#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 (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)

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

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

inline

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

override

Member Function Documentation

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_.

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

Referenced by compute().

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

static

Referenced by name(), and provide_xml_schema().

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

inlineoverridevirtual

Implements protocols::filters::Filter.

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().

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::pack::dunbrack::c, core::id::D, protocols::antibody::l1, protocols::antibody::l2, protocols::simple_filters::TR(), and protocols::hybridization::u.

Referenced by compute().

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 protocols::kinmatch::xyz().

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::pose::center_of_mass(), core::scoring::constraints::closest_point_on_line(), protocols::membrane::com(), core::sequence::end, and core::pose::Pose::residue().

Referenced by compute().

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

inlineoverridevirtual

Implements protocols::filters::Filter.

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