filename_.

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

inlinevirtual

Implements protocols::filters::Filter.

References SSMotifFinder().

core::Size protocols::simple_filters::SSMotifFinder::from_res ( ) const

inline

References from_res_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::SSMotifFinder::from_res ( core::Size const r )

inline

References from_res_.

core::kinematics::Jump protocols::simple_filters::SSMotifFinder::jump ( ) const

References jump_.

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

virtual

Reimplemented from protocols::filters::Filter.

References compute_jump(), filename(), from_res(), jump_, core::pose::parse_resnum(), pdbname(), core::import_pose::pose_from_pdb(), rmsd(), template_pose_, template_stem1(), template_stem2(), to_res(), and protocols::simple_filters::TR.

std::string protocols::simple_filters::SSMotifFinder::pdbname ( ) const

inline

References pdbname_.

Referenced by parse_my_tag().

void protocols::simple_filters::SSMotifFinder::pdbname ( std::string const s )

inline

References pdbname_.

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

virtual

Reimplemented from protocols::filters::Filter.

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

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

core::Real protocols::simple_filters::SSMotifFinder::rmsd ( ) const

inline

References rmsd_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::SSMotifFinder::rmsd ( core::Real const c )

inline

References rmsd_.

void protocols::simple_filters::SSMotifFinder::superimpose_pose_on_template	(	core::pose::Pose const &	template_pose,
		core::pose::Pose &	copy_pose,
		core::Size const	pose_stem1,
		core::Size const	pose_stem2
	)		const