#include <SSMotifFinderFilter.hh>

Inheritance diagram for protocols::simple_filters::SSMotifFinder:

Public Member Functions
	SSMotifFinder ()

	~SSMotifFinder () override

filters::FilterOP	clone () const override

filters::FilterOP	fresh_instance () const override

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

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

core::Real	report_sm (core::pose::Pose const &pose) const override
	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 &) override

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)

std::string	name () const override

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

	Filter (std::string const &)

	Filter (Filter const &)

	~Filter () override

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 core::Real	score (core::pose::Pose &pose)

virtual bool	filter_provides_citation_info () const
	Does this filter provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	filter_is_unpublished () const
	Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Static Public Member Functions
static std::string	class_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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 ( )

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

overridedefault

Member Function Documentation

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

overridevirtual

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(), core::scoring::pair, pdbname_, protocols::simple_filters::res_rmsd(), core::conformation::Conformation::residue(), rmsd(), core::pose::Pose::size(), superimpose_pose_on_template(), template_pose_, template_stem1(), template_stem2(), to_res(), protocols::simple_filters::TR(), and protocols::simple_filters::write_to_file().

std::string protocols::simple_filters::SSMotifFinder::class_name ( )

static

Referenced by protocols::simple_filters::SSMotifFinderFilterCreator::keyname(), name(), and provide_xml_schema().

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

inlineoverridevirtual

Implements protocols::filters::Filter.

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(), 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

inlineoverridevirtual

Implements protocols::filters::Filter.

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_.

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

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 &
	)

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute_jump(), filename(), from_res(), jump_, core::pose::parse_resnum(), core::import_pose::PDB_file, pdbname(), core::import_pose::pose_from_file(), 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::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::simple_filters::SSMotifFinderFilterCreator::provide_xml_schema().

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

overridevirtual

Reimplemented from protocols::filters::Filter.

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

overridevirtual

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 core::pack::dunbrack::c, and 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