#include <SequenceComparison.hh>

Public Member Functions
	SequenceComparison (core::Size surface, core::Size core)

	SequenceComparison ()

void	get_sequence_recovery (utility::vector1< core::pose::Pose > &native_poses, utility::vector1< core::pose::Pose > &redesign_poses)
	main function that is called. calls measure_sequence_recovery More...

void	get_sequence_recovery (core::pose::Pose &native, core::pose::Pose &designed)
	overflowed main function to compare only two proteins More...

void	measure_sequence_recovery (utility::vector1< core::pose::Pose > &native_poses, utility::vector1< core::pose::Pose > &redesign_poses)
	measures the sequence recovery of a list of native proteins and a list of designed proteins. Outputs files to sequencerecovery.txt More...

void	fill_num_neighbors (core::pose::Pose &pose, utility::vector1< core::Size > &num_nbs)
	helper method which uses the tenA nb graph in the pose object to fill a vector with nb counts More...

core::pack::task::TaskFactoryOP	setup_tf (core::pack::task::TaskFactoryOP task_factory_)
	sets up the task factory used for determing what the neighbor counts...what is on the surface and what is in the core More...

std::set< core::Size >	fill_designable_set (core::pose::Pose &pose, core::pack::task::TaskFactoryOP &tf)
	return the set of residues that are designable based given pose More...

Private Attributes
core::Size	surface_exposure_
	what is the surface cutoff that you are using? default 16 More...

core::Size	core_cutoff_
	what is the core cutoff that you are using? default 24 More...

Constructor & Destructor Documentation

◆ SequenceComparison() [1/2]

protocols::pose_metric_calculators::SequenceComparison::SequenceComparison	(	core::Size	surface,
		core::Size	core
	)

inline

◆ SequenceComparison() [2/2]

protocols::pose_metric_calculators::SequenceComparison::SequenceComparison ( )

inline

Member Function Documentation

◆ fill_designable_set()

std::set< core::Size > protocols::pose_metric_calculators::SequenceComparison::fill_designable_set	(	core::pose::Pose &	pose,
		core::pack::task::TaskFactoryOP &	tf
	)

return the set of residues that are designable based given pose

References protocols::pose_metric_calculators::TR().

◆ fill_num_neighbors()

void protocols::pose_metric_calculators::SequenceComparison::fill_num_neighbors	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > &	num_nbs
	)

helper method which uses the tenA nb graph in the pose object to fill a vector with nb counts

References core::pose::Pose::conformation(), core::conformation::residue_point_graph_from_conformation(), and core::pose::Pose::size().

◆ get_sequence_recovery() [1/2]

void protocols::pose_metric_calculators::SequenceComparison::get_sequence_recovery	(	core::pose::Pose &	native,
		core::pose::Pose &	designed
	)

overflowed main function to compare only two proteins

◆ get_sequence_recovery() [2/2]

void protocols::pose_metric_calculators::SequenceComparison::get_sequence_recovery	(	utility::vector1< core::pose::Pose > &	native_poses,
		utility::vector1< core::pose::Pose > &	redesign_poses
	)

main function that is called. calls measure_sequence_recovery

References protocols::pose_metric_calculators::TR().

◆ measure_sequence_recovery()

void protocols::pose_metric_calculators::SequenceComparison::measure_sequence_recovery	(	utility::vector1< core::pose::Pose > &	native_poses,
		utility::vector1< core::pose::Pose > &	redesign_poses
	)

measures the sequence recovery of a list of native proteins and a list of designed proteins. Outputs files to sequencerecovery.txt

iterates over all designed positions and determines identity to native. outputs recoveries to file.

References core::conformation::Residue::aa(), core::chemical::aa_unk, core::chemical::element::F, core::conformation::Residue::is_protein(), core::chemical::name_from_aa(), core::chemical::num_canonical_aas, core::pose::Pose::residue(), and core::pose::Pose::size().

◆ setup_tf()

core::pack::task::TaskFactoryOP protocols::pose_metric_calculators::SequenceComparison::setup_tf ( core::pack::task::TaskFactoryOP task_factory_ )

sets up the task factory used for determing what the neighbor counts...what is on the surface and what is in the core

load custom TaskOperations according to an xml-like utility::tag file

Member Data Documentation

◆ core_cutoff_

core::Size protocols::pose_metric_calculators::SequenceComparison::core_cutoff_

private

what is the core cutoff that you are using? default 24

◆ surface_exposure_

core::Size protocols::pose_metric_calculators::SequenceComparison::surface_exposure_