test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts. More...

#include <AlignmentAAFinderFilter.hh>

Inheritance diagram for protocols::evolution::AlignmentAAFinder:

[legend]

Public Member Functions
	AlignmentAAFinder ()

	~AlignmentAAFinder () override

filters::FilterOP	clone () const override

filters::FilterOP	fresh_instance () const override

bool	apply (core::pose::Pose const &p) 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 &data) override
	Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...

core::Real	exclude_AA_threshold () const

void	exclude_AA_threshold (core::Real const &t)

std::string	alignment_file () const

void	alignment_file (std::string const &a)

std::string	available_AAs_file () const

void	available_AAs_file (std::string const &a)

core::Size	indel_motif_radius () const

void	indel_motif_radius (core::Size const &r)

core::Real	loop_seqid_threshold () const

void	loop_seqid_threshold (core::Real const &t)

core::scoring::ScoreFunctionOP	scorefxn () const

void	scorefxn (core::scoring::ScoreFunctionOP scorefxn)

protocols::moves::MoverOP	relax_mover () const

void	relax_mover (protocols::moves::MoverOP mover)

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 Attributes
core::Real	exclude_AA_threshold_

std::string	alignment_file_

std::string	available_AAs_file_

core::Size	indel_motif_radius_

core::Real	loop_seqid_threshold_

core::scoring::ScoreFunctionOP	scorefxn_

protocols::moves::MoverOP	relax_mover_

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

Detailed Description

test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts.

Constructor & Destructor Documentation

◆ AlignmentAAFinder()

protocols::evolution::AlignmentAAFinder::AlignmentAAFinder ( )

◆ ~AlignmentAAFinder()

protocols::evolution::AlignmentAAFinder::~AlignmentAAFinder ( )

overridedefault

Member Function Documentation

◆ alignment_file() [1/2]

std::string protocols::evolution::AlignmentAAFinder::alignment_file ( ) const

inline

References alignment_file_.

Referenced by apply(), and parse_my_tag().

◆ alignment_file() [2/2]

void protocols::evolution::AlignmentAAFinder::alignment_file ( std::string const & a )

inline

References core::pose::motif::a(), and alignment_file_.

◆ apply()

bool protocols::evolution::AlignmentAAFinder::apply ( core::pose::Pose const & pose ) const

overridevirtual

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

Implements protocols::filters::Filter.

References alignment_file(), available_AAs_file(), protocols::simple_filters::dssp(), core::pose::Pose::energies(), exclude_AA_threshold(), protocols::evolution::AlignmentCleanerTools::indel_motif(), indel_motif_radius(), protocols::evolution::AlignmentCleanerTools::indel_motif_seq_id(), loop_seqid_threshold(), core::sequence::read_fasta_file(), core::scoring::Energies::residue_total_energy(), scorefxn(), core::pose::Pose::sequence(), protocols::evolution::AlignmentCleanerTools::short_ss_loop_filter(), core::pose::Pose::size(), protocols::evolution::AlignmentCleanerTools::thread_sequence_on_pose(), and protocols::evolution::TR().

◆ available_AAs_file() [1/2]

std::string protocols::evolution::AlignmentAAFinder::available_AAs_file ( ) const

inline

References available_AAs_file_.

Referenced by apply(), and parse_my_tag().

◆ available_AAs_file() [2/2]

void protocols::evolution::AlignmentAAFinder::available_AAs_file ( std::string const & a )

inline

References core::pose::motif::a(), and available_AAs_file_.

◆ class_name()

std::string protocols::evolution::AlignmentAAFinder::class_name ( )

static

Referenced by protocols::evolution::AlignmentAAFinderFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

filters::FilterOP protocols::evolution::AlignmentAAFinder::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ exclude_AA_threshold() [1/2]

core::Real protocols::evolution::AlignmentAAFinder::exclude_AA_threshold ( ) const

inline

References exclude_AA_threshold_.

Referenced by apply(), and parse_my_tag().

◆ exclude_AA_threshold() [2/2]

void protocols::evolution::AlignmentAAFinder::exclude_AA_threshold ( core::Real const & t )

inline

References exclude_AA_threshold_, and protocols::hybridization::t.

◆ fresh_instance()

filters::FilterOP protocols::evolution::AlignmentAAFinder::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ indel_motif_radius() [1/2]

core::Size protocols::evolution::AlignmentAAFinder::indel_motif_radius ( ) const

inline

References indel_motif_radius_.

