Rosetta 3.3
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src/apps/public/design/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 <protocols/init.hh>
#include <core/conformation/PointGraph.hh>
#include <core/conformation/find_neighbors.hh>
#include <core/io/pdb/pose_io.hh>
#include <basic/options/util.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/pose/metrics/CalculatorFactory.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <protocols/moves/PackRotamersMover.hh>
#include <basic/Tracer.hh>
#include <basic/MetricValue.hh>
#include <basic/prof.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/io/ozstream.hh>
#include <utility/vector1.hh>
#include <basic/options/keys/optE.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <sstream>
#include <core/import_pose/import_pose.hh>

Namespaces

namespace  sequence_recovery

Functions

void init_usage_prompt (std::string exe)
core::pack::task::TaskFactoryOP setup_tf (core::pack::task::TaskFactoryOP task_factory_)
 load custom TaskOperations according to an xml-like utility::tag file
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
std::set< Size > fill_designable_set (pose::Pose &pose, pack::task::TaskFactoryOP &tf)
 return the set of residues that are designable based given pose
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.
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 (renfrew@unc.edu) ( 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  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

References option, sequence_recovery::parse_taskops_file, and basic::options::OptionKeys::mysql::user.

Referenced by measure_sequence_recovery().


Variable Documentation

basic::Tracer TR("sequence_recovery") [static]
std::string usage_string

Referenced by init_usage_prompt(), and main().

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