protocols::simple_filters::SequenceDistance Class Reference

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

#include <SequenceDistanceFilter.hh>

Inheritance diagram for protocols::simple_filters::SequenceDistance:

Public Member Functions
	SequenceDistance ()
	~SequenceDistance () 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	compute (core::pose::Pose const &pose) const
std::string const &	sequence_comment_id () const
void	sequence_comment_id (std::string const &s)
std::string const &	target_seq () const
void	target_seq (std::string const &s)
core::Size	threshold () const
void	threshold (core::Size const &t)
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	sequence_comment_id_
std::string	target_seq_
core::Size	threshold_

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

SequenceDistance()

protocols::simple_filters::SequenceDistance::SequenceDistance

(

)

~SequenceDistance()

protocols::simple_filters::SequenceDistance::~SequenceDistance ( )

overridedefault

Member Function Documentation

apply()

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

overridevirtual

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

Implements protocols::filters::Filter.

References compute(), threshold(), protocols::simple_filters::TR(), and protocols::hybridization::val.

class_name()

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

static

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

clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

core::Size protocols::simple_filters::SequenceDistance::compute

(

core::pose::Pose const &

pose

)

const

References core::kinematics::distance(), core::pose::get_all_comments(), core::pose::Pose::sequence(), sequence_comment_id(), target_seq(), and protocols::simple_filters::TR().

Referenced by apply(), report(), and report_sm().

fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

void protocols::simple_filters::SequenceDistance::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 sequence_comment_id(), target_seq(), and threshold().

provide_xml_schema()

void protocols::simple_filters::SequenceDistance::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

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

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

report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), threshold(), and protocols::hybridization::val.

report_sm()

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

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

sequence_comment_id() [1/2]

std::string const& protocols::simple_filters::SequenceDistance::sequence_comment_id ( ) const

inline

References sequence_comment_id_.

Referenced by compute(), and parse_my_tag().

sequence_comment_id() [2/2]

void protocols::simple_filters::SequenceDistance::sequence_comment_id ( std::string const &  s )

inline

References sequence_comment_id_.

target_seq() [1/2]

std::string const& protocols::simple_filters::SequenceDistance::target_seq ( ) const

inline

References target_seq_.

Referenced by compute(), and parse_my_tag().

target_seq() [2/2]

void protocols::simple_filters::SequenceDistance::target_seq ( std::string const &  s )

inline

References target_seq_.

threshold() [1/2]

core::Size protocols::simple_filters::SequenceDistance::threshold ( ) const

inline

References threshold_.

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

threshold() [2/2]

void protocols::simple_filters::SequenceDistance::threshold ( core::Size const &  t )

inline

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

Member Data Documentation

sequence_comment_id_

std::string protocols::simple_filters::SequenceDistance::sequence_comment_id_

private

Referenced by sequence_comment_id().

target_seq_

std::string protocols::simple_filters::SequenceDistance::target_seq_

private

Referenced by target_seq().

threshold_

core::Size protocols::simple_filters::SequenceDistance::threshold_

private

Referenced by threshold().

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

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