protocols::toolbox::pose_metric_calculators::SequenceComparison Class Reference

#include <SequenceComparison.hh>

Collaboration diagram for protocols::toolbox::pose_metric_calculators::SequenceComparison:

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...

Detailed Description

Definition at line 60 of file SequenceComparison.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 63 of file SequenceComparison.hh.

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

inline

Definition at line 72 of file SequenceComparison.hh.

Member Function Documentation

std::set< core::Size > protocols::toolbox::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

Definition at line 117 of file SequenceComparison.cc.

References protocols::toolbox::pose_metric_calculators::TR().

void protocols::toolbox::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

Definition at line 139 of file SequenceComparison.cc.

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

void protocols::toolbox::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

Definition at line 373 of file SequenceComparison.cc.

References protocols::toolbox::pose_metric_calculators::TR().

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

overflowed main function to compare only two proteins

Definition at line 362 of file SequenceComparison.cc.

void protocols::toolbox::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.

Definition at line 166 of file SequenceComparison.cc.

References core::conformation::Residue::aa(), core::chemical::aa_unk, core::sequence::end, core::conformation::Residue::is_protein(), core::chemical::name_from_aa(), core::chemical::num_canonical_aas, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

core::pack::task::TaskFactoryOP protocols::toolbox::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

Definition at line 106 of file SequenceComparison.cc.

Member Data Documentation

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

private

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

Definition at line 100 of file SequenceComparison.hh.

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

private

what is the surface cutoff that you are using? default 16

Definition at line 97 of file SequenceComparison.hh.

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

• src/protocols/toolbox/pose_metric_calculators/SequenceComparison.hh
• src/protocols/toolbox/pose_metric_calculators/SequenceComparison.cc