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

#include <AlignmentGapInserterFilter.hh>

Inheritance diagram for protocols::evolution::AlignmentGapInserter:

[legend]

Public Member Functions
	AlignmentGapInserter ()

	~AlignmentGapInserter () override

filters::FilterOP	clone () const override

filters::FilterOP	fresh_instance () const override

utility::vector0< core::Size >	find_char_location_in_string (std::string const &string, char const findIt) const

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...

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)

std::string	cleaned_alignment_file () const

void	cleaned_alignment_file (std::string const &a)

core::Real	nbr_e_threshold () const

void	nbr_e_threshold (core::Real const &t)

utility::vector1< core::Real >	loop_seqid_thresholds () const

void	loop_seqid_thresholds (utility::vector1< core::Real > const &v)

core::Size	indel_motif_radius () const

void	indel_motif_radius (core::Size const &r)

core::Size	only_clean_seq_num () const

void	only_clean_seq_num (core::Size const &t)

core::scoring::ScoreFunctionOP	scorefxn () const

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

utility::vector1< core::Real >	max_score_diffs () const

void	max_score_diffs (utility::vector1< core::Real > const &v)

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
std::string	alignment_file_

std::string	available_AAs_file_

std::string	cleaned_alignment_file_

core::Real	nbr_e_threshold_

utility::vector1< core::Real >	loop_seqid_thresholds_

core::Size	indel_motif_radius_

core::Real	only_clean_seq_num_

core::scoring::ScoreFunctionOP	scorefxn_

utility::vector1< core::Real >	max_score_diffs_

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

◆ AlignmentGapInserter()

protocols::evolution::AlignmentGapInserter::AlignmentGapInserter ( )

References loop_seqid_thresholds_, and max_score_diffs_.

◆ ~AlignmentGapInserter()

protocols::evolution::AlignmentGapInserter::~AlignmentGapInserter ( )

overridedefault

Member Function Documentation

◆ alignment_file() [1/2]

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

inline

References alignment_file_.

Referenced by apply(), and parse_my_tag().

◆ alignment_file() [2/2]

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

inline

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

◆ apply()

bool protocols::evolution::AlignmentGapInserter::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(), cleaned_alignment_file(), protocols::simple_filters::dssp(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), find_char_location_in_string(), protocols::evolution::AlignmentCleanerTools::indel_motif(), indel_motif_radius(), protocols::evolution::AlignmentCleanerTools::indel_motif_seq_id(), loop_seqid_thresholds(), max_score_diffs(), nbr_e_threshold(), only_clean_seq_num(), core::sequence::read_fasta_file(), core::scoring::Energies::residue_total_energy(), scorefxn(), core::pose::Pose::sequence(), protocols::evolution::AlignmentCleanerTools::short_ss_loop_filter(), protocols::evolution::AlignmentCleanerTools::thread_sequence_on_pose(), protocols::evolution::TR(), and core::scoring::Energies::weights().

◆ available_AAs_file() [1/2]

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

inline

References available_AAs_file_.

Referenced by apply(), and parse_my_tag().

◆ available_AAs_file() [2/2]

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

inline

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

◆ class_name()

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

static

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

◆ cleaned_alignment_file() [1/2]

std::string protocols::evolution::AlignmentGapInserter::cleaned_alignment_file ( ) const

inline

References cleaned_alignment_file_.

Referenced by apply(), and parse_my_tag().

◆ cleaned_alignment_file() [2/2]

void protocols::evolution::AlignmentGapInserter::cleaned_alignment_file ( std::string const & a )

inline

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

◆ clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ find_char_location_in_string()

utility::vector0< core::Size > protocols::evolution::AlignmentGapInserter::find_char_location_in_string	(	std::string const &	string,
		char const	findIt
	)		const

Referenced by apply().

◆ fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ indel_motif_radius() [1/2]

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

inline

References indel_motif_radius_.

Referenced by apply(), and parse_my_tag().

◆ indel_motif_radius() [2/2]

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

inline

References indel_motif_radius_.

◆ loop_seqid_thresholds() [1/2]

utility::vector1< core::Real > protocols::evolution::AlignmentGapInserter::loop_seqid_thresholds ( ) const

inline

References loop_seqid_thresholds_.

Referenced by apply(), and parse_my_tag().

◆ loop_seqid_thresholds() [2/2]

void protocols::evolution::AlignmentGapInserter::loop_seqid_thresholds ( utility::vector1< core::Real > const & v )

inline

References loop_seqid_thresholds_.

◆ max_score_diffs() [1/2]

utility::vector1< core::Real > protocols::evolution::AlignmentGapInserter::max_score_diffs ( ) const

inline

References max_score_diffs_.

Referenced by apply(), and parse_my_tag().

