protocols::pose_sewing Namespace Reference

Namespaces
	data_storage
	filters
	movers
	simple_metrics

Typedefs
using	Block = utility::StrongSize< struct Block_ >

Functions
void	identify_ss_blocks (std::set< core::select::residue_selector::ResidueSubset > &outset, utility::vector1< bool > const &subset)
	Get residues in each block through a set of equal subsets. Number of subsets are the number of SS blocks. More...
void	identify_ss_blocks_vec (utility::vector1< core::select::residue_selector::ResidueSubset > &out_vec, utility::vector1< bool > const &subset)
	Will eventually replace standard function. More...
void	calculate_blocks (std::map< core::Size, core::Size > &outmap, core::pose::Pose const &pose)
	Assign E/H blocks in the given pose. More...
void	calculate_helices (std::map< core::Size, core::Size > &outmap, core::pose::Pose const &pose, core::Size min_length)
void	calculate_blocks_from_subset (std::map< core::Size, core::Size > &outmap, utility::vector1< bool > const &subset)
	Assign arbitrary blocks from a Residue subset. More...
bool	all_L_dssp (core::pose::Pose const &pose)
	Is the DSSP all loop? A pose unfortunately starts with all L as the DSSP when creating a pose from seq and inserting residues as is done for segments. More...
core::Real	calculate_motif_score_bt_residues (sewing::scoring::MotifScorer const &scorer, core::conformation::Residue const &res1, core::conformation::Residue const &res2, char res1_SS, char res2_SS)
	Calculate the motif score between two residues. More...
core::Real	calculate_distance_score_bt_residues (core::conformation::Residue const &N_res, core::conformation::Residue const &C_res, core::Real min_score, core::Real min_distance, core::Real dist_mult)
void	calculate_bw_pose_compat_motifs (std::map< std::string, core::Real > &outmap, core::pose::Pose const &pose, std::set< core::select::residue_selector::ResidueSubset > const &block_selections, bool drop_best=true, bool normalize_by_residues=false, core::Real max_pair_score=0, bool use_motifs=true)
	Core code to calculate BlockWise/Elementwise Pose Compatable Motif Metrics. Reports worst score found for each block (Number as a string for the metric) If max_pair_score is something not 0, will use it (essentially used for filtering outside of metrics). More...
void	calculate_bw_window_motifs (std::map< std::string, core::Real > &outmap, core::pose::Pose const &pose, std::set< core::select::residue_selector::ResidueSubset > const &block_selections, core::Size window_width=3, bool use_motifs=true)
	Core code to calculate window metrics. Returns worst score for each window, represented as a string for the metric. More...

Typedef Documentation

Block

using protocols::pose_sewing::Block = typedef utility::StrongSize< struct Block_ >

Function Documentation

all_L_dssp()

bool protocols::pose_sewing::all_L_dssp

(

core::pose::Pose const &

pose

)

Is the DSSP all loop? A pose unfortunately starts with all L as the DSSP when creating a pose from seq and inserting residues as is done for segments.

References core::pose::Pose::secstruct(), and core::pose::Pose::size().

Referenced by protocols::pose_sewing::movers::PickRandomSegmentMover::apply().

calculate_blocks()

void protocols::pose_sewing::calculate_blocks	(	std::map< core::Size, core::Size > &	outmap,
		core::pose::Pose const &	pose
	)

Assign E/H blocks in the given pose.

References identify_ss_blocks_vec(), core::conformation::Residue::is_virtual_residue(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::pose::Pose::size(), and core::pose::Pose::total_residue().

calculate_blocks_from_subset()

void protocols::pose_sewing::calculate_blocks_from_subset	(	std::map< core::Size, core::Size > &	outmap,
		utility::vector1< bool > const &	selection
	)

Assign arbitrary blocks from a Residue subset.

Referenced by protocols::pose_sewing::filters::CoreScorer::report_sm().

calculate_bw_pose_compat_motifs()

void protocols::pose_sewing::calculate_bw_pose_compat_motifs	(	std::map< std::string, core::Real > &	outmap,
		core::pose::Pose const &	pose,
		std::set< core::select::residue_selector::ResidueSubset > const &	block_selections,
		bool	drop_best,
		bool	normalize_by_residues,
		core::Real	max_pair_score,
		bool	use_motifs
	)

Core code to calculate BlockWise/Elementwise Pose Compatable Motif Metrics. Reports worst score found for each block (Number as a string for the metric) If max_pair_score is something not 0, will use it (essentially used for filtering outside of metrics).

References calculate_distance_score_bt_residues(), calculate_motif_score_bt_residues(), core::conformation::Residue::is_virtual_residue(), core::pose::Pose::residue(), protocols::hybridization::score, core::pose::Pose::secstruct(), core::pose::Pose::size(), core::id::to_string(), and protocols::TR().

Referenced by protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::calculate().

calculate_bw_window_motifs()

void protocols::pose_sewing::calculate_bw_window_motifs	(	std::map< std::string, core::Real > &	outmap,
		core::pose::Pose const &	pose,
		std::set< core::select::residue_selector::ResidueSubset > const &	block_selections,
		core::Size	window_width,
		bool	use_motifs
	)

Core code to calculate window metrics. Returns worst score for each window, represented as a string for the metric.

References calculate_distance_score_bt_residues(), calculate_motif_score_bt_residues(), core::conformation::Residue::is_virtual_residue(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::pose::Pose::size(), and core::id::to_string().

Referenced by protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::calculate().

calculate_distance_score_bt_residues()

core::Real protocols::pose_sewing::calculate_distance_score_bt_residues	(	core::conformation::Residue const &	N_res,
		core::conformation::Residue const &	C_res,
		core::Real	min_score,
		core::Real	min_distance,
		core::Real	dist_mult
	)

References core::conformation::Residue::atom().

Referenced by protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), calculate_bw_pose_compat_motifs(), and calculate_bw_window_motifs().

calculate_helices()

void protocols::pose_sewing::calculate_helices	(	std::map< core::Size, core::Size > &	outmap,
		core::pose::Pose const &	pose,
		core::Size	min_length
	)

References core::pose::Pose::secstruct(), and core::pose::Pose::size().

Referenced by protocols::pose_sewing::movers::BlockwiseAnalysisMover::apply(), and protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply().

calculate_motif_score_bt_residues()

core::Real protocols::pose_sewing::calculate_motif_score_bt_residues	(	sewing::scoring::MotifScorer const &	scorer,
		core::conformation::Residue const &	N_res,
		core::conformation::Residue const &	C_res,
		char	ss1,
		char	ss2
	)

Calculate the motif score between two residues.

References core::conformation::Residue::atoms(), core::pose::motif::get_backbone_reference_frame(), protocols::sewing::scoring::MotifScorer::get_score(), core::conformation::Residue::name1(), and protocols::kinmatch::xyz().

Referenced by protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), calculate_bw_pose_compat_motifs(), and calculate_bw_window_motifs().

identify_ss_blocks()

void protocols::pose_sewing::identify_ss_blocks	(	std::set< core::select::residue_selector::ResidueSubset > &	outset,
		core::select::residue_selector::ResidueSubset const &	selection
	)

Get residues in each block through a set of equal subsets. Number of subsets are the number of SS blocks.

Referenced by protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::calculate(), protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::calculate(), and protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::calculate().

identify_ss_blocks_vec()

void protocols::pose_sewing::identify_ss_blocks_vec	(	utility::vector1< core::select::residue_selector::ResidueSubset > &	out_vec,
		core::select::residue_selector::ResidueSubset const &	selection
	)

Will eventually replace standard function.

Referenced by calculate_blocks().