protocols::simple_filters::HelixHelixAngleFilter Class Reference

#include <HelixHelixAngleFilter.hh>

Inheritance diagram for protocols::simple_filters::HelixHelixAngleFilter:

Public Member Functions
	HelixHelixAngleFilter ()
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...
core::Real	compute (core::pose::Pose const &pose) const
core::Real	calc_shortest_dist_by_atoms (core::pose::Pose const &pose, core::Size start_helix_1, core::Size end_helix_1, core::Size start_helix_2, core::Size end_helix_2) const
std::pair< numeric::xyzVector< core::Real >, numeric::xyzVector< core::Real > >	find_closest_pnts (utility::vector1< numeric::xyzVector< core::Real >> l1, utility::vector1< numeric::xyzVector< core::Real >> l2) const
utility::vector1< numeric::xyzVector< core::Real > >	find_helix_vector (core::pose::Pose const &pose, core::Size start, core::Size end) const
filters::FilterOP	clone () const override
filters::FilterOP	fresh_instance () const override
	~HelixHelixAngleFilter () override
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...
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)

Protected Member Functions
void	get_helix_start_stop (core::pose::Pose const &pose, core::Size &start_helix_1, core::Size &end_helix_1, core::Size &start_helix_2, core::Size &end_helix_2) const
	Calculate the extent of helicies for this pose Returns values by reference. More...

Private Member Functions
std::pair< core::Size, core::Size >	find_closest_res (core::pose::Pose const &pose, core::Size s1, core::Size e1, core::Size s2, core::Size e2) const

Private Attributes
core::Size	start_helix_1_ = 0
core::Size	start_helix_2_ = 0
core::Size	end_helix_1_ = 0
core::Size	end_helix_2_ = 0
core::Real	angle_min_ = 40.0
core::Real	angle_max_ = 100.0
core::Size	helix_num_1_ = 1
core::Size	helix_num_2_ = 2
core::Real	dist_min_ = 0.0
core::Real	dist_max_ = 5.0
std::string	angle_or_dist_ = "angle"
bool	by_helices_ = false
bool	dist_by_atom_ = true

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

Constructor & Destructor Documentation

HelixHelixAngleFilter()

protocols::simple_filters::HelixHelixAngleFilter::HelixHelixAngleFilter ( )

inline

~HelixHelixAngleFilter()

protocols::simple_filters::HelixHelixAngleFilter::~HelixHelixAngleFilter ( )

override

Member Function Documentation

apply()

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

overridevirtual

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

Implements protocols::filters::Filter.

References angle_max_, angle_min_, angle_or_dist_, compute(), dist_max_, and dist_min_.

calc_shortest_dist_by_atoms()

core::Real protocols::simple_filters::HelixHelixAngleFilter::calc_shortest_dist_by_atoms	(	core::pose::Pose const &	pose,
		core::Size	start_helix_1,
		core::Size	end_helix_1,
		core::Size	start_helix_2,
		core::Size	end_helix_2
	)		const

References core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), core::pose::Pose::residue(), protocols::simple_filters::TR(), and core::conformation::Residue::xyz().

Referenced by compute().

class_name()

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

static

Referenced by name(), and provide_xml_schema().

clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

core::Real protocols::simple_filters::HelixHelixAngleFilter::compute

(

core::pose::Pose const &

pose

)

const

References angle_or_dist_, calc_shortest_dist_by_atoms(), dist_by_atom_, core::kinematics::distance(), find_closest_pnts(), find_helix_vector(), get_helix_start_stop(), protocols::antibody::l1, protocols::antibody::l2, and protocols::simple_filters::TR().

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

find_closest_pnts()

std::pair< numeric::xyzVector< core::Real >, numeric::xyzVector< core::Real > > protocols::simple_filters::HelixHelixAngleFilter::find_closest_pnts	(	utility::vector1< numeric::xyzVector< core::Real >>	l1,
		utility::vector1< numeric::xyzVector< core::Real >>	l2
	)		const

References core::pose::motif::a(), protocols::match::upstream::b, core::id::D, protocols::antibody::l1, protocols::antibody::l2, protocols::simple_filters::TR(), and protocols::hybridization::u.

