protocols::simple_filters::SSMotifFinder Class Reference

#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 &) override
	Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
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 () 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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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

SSMotifFinder()

protocols::simple_filters::SSMotifFinder::SSMotifFinder

(

)

~SSMotifFinder()

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

overridedefault

Member Function Documentation

apply()

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().

class_name()

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

static

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

clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

compute_jump()

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::conformation::Conformation::append_residue_by_jump(), core::pose::Pose::conformation(), core::sequence::end, core::pose::Pose::fold_tree(), core::pose::Pose::jump(), core::conformation::Conformation::num_chains(), core::conformation::Conformation::residue(), protocols::loops::start, and protocols::simple_filters::TR().

Referenced by parse_my_tag().

filename() [1/2]

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

inline

References filename_.

Referenced by parse_my_tag().

filename() [2/2]

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

inline

References filename_.

fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

from_res() [1/2]

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

inline

References from_res_.

Referenced by apply(), and parse_my_tag().

from_res() [2/2]

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

inline

References from_res_.

jump()

core::kinematics::Jump protocols::simple_filters::SSMotifFinder::jump

(

)

const

References jump_.

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

void protocols::simple_filters::SSMotifFinder::parse_my_tag ( utility::tag::TagCOP  , basic::datacache::DataMap &    )

overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

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().

pdbname() [1/2]

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

inline

References pdbname_.

Referenced by parse_my_tag().

pdbname() [2/2]

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

inline

References pdbname_.

provide_xml_schema()

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().

report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

report_sm()

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.

rmsd() [1/2]

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

inline

References rmsd_.

Referenced by apply(), and parse_my_tag().

rmsd() [2/2]

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

inline

References rmsd_.

superimpose_pose_on_template()

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

private

References protocols::toolbox::apply_superposition_transform(), protocols::simple_filters::coords(), protocols::seeded_abinitio::superposition_transform(), template_stem1(), and template_stem2().

Referenced by apply().

template_stem1() [1/2]

core::Size protocols::simple_filters::SSMotifFinder::template_stem1 ( ) const

inline

References template_stem1_.

Referenced by apply(), parse_my_tag(), and superimpose_pose_on_template().

template_stem1() [2/2]

void protocols::simple_filters::SSMotifFinder::template_stem1 ( core::Size const  r )

inline

References template_stem1_.

template_stem2() [1/2]

core::Size protocols::simple_filters::SSMotifFinder::template_stem2 ( ) const

inline

References template_stem2_.

Referenced by apply(), parse_my_tag(), and superimpose_pose_on_template().

template_stem2() [2/2]

void protocols::simple_filters::SSMotifFinder::template_stem2 ( core::Size const  r )

inline

References template_stem2_.

to_res() [1/2]

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

inline

References to_res_.

Referenced by apply(), and parse_my_tag().

to_res() [2/2]

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

inline

References to_res_.

Member Data Documentation

filename_

std::string protocols::simple_filters::SSMotifFinder::filename_

private

Referenced by apply(), and filename().

from_res_

core::Size protocols::simple_filters::SSMotifFinder::from_res_

private

Referenced by from_res().

jump_

core::kinematics::Jump protocols::simple_filters::SSMotifFinder::jump_

private

Referenced by jump(), and parse_my_tag().

pdbname_

std::string protocols::simple_filters::SSMotifFinder::pdbname_

private

Referenced by apply(), and pdbname().

rmsd_

core::Real protocols::simple_filters::SSMotifFinder::rmsd_

private

Referenced by rmsd().

template_pose_

core::pose::PoseOP protocols::simple_filters::SSMotifFinder::template_pose_

private

Referenced by apply(), and parse_my_tag().

template_stem1_

core::Size protocols::simple_filters::SSMotifFinder::template_stem1_

private

Referenced by template_stem1().

template_stem2_

core::Size protocols::simple_filters::SSMotifFinder::template_stem2_

private

Referenced by template_stem2().

to_res_

core::Size protocols::simple_filters::SSMotifFinder::to_res_

private

Referenced by to_res().

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

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