#include <RepeatParameterFilter.hh>

Inheritance diagram for protocols::simple_filters::RepeatParameterFilter:

Public Member Functions
	RepeatParameterFilter ()

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

core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...

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

void	calculate_helical_parameters (core::pose::Pose const &pose, std::string &handedness, Real &rise_out, Real &radius_out, Real &omega_out) const

void	apply_transformation (core::pose::Pose &mod_pose, std::list< core::Size > const &residue_list, numeric::xyzMatrix< core::Real > const &R, numeric::xyzVector< core::Real > const &preT, numeric::xyzVector< core::Real > const &postT) const

void	matrix3f_to_xyzMatrix (Eigen::Matrix3f const &Re, numeric::xyzMatrix< core::Real > &R) const

void	identity_matrix (numeric::xyzMatrix< core::Real > &R) const

void	calculate_helical_parameters_helper (core::pose::Pose const &pose, std::string &handedness, Real &rise_out, Real &radius_out, Real &omega_out) const

filters::FilterOP	clone () const

filters::FilterOP	fresh_instance () const

virtual	~RepeatParameterFilter ()

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string const &)

	Filter (Filter const &)

virtual	~Filter ()

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 std::string	name () const

Private Attributes
Size	numb_repeats_

Size	startAtRepeat_

std::string	param_type_

Real	min_

Real	max_

bool	r_handed_

bool	filter_

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

Constructor & Destructor Documentation

protocols::simple_filters::RepeatParameterFilter::RepeatParameterFilter ( )

protocols::simple_filters::RepeatParameterFilter::~RepeatParameterFilter ( )

virtual

Member Function Documentation

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

virtual

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

Implements protocols::filters::Filter.

References calculate_helical_parameters(), filter_, max_, min_, core::scoring::omega, and param_type_.

void protocols::simple_filters::RepeatParameterFilter::apply_transformation	(	core::pose::Pose &	mod_pose,
		std::list< core::Size > const &	residue_list,
		numeric::xyzMatrix< core::Real > const &	R,
		numeric::xyzVector< core::Real > const &	preT,
		numeric::xyzVector< core::Real > const &	postT
	)		const

References core::pose::Pose::batch_set_xyz(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::pose::Pose::xyz().

void protocols::simple_filters::RepeatParameterFilter::calculate_helical_parameters	(	core::pose::Pose const &	pose,
		std::string &	handedness,
		Real &	rise_out,
		Real &	radius_out,
		Real &	omega_out
	)		const

References calculate_helical_parameters_helper(), and core::pose::Pose::clone().

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

void protocols::simple_filters::RepeatParameterFilter::calculate_helical_parameters_helper	(	core::pose::Pose const &	pose,
		std::string &	handedness,
		Real &	rise_out,
		Real &	radius_out,
		Real &	omega_out
	)		const

References protocols::comparative_modeling::features::A, core::chemical::element::B, core::chemical::element::H, core::chemical::element::I, protocols::features::L, core::chemical::element::N, numb_repeats_, core::scoring::omega, core::pose::Pose::residue(), startAtRepeat_, protocols::hybridization::t, core::pose::Pose::total_residue(), protocols::simple_filters::TR(), and core::conformation::Residue::xyz().

Referenced by calculate_helical_parameters().

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

inlinevirtual

Implements protocols::filters::Filter.

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

inlinevirtual

Implements protocols::filters::Filter.

void protocols::simple_filters::RepeatParameterFilter::identity_matrix ( numeric::xyzMatrix< core::Real > & R ) const

void protocols::simple_filters::RepeatParameterFilter::matrix3f_to_xyzMatrix	(	Eigen::Matrix3f const &	Re,
		numeric::xyzMatrix< core::Real > &	R
	)		const

References core::chemical::element::Re.

void protocols::simple_filters::RepeatParameterFilter::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &
	)