Newer version of filter used in Marcos & Basanta et al. 2017. More...

#include <StrandCurvatureByLevels.hh>

Inheritance diagram for protocols::fldsgn::filters::StrandCurvatureByLevels:

Public Types
typedef core::Real	Real

typedef protocols::filters::Filter	Super

typedef protocols::filters::Filter	Filter

typedef std::string	String

typedef protocols::filters::FilterOP	FilterOP

typedef core::pose::Pose	Pose

typedef protocols::fldsgn::topology::StrandPairingSet	StrandPairingSet

typedef protocols::fldsgn::topology::StrandPairingSetOP	StrandPairingSetOP

typedef protocols::fldsgn::topology::SS_Info2	SS_Info2

typedef protocols::fldsgn::topology::SS_Info2_OP	SS_Info2_OP

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

Public Member Functions
	StrandCurvatureByLevels ()

	~StrandCurvatureByLevels () override

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

core::Real	report_sm (core::pose::Pose const &pose) const override
	required for reporting score values More...

void	report (std::ostream &os, core::pose::Pose const &pose) const override
	allows printing data to a stream More...

std::string	name () const override

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Filter in Rosetta Scripts) More...

protocols::filters::FilterOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::filters::FilterOP	clone () const override
	required in the context of the parser/scripting scheme More...

void	secstruct (String const &ss)
	miniimum angle for filtering More...

void	bend_level (core::Size const r)

void	filter_min_bend (Real const r)
	miniimum angle for filtering More...

void	filter_max_bend (Real const r)
	maximum angle for filtering More...

void	twist_level (core::Size const r)

void	filter_min_twist (Real const r)
	miniimum twist for filtering More...

void	filter_max_twist (Real const r)
	maximum twist for filtering More...

void	strand_id (core::Size const r)
	miniimum angle for filtering More...

void	output_type (String const &s)
	set output type More...

void	concavity_reference_residue (String const &ss)

void	concavity_direction (bool const &r)

virtual core::Real	compute (Pose const &pose) const

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 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
String	secstruct_
	if value is empty, dssp will run for ss definition ( default is emptry ) More...

core::Size	bend_level_

Real	filter_min_bend_
	filtered min angle between helix and sheet More...

Real	filter_max_bend_
	filtered max angle between helix and sheet More...

core::Size	twist_level_

Real	filter_min_twist_
	filtered min twist between helix and sheet More...

Real	filter_max_twist_
	filtered max twist between helix and sheet More...

core::Size	strand_id_
	strand id More...

String	output_type_
	output_type More...

Real	output_value_
	output value, the result of filterring calculation More...

String	concavity_reference_residue_

bool	concavity_direction_

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

Detailed Description

Newer version of filter used in Marcos & Basanta et al. 2017.

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::fldsgn::filters::StrandCurvatureByLevels::DataMap

typedef protocols::filters::Filter protocols::fldsgn::filters::StrandCurvatureByLevels::Filter

typedef protocols::filters::FilterOP protocols::fldsgn::filters::StrandCurvatureByLevels::FilterOP

typedef core::pose::Pose protocols::fldsgn::filters::StrandCurvatureByLevels::Pose

typedef core::Real protocols::fldsgn::filters::StrandCurvatureByLevels::Real

typedef protocols::fldsgn::topology::SS_Info2 protocols::fldsgn::filters::StrandCurvatureByLevels::SS_Info2

typedef protocols::fldsgn::topology::SS_Info2_OP protocols::fldsgn::filters::StrandCurvatureByLevels::SS_Info2_OP

typedef protocols::fldsgn::topology::StrandPairingSet protocols::fldsgn::filters::StrandCurvatureByLevels::StrandPairingSet

typedef protocols::fldsgn::topology::StrandPairingSetOP protocols::fldsgn::filters::StrandCurvatureByLevels::StrandPairingSetOP

typedef std::string protocols::fldsgn::filters::StrandCurvatureByLevels::String

typedef protocols::filters::Filter protocols::fldsgn::filters::StrandCurvatureByLevels::Super

typedef utility::tag::TagCOP protocols::fldsgn::filters::StrandCurvatureByLevels::TagCOP

Constructor & Destructor Documentation

protocols::fldsgn::filters::StrandCurvatureByLevels::StrandCurvatureByLevels ( )

protocols::fldsgn::filters::StrandCurvatureByLevels::~StrandCurvatureByLevels ( )

overridedefault

Member Function Documentation

bool protocols::fldsgn::filters::StrandCurvatureByLevels::apply ( core::pose::Pose const & pose ) const

overridevirtual

returns true if the structure passes the filter, false otherwise

Implements protocols::filters::Filter.