◆ max_score_diffs() [2/2]

void protocols::evolution::AlignmentGapInserter::max_score_diffs ( utility::vector1< core::Real > const & v )

inline

References max_score_diffs_.

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ nbr_e_threshold() [1/2]

core::Real protocols::evolution::AlignmentGapInserter::nbr_e_threshold ( ) const

inline

References nbr_e_threshold_.

Referenced by apply(), and parse_my_tag().

◆ nbr_e_threshold() [2/2]

void protocols::evolution::AlignmentGapInserter::nbr_e_threshold ( core::Real const & t )

inline

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

◆ only_clean_seq_num() [1/2]

core::Size protocols::evolution::AlignmentGapInserter::only_clean_seq_num ( ) const

inline

References only_clean_seq_num_.

Referenced by apply(), and parse_my_tag().

◆ only_clean_seq_num() [2/2]

void protocols::evolution::AlignmentGapInserter::only_clean_seq_num ( core::Size const & t )

inline

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

◆ parse_my_tag()

void protocols::evolution::AlignmentGapInserter::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(), cleaned_alignment_file(), indel_motif_radius(), loop_seqid_thresholds(), max_score_diffs(), nbr_e_threshold(), only_clean_seq_num(), core::scoring::parse_score_function(), scorefxn(), and protocols::evolution::TR().

◆ provide_xml_schema()

void protocols::evolution::AlignmentGapInserter::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::AlignmentGapInserterFilterCreator::provide_xml_schema().

◆ report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

◆ report_sm()

core::Real protocols::evolution::AlignmentGapInserter::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::AlignmentGapInserter::scorefxn ( ) const

inline

References scorefxn_.

Referenced by apply(), and parse_my_tag().

◆ scorefxn() [2/2]

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

inline

References scorefxn(), and scorefxn_.

Referenced by scorefxn().

Member Data Documentation

◆ alignment_file_

std::string protocols::evolution::AlignmentGapInserter::alignment_file_

private

Referenced by alignment_file().

◆ available_AAs_file_

std::string protocols::evolution::AlignmentGapInserter::available_AAs_file_

private

Referenced by available_AAs_file().

◆ cleaned_alignment_file_

std::string protocols::evolution::AlignmentGapInserter::cleaned_alignment_file_

private

Referenced by cleaned_alignment_file().

◆ indel_motif_radius_

core::Size protocols::evolution::AlignmentGapInserter::indel_motif_radius_

private

Referenced by indel_motif_radius().

◆ loop_seqid_thresholds_

utility::vector1< core::Real > protocols::evolution::AlignmentGapInserter::loop_seqid_thresholds_

private

Referenced by AlignmentGapInserter(), and loop_seqid_thresholds().

◆ max_score_diffs_

utility::vector1< core::Real > protocols::evolution::AlignmentGapInserter::max_score_diffs_

private

Referenced by AlignmentGapInserter(), and max_score_diffs().

◆ nbr_e_threshold_

core::Real protocols::evolution::AlignmentGapInserter::nbr_e_threshold_

private

Referenced by nbr_e_threshold().

◆ only_clean_seq_num_

core::Real protocols::evolution::AlignmentGapInserter::only_clean_seq_num_

private

Referenced by only_clean_seq_num().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::evolution::AlignmentGapInserter::scorefxn_

private

Referenced by scorefxn().

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

src/protocols/evolution/AlignmentGapInserterFilter.hh
src/protocols/evolution/AlignmentGapInserterFilter.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ AlignmentGapInserter()

◆ ~AlignmentGapInserter()

Member Function Documentation

◆ alignment_file() [1/2]

◆ alignment_file() [2/2]

◆ apply()

◆ available_AAs_file() [1/2]

◆ available_AAs_file() [2/2]

◆ class_name()

◆ cleaned_alignment_file() [1/2]

◆ cleaned_alignment_file() [2/2]

◆ clone()

◆ find_char_location_in_string()

◆ fresh_instance()

◆ indel_motif_radius() [1/2]

◆ indel_motif_radius() [2/2]

◆ loop_seqid_thresholds() [1/2]

◆ loop_seqid_thresholds() [2/2]

◆ max_score_diffs() [1/2]

◆ max_score_diffs() [2/2]

◆ name()

◆ nbr_e_threshold() [1/2]

◆ nbr_e_threshold() [2/2]

◆ only_clean_seq_num() [1/2]

◆ only_clean_seq_num() [2/2]

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ scorefxn() [1/2]

◆ scorefxn() [2/2]

Member Data Documentation

◆ alignment_file_

◆ available_AAs_file_

◆ cleaned_alignment_file_

◆ indel_motif_radius_

◆ loop_seqid_thresholds_

◆ max_score_diffs_

◆ nbr_e_threshold_

◆ only_clean_seq_num_

◆ scorefxn_