Referenced by apply(), and parse_my_tag().

◆ indel_motif_radius() [2/2]

void protocols::evolution::AlignmentAAFinder::indel_motif_radius ( core::Size const & r )

inline

References indel_motif_radius_.

◆ loop_seqid_threshold() [1/2]

core::Real protocols::evolution::AlignmentAAFinder::loop_seqid_threshold ( ) const

inline

References loop_seqid_threshold_.

Referenced by apply(), and parse_my_tag().

◆ loop_seqid_threshold() [2/2]

void protocols::evolution::AlignmentAAFinder::loop_seqid_threshold ( core::Real const & t )

inline

References loop_seqid_threshold_, and protocols::hybridization::t.

◆ name()

std::string protocols::evolution::AlignmentAAFinder::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::evolution::AlignmentAAFinder::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 alignment_file(), available_AAs_file(), exclude_AA_threshold(), indel_motif_radius(), loop_seqid_threshold(), protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), relax_mover(), and scorefxn().

◆ provide_xml_schema()

void protocols::evolution::AlignmentAAFinder::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::evolution::AlignmentAAFinderFilterCreator::provide_xml_schema().

◆ relax_mover() [1/2]

protocols::moves::MoverOP protocols::evolution::AlignmentAAFinder::relax_mover ( ) const

inline

References relax_mover_.

Referenced by parse_my_tag().

◆ relax_mover() [2/2]

void protocols::evolution::AlignmentAAFinder::relax_mover ( protocols::moves::MoverOP mover )

inline

References relax_mover_.

◆ report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

◆ report_sm()

core::Real protocols::evolution::AlignmentAAFinder::report_sm ( core::pose::Pose const & ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

◆ scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::evolution::AlignmentAAFinder::scorefxn ( ) const

inline

References scorefxn_.

Referenced by apply(), and parse_my_tag().

◆ scorefxn() [2/2]

void protocols::evolution::AlignmentAAFinder::scorefxn ( core::scoring::ScoreFunctionOP scorefxn )

inline

References scorefxn(), and scorefxn_.

Referenced by scorefxn().

Member Data Documentation

◆ alignment_file_

std::string protocols::evolution::AlignmentAAFinder::alignment_file_

private

Referenced by alignment_file().

◆ available_AAs_file_

std::string protocols::evolution::AlignmentAAFinder::available_AAs_file_

private

Referenced by available_AAs_file().

◆ exclude_AA_threshold_

core::Real protocols::evolution::AlignmentAAFinder::exclude_AA_threshold_

private

Referenced by exclude_AA_threshold().

◆ indel_motif_radius_

core::Size protocols::evolution::AlignmentAAFinder::indel_motif_radius_

private

Referenced by indel_motif_radius().

◆ loop_seqid_threshold_

core::Real protocols::evolution::AlignmentAAFinder::loop_seqid_threshold_

private

Referenced by loop_seqid_threshold().

◆ relax_mover_

protocols::moves::MoverOP protocols::evolution::AlignmentAAFinder::relax_mover_

private

Referenced by relax_mover().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::evolution::AlignmentAAFinder::scorefxn_

private

Referenced by scorefxn().

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

src/protocols/evolution/AlignmentAAFinderFilter.hh
src/protocols/evolution/AlignmentAAFinderFilter.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ AlignmentAAFinder()

◆ ~AlignmentAAFinder()

Member Function Documentation

◆ alignment_file() [1/2]

◆ alignment_file() [2/2]

◆ apply()

◆ available_AAs_file() [1/2]

◆ available_AAs_file() [2/2]

◆ class_name()

◆ clone()

◆ exclude_AA_threshold() [1/2]

◆ exclude_AA_threshold() [2/2]

◆ fresh_instance()

◆ indel_motif_radius() [1/2]

◆ indel_motif_radius() [2/2]

◆ loop_seqid_threshold() [1/2]

◆ loop_seqid_threshold() [2/2]

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ relax_mover() [1/2]

◆ relax_mover() [2/2]

◆ report()

◆ report_sm()

◆ scorefxn() [1/2]

◆ scorefxn() [2/2]

Member Data Documentation

◆ alignment_file_

◆ available_AAs_file_

◆ exclude_AA_threshold_

◆ indel_motif_radius_

◆ loop_seqid_threshold_

◆ relax_mover_

◆ scorefxn_