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Public Member Functions | Private Attributes | List of all members
protocols::pose_metric_calculators::SequenceComparison Class Reference

#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::Sizefill_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

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

Member Function Documentation

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().

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().

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().

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

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().

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::Size protocols::pose_metric_calculators::SequenceComparison::core_cutoff_
private

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

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

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


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