Referenced by compute().

find_closest_res()

std::pair< core::Size, core::Size > protocols::simple_filters::HelixHelixAngleFilter::find_closest_res ( core::pose::Pose const &  pose, core::Size  s1, core::Size  e1, core::Size  s2, core::Size  e2  ) const

private

References core::conformation::Residue::atom(), core::kinematics::distance(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), protocols::simple_filters::TR(), and core::conformation::Atom::xyz().

find_helix_vector()

utility::vector1< numeric::xyzVector< core::Real > > protocols::simple_filters::HelixHelixAngleFilter::find_helix_vector	(	core::pose::Pose const &	pose,
		core::Size	start,
		core::Size	end
	)		const

References core::conformation::Residue::atom_is_backbone(), core::pose::center_of_mass(), core::scoring::constraints::closest_point_on_line(), protocols::membrane::com(), core::sequence::end, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), protocols::loops::start, and core::conformation::Residue::xyz().

Referenced by compute().

fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

get_helix_start_stop()

void protocols::simple_filters::HelixHelixAngleFilter::get_helix_start_stop ( core::pose::Pose const &  pose, core::Size &  start_helix_1, core::Size &  end_helix_1, core::Size &  start_helix_2, core::Size &  end_helix_2  ) const

protected

Calculate the extent of helicies for this pose Returns values by reference.

References by_helices_, core::pose::Pose::chain(), protocols::simple_filters::dssp(), core::sequence::end, end_helix_1_, end_helix_2_, helix_num_1_, helix_num_2_, protocols::loops::start, start_helix_1_, start_helix_2_, and protocols::simple_filters::TR().

Referenced by compute().

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

void protocols::simple_filters::HelixHelixAngleFilter::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 angle_max_, angle_min_, angle_or_dist_, by_helices_, dist_by_atom_, dist_max_, dist_min_, end_helix_1_, end_helix_2_, helix_num_1_, helix_num_2_, start_helix_1_, and start_helix_2_.

provide_xml_schema()

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

static

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

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

report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References angle_or_dist_, compute(), and core::conformation::membrane::out.

report_sm()

core::Real protocols::simple_filters::HelixHelixAngleFilter::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().

Member Data Documentation

angle_max_

core::Real protocols::simple_filters::HelixHelixAngleFilter::angle_max_ = 100.0

private

Referenced by apply(), and parse_my_tag().

angle_min_

core::Real protocols::simple_filters::HelixHelixAngleFilter::angle_min_ = 40.0

private

Referenced by apply(), and parse_my_tag().

angle_or_dist_

std::string protocols::simple_filters::HelixHelixAngleFilter::angle_or_dist_ = "angle"

private

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

by_helices_

bool protocols::simple_filters::HelixHelixAngleFilter::by_helices_ = false

private

Referenced by get_helix_start_stop(), and parse_my_tag().

dist_by_atom_

bool protocols::simple_filters::HelixHelixAngleFilter::dist_by_atom_ = true

private

Referenced by compute(), and parse_my_tag().

dist_max_

core::Real protocols::simple_filters::HelixHelixAngleFilter::dist_max_ = 5.0

private

Referenced by apply(), and parse_my_tag().

dist_min_

core::Real protocols::simple_filters::HelixHelixAngleFilter::dist_min_ = 0.0

private

Referenced by apply(), and parse_my_tag().

end_helix_1_

core::Size protocols::simple_filters::HelixHelixAngleFilter::end_helix_1_ = 0

private

Referenced by get_helix_start_stop(), and parse_my_tag().

end_helix_2_

core::Size protocols::simple_filters::HelixHelixAngleFilter::end_helix_2_ = 0

private

Referenced by get_helix_start_stop(), and parse_my_tag().

helix_num_1_

core::Size protocols::simple_filters::HelixHelixAngleFilter::helix_num_1_ = 1

private

Referenced by get_helix_start_stop(), and parse_my_tag().

helix_num_2_

core::Size protocols::simple_filters::HelixHelixAngleFilter::helix_num_2_ = 2

private

Referenced by get_helix_start_stop(), and parse_my_tag().

start_helix_1_

core::Size protocols::simple_filters::HelixHelixAngleFilter::start_helix_1_ = 0

private

Referenced by get_helix_start_stop(), and parse_my_tag().

start_helix_2_

core::Size protocols::simple_filters::HelixHelixAngleFilter::start_helix_2_ = 0

private

Referenced by get_helix_start_stop(), and parse_my_tag().

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

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