sequencerecovery.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 <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/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/minimization_packing/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 <core/pose/metrics/simple_calculators/SasaCalculatorLegacy.hh>
#include <protocols/simple_pose_metric_calculators/NumberHBondsCalculator.hh>
#include <protocols/simple_pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.hh>
#include <protocols/pose_metric_calculators/SaltBridgeCalculator.hh>
#include <protocols/pose_metric_calculators/CatPiCalculator.hh>
#include <protocols/pose_metric_calculators/PiPiCalculator.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <protocols/analysis/PackStatMover.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
	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 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 ("seqrecovery")
FileOptionKey const	sequence_recovery::native_pdb_list ("sequence_recovery::native_pdb_list")
FileOptionKey const	sequence_recovery::redesign_pdb_list ("sequence_recovery::redesign_pdb_list")
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 )

Steven Combs - added pose metrics

Function Documentation

fill_designable_set()

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

return the set of residues that are designable based given pose

References create_a3b_hbs::ii, option, optE::parse_tagfile(), beta_nonlocal::pose, oop_conformations::scorefxn, test.G200_Module_Region::tf, TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by XMLprinterMover::apply(), and measure_sequence_recovery().

fill_num_neighbors()

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 create_a3b_hbs::ii, and beta_nonlocal::pose.

Referenced by measure_sequence_recovery().

init_usage_prompt()

void init_usage_prompt

(

std::string

exe

)

References usage_string.

Referenced by main().

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, test.T009_Exceptions::e, utility::file::file_exists(), file_exists(), getline(), basic::init(), init_usage_prompt(), subloop_histogram::iterator, measure_rotamer_recovery(), measure_sequence_recovery(), sequence_recovery::native_pdb_list, docking::native_pose, option, pyrosetta.distributed.io::pose_from_file, sequence_recovery::redesign_pdb_list, sequence_recovery::rotamer_recovery, sequence_recovery::se_cutoff, sequence_recovery::seq_recov_filename, sequence_recovery::sub_matrix_filename, TR, usage_string, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, utility_exit_with_message_status, and value.

measure_rotamer_recovery()

void measure_rotamer_recovery	(	utility::vector1< core::pose::Pose > &	,
		utility::vector1< core::pose::Pose > &
	)

Referenced by main().

measure_sequence_recovery()

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.

References basic::options::OptionKeys::remodel::core_cutoff, utility::io::oc::cout, end, ObjexxFCL::format::F(), fill_designable_set(), fill_num_neighbors(), create_a3b_hbs::i, create_a3b_hbs::ii, beta_nonlocal::jj, n_total, docking::native_pose, usec::native_sequence, create_a3b_hbs::nres, option, oop_conformations::scorefxn, sequence_recovery::se_cutoff, sequence_recovery::seq_recov_filename, setup_tf(), sequence_recovery::sub_matrix_filename, and value.

Referenced by main().

setup_tf()

core::pack::task::TaskFactoryOP setup_tf

(

core::pack::task::TaskFactoryOP

task_factory_

)

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

References subloop_histogram::iterator, option, optE::parse_tagfile(), test.G204_Module_ScoreAnalysis::tops, and basic::options::OptionKeys::inout::dbms::user.

Referenced by XMLprinterMover::apply(), and measure_sequence_recovery().

Variable Documentation

TR

basic::Tracer TR("seqrecovery") ( "seqrecovery"  )

static

Referenced by fill_designable_set(), and main().

usage_string

std::string usage_string

Referenced by init_usage_prompt(), and main().