References core::conformation::Residue::aa(), core::chemical::aa_gly, bend_level_, core::conformation::membrane::center, concavity_direction_, concavity_reference_residue_, protocols::simple_filters::dssp(), core::sequence::end, filter_max_bend_, filter_max_twist_, protocols::fldsgn::topology::NO_STRANDS, output_type_, output_value_, core::pose::Pose::residue(), secstruct_, strand_id_, protocols::fldsgn::TR(), twist_level_, and core::conformation::Residue::xyz().

Referenced by compute().

void protocols::fldsgn::filters::StrandCurvatureByLevels::bend_level ( core::Size const r )

References bend_level_.

std::string protocols::fldsgn::filters::StrandCurvatureByLevels::class_name ( )

static

Referenced by protocols::fldsgn::filters::StrandCurvatureByLevelsCreator::keyname(), name(), and provide_xml_schema().

protocols::filters::FilterOP protocols::fldsgn::filters::StrandCurvatureByLevels::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

StrandCurvatureByLevels::Real protocols::fldsgn::filters::StrandCurvatureByLevels::compute ( Pose const & pose ) const

virtual

References apply(), and output_value_.

Referenced by report_sm().

void protocols::fldsgn::filters::StrandCurvatureByLevels::concavity_direction ( bool const & r )

References concavity_direction_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::concavity_reference_residue ( String const & ss )

References concavity_reference_residue_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::filter_max_bend ( core::Real const r )

maximum angle for filtering

References filter_max_bend_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::filter_max_twist ( core::Real const r )

maximum twist for filtering

References filter_max_twist_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::filter_min_bend ( core::Real const r )

miniimum angle for filtering

minimum angle for filtering

References filter_min_bend_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::filter_min_twist ( core::Real const r )

miniimum twist for filtering

References filter_min_twist_.

protocols::filters::FilterOP protocols::fldsgn::filters::StrandCurvatureByLevels::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

std::string protocols::fldsgn::filters::StrandCurvatureByLevels::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::fldsgn::filters::StrandCurvatureByLevels::output_type ( String const & s )

set output type

References output_type_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Filter in Rosetta Scripts)

Reimplemented from protocols::filters::Filter.

References bend_level_, concavity_direction_, concavity_reference_residue_, filter_max_bend_, filter_max_twist_, filter_min_bend_, filter_min_twist_, output_type_, protocols::parser::BluePrint::secstruct(), secstruct_, strand_id_, and twist_level_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::fldsgn::filters::StrandCurvatureByLevelsCreator::provide_xml_schema().

void protocols::fldsgn::filters::StrandCurvatureByLevels::report	(	std::ostream &	os,
		core::pose::Pose const &	pose
	)		const

overridevirtual

allows printing data to a stream

Reimplemented from protocols::filters::Filter.

core::Real protocols::fldsgn::filters::StrandCurvatureByLevels::report_sm ( core::pose::Pose const & pose ) const

overridevirtual

required for reporting score values

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::fldsgn::filters::StrandCurvatureByLevels::secstruct ( String const & ss )

miniimum angle for filtering

References secstruct_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::strand_id ( core::Size const r )

miniimum angle for filtering

Strand id number.

References strand_id_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::twist_level ( core::Size const r )

References twist_level_.

Member Data Documentation

core::Size protocols::fldsgn::filters::StrandCurvatureByLevels::bend_level_

private

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

bool protocols::fldsgn::filters::StrandCurvatureByLevels::concavity_direction_

private

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

String protocols::fldsgn::filters::StrandCurvatureByLevels::concavity_reference_residue_

private

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

Real protocols::fldsgn::filters::StrandCurvatureByLevels::filter_max_bend_

private

filtered max angle between helix and sheet

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

Real protocols::fldsgn::filters::StrandCurvatureByLevels::filter_max_twist_

private

filtered max twist between helix and sheet

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

Real protocols::fldsgn::filters::StrandCurvatureByLevels::filter_min_bend_

private

filtered min angle between helix and sheet

Referenced by filter_min_bend(), and parse_my_tag().

Real protocols::fldsgn::filters::StrandCurvatureByLevels::filter_min_twist_

private

filtered min twist between helix and sheet

Referenced by filter_min_twist(), and parse_my_tag().

String protocols::fldsgn::filters::StrandCurvatureByLevels::output_type_

private

output_type

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

Real protocols::fldsgn::filters::StrandCurvatureByLevels::output_value_

mutableprivate

output value, the result of filterring calculation

Referenced by apply(), and compute().

String protocols::fldsgn::filters::StrandCurvatureByLevels::secstruct_

mutableprivate

if value is empty, dssp will run for ss definition ( default is emptry )

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

core::Size protocols::fldsgn::filters::StrandCurvatureByLevels::strand_id_

private

strand id

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

core::Size protocols::fldsgn::filters::StrandCurvatureByLevels::twist_level_

private

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

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

src/protocols/fldsgn/filters/StrandCurvatureByLevels.hh
src/protocols/fldsgn/filters/StrandCurvatureByLevels.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation