ClosabilityScore Class Reference

#include <closability_score.hh>

Public Member Functions
	ClosabilityScore ()
core::Real	closability_score (core::pose::Pose const &pose1, core::Size const pos1, core::pose::Pose const &pose2, core::Size const pos2, core::Size &counts, int &gap_size, core::Size radius=2)
core::Real	closability_score (core::pose::Pose const &pose1, core::Size const pos1, core::pose::Pose const &pose2, core::Size const pos2, int &gap_size, bool stringent=false)
void	set_db_to_use_threshold (core::Size threshold)
bool	get_rt_over_leap (const core::pose::Pose &orig_pose, core::Size const ir, core::Size const jr, numeric::geometry::hashing::Real6 &rt_6)
void	miniPose_creator (core::pose::Pose &miniPose, core::pose::Pose pose1, core::pose::Pose pose2, core::Size pos2_start=1)
core::Real	gap_bound_cst_score (core::pose::Pose const &pose, core::Size const gap_size, core::Real stdev=1, core::Real cst_weight=1)
core::Real	gap_upper_boundary (core::Size seq_gap)
core::Size	loophash_query (core::pose::Pose const &miniPose, core::Size const db_to_use, core::Size const radius)

Private Attributes
boost::unordered_map< core::Size, protocols::loophash::LoopHashLibraryOP >	LH_Lib_Map_
core::Size	db_to_use_threshold_

Constructor & Destructor Documentation

ClosabilityScore()

ClosabilityScore::ClosabilityScore ( )

inline

References db_to_use_threshold_.

Member Function Documentation

closability_score() [1/2]

core::Real ClosabilityScore::closability_score	(	core::pose::Pose const &	pose1,
		core::Size const	pos1,
		core::pose::Pose const &	pose2,
		core::Size const	pos2,
		core::Size &	counts,
		int &	gap_size,
		core::Size	radius = 2
	)

References cal_distance(), bin_torsions::counts, db_to_use_threshold_, gap_bound_cst_score(), loophash_query(), max(), min(), miniPose_creator(), test.T008_Serialization::pose1, test.T008_Serialization::pose2, basic::options::OptionKeys::cluster::radius, and tr.

Referenced by main().

closability_score() [2/2]

core::Real ClosabilityScore::closability_score	(	core::pose::Pose const &	pose1,
		core::Size const	pos1,
		core::pose::Pose const &	pose2,
		core::Size const	pos2,
		int &	gap_size,
		bool	stringent = false
	)

References val2thr::atom, gap_upper_boundary(), oop_conformations::length, max(), min(), test.T008_Serialization::pose1, and test.T008_Serialization::pose2.

gap_bound_cst_score()

core::Real ClosabilityScore::gap_bound_cst_score	(	core::pose::Pose const &	pose,
		core::Size const	gap_size,
		core::Real	stdev = 1,
		core::Real	cst_weight = 1
	)

References basic::options::OptionKeys::constraints::cst_weight, gap_upper_boundary(), beta_nonlocal::pose, oop_conformations::scorefxn, myspace::stdev(), and tr.

Referenced by closability_score().

gap_upper_boundary()

core::Real ClosabilityScore::gap_upper_boundary

(

core::Size

seq_gap

)

References enumerate_junctions::default.

Referenced by closability_score(), and gap_bound_cst_score().

get_rt_over_leap()

bool ClosabilityScore::get_rt_over_leap	(	const core::pose::Pose &	orig_pose,
		core::Size const	ir,
		core::Size const	jr,
		numeric::geometry::hashing::Real6 &	rt_6
	)

References loops::cutpoint, basic::Tracer::Error, numeric::HomogeneousTransform< T >::euler_angles_rad(), create_a3b_hbs::f, create_a3b_hbs::i, make_symmdef_file_denovo::jump_num, create_a3b_hbs::nres, numeric::constants::d::pi, beta_nonlocal::pose, tr, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

Referenced by loophash_query().

loophash_query()

core::Size ClosabilityScore::loophash_query	(	core::pose::Pose const &	miniPose,
		core::Size const	db_to_use,
		core::Size const	radius
	)

References basic::options::OptionKeys::lh::db_path, get_rt_over_leap(), LH_Lib_Map_, basic::options::option, basic::options::OptionKeys::cluster::radius, tr, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by closability_score().

miniPose_creator()

void ClosabilityScore::miniPose_creator	(	core::pose::Pose &	miniPose,
		core::pose::Pose	pose1,
		core::pose::Pose	pose2,
		core::Size	pos2_start = 1
	)

References test.T008_Serialization::pose1, test.T008_Serialization::pose2, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, and tr.

Referenced by closability_score().

set_db_to_use_threshold()

void ClosabilityScore::set_db_to_use_threshold

(

core::Size

threshold

)

References db_to_use_threshold_, and revert_app::threshold.

Member Data Documentation

db_to_use_threshold_

core::Size ClosabilityScore::db_to_use_threshold_

private

Referenced by closability_score(), ClosabilityScore(), and set_db_to_use_threshold().

LH_Lib_Map_

boost::unordered_map<core::Size, protocols::loophash::LoopHashLibraryOP> ClosabilityScore::LH_Lib_Map_

private

Referenced by loophash_query().

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

• src/apps/pilot/rayyrw/closability_score.hh