Rosetta  2020.37
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sequence_recovery.cc File Reference

A protocol which outputs sequence recovery statistics ala the table in the "Native sequences are close to optimal" paper. More...

#include <devel/init.hh>
#include <core/conformation/PointGraph.hh>
#include <core/conformation/find_neighbors.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/operation/TaskOperationFactory.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <basic/Tracer.hh>
#include <basic/prof.hh>
#include <basic/options/util.hh>
#include <basic/datacache/DataMap.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/io/ozstream.hh>
#include <utility/vector1.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <sstream>
#include <core/conformation/PointGraphData.hh>
#include <utility/graph/UpperEdgeGraph.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/filters/Filter.fwd.hh>
#include <utility/vector0.hh>

Namespaces

 sequence_recovery
 

Functions

void init_usage_prompt (std::string const &exe)
 
core::pack::task::TaskFactoryOP setup_tf (core::pack::task::TaskFactoryOP task_factory_)
 load custom TaskOperations according to an xml-like utility::tag file More...
 
void fill_num_neighbors (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...
 
std::set< Size > fill_designable_set (pose::Pose &pose, pack::task::TaskFactoryOP &tf)
 return the set of residues that are designable based given pose More...
 
void measure_sequence_recovery (utility::vector1< core::pose::Pose > &native_poses, utility::vector1< core::pose::Pose > &redesign_poses)
 iterates over all designed positions and determines identity to native. outputs recoveries to file. More...
 
void measure_rotamer_recovery (utility::vector1< core::pose::Pose > &, utility::vector1< core::pose::Pose > &)
 
int main (int argc, char *argv[])
 

Variables

static basic::Tracer TR ("sequence_recovery")
 
FileOptionKey const sequence_recovery::native_pdb_list ("sequence_recovery::native_pdb_list")
 
FileOptionKey const sequence_recovery::redesign_pdb_list ("sequence_recovery::redesign_pdb_list")
 
FileOptionKey const sequence_recovery::parse_taskops_file ("sequence_recovery::parse_taskops_file")
 
BooleanOptionKey const sequence_recovery::rotamer_recovery ("sequence_recovery::rotamer_recovery")
 
StringOptionKey const sequence_recovery::seq_recov_filename ("sequence_recovery::seq_recov_filename")
 
StringOptionKey const sequence_recovery::sub_matrix_filename ("sequence_recovery::sub_matrix_filename")
 
IntegerOptionKey const sequence_recovery::se_cutoff ("sequence_recovery::se_cutoff")
 
std::string usage_string
 

Detailed Description

A protocol which outputs sequence recovery statistics ala the table in the "Native sequences are close to optimal" paper.

Author
Ron Jacak
P. Douglas Renfrew (renfr.nosp@m.ew@n.nosp@m.yu.ed.nosp@m.u) ( added rotamer recovery, cleanup )

Function Documentation

std::set< Size > fill_designable_set ( pose::Pose pose,
pack::task::TaskFactoryOP &  tf 
)
void fill_num_neighbors ( 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 test.T200_Scoring::ii.

Referenced by measure_sequence_recovery().

void init_usage_prompt ( std::string const &  exe)

References usage_string.

Referenced by main().

int main ( int  argc,
char *  argv[] 
)
void measure_rotamer_recovery ( utility::vector1< core::pose::Pose > &  ,
utility::vector1< core::pose::Pose > &   
)

Referenced by main().

void measure_sequence_recovery ( utility::vector1< core::pose::Pose > &  native_poses,
utility::vector1< core::pose::Pose > &  redesign_poses 
)
core::pack::task::TaskFactoryOP setup_tf ( core::pack::task::TaskFactoryOP  task_factory_)

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

The sequence recovery app can only handle taskops that do not use ResidueSelectors, unless they are anonymous (i.e. unnamed) ResidueSelectors that are declared as subtags of TaskOperations.

References option, sequence_recovery::parse_taskops_file, top, test.G204_Module_ScoreAnalysis::tops, and basic::options::OptionKeys::inout::dbms::user.

Referenced by measure_sequence_recovery().

Variable Documentation

basic::Tracer TR("sequence_recovery")
static

Referenced by fill_designable_set(), and main().

std::string usage_string

Referenced by init_usage_prompt(), and main().