bur_nodon_tyr.cc File Reference

#include <devel/init.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/chemical/ResidueType.fwd.hh>
#include <core/pose/PDBInfo.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/metrics/simple_calculators/SasaCalculator.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <devel/vardist_solaccess/VarSolDRotamerDots.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <basic/Tracer.hh>
#include <basic/MetricValue.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
	bur_nodon_tyr

Functions
core::pack::task::TaskFactoryOP	setup_tf (core::pack::task::TaskFactoryOP task_factory_)
	load custom TaskOperations according to an xml-like utility::tag file 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 (core::pose::Pose &pose)
	iterates over all designed positions and determines identity to native. outputs recoveries to file. More...
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("bur_nodon_tyr")
FileOptionKey const	bur_nodon_tyr::pdb_list ("bur_nodon_tyr:pdb_list")
FileOptionKey const	bur_nodon_tyr::parse_taskops_file ("bur_nodon_tyr:parse_taskops_file")
RealOptionKey const	bur_nodon_tyr::probe_radius ("bur_nodon_tyr:probe_radius")
BooleanOptionKey const	bur_nodon_tyr::layered_sasa ("bur_nodon_tyr:layered_sasa")
RealOptionKey const	bur_nodon_tyr::sasa_bur_cutoff ("bur_nodon_tyr:sasa_bur_cutoff")

Detailed Description

Author

Kevin Houlihan (khoul.nosp@m.i@un.nosp@m.c.edu)

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, bur_nodon_tyr::parse_taskops_file, beta_nonlocal::pose, oop_conformations::scorefxn, test.G200_Module_Region::tf, and basic::options::OptionKeys::inout::dbms::user.

Referenced by measure_sequence_recovery().

main()

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

References argv, test.T009_Exceptions::e, utility::file::file_exists(), file_exists(), getline(), basic::init(), subloop_histogram::iterator, bur_nodon_tyr::layered_sasa, measure_sequence_recovery(), option, bur_nodon_tyr::parse_taskops_file, kic_runner::pdb, bur_nodon_tyr::pdb_list, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, bur_nodon_tyr::probe_radius, bur_nodon_tyr::sasa_bur_cutoff, TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, utility_exit_with_message_status, and value.

measure_sequence_recovery()

void measure_sequence_recovery

(

core::pose::Pose &

pose

)

iterates over all designed positions and determines identity to native. outputs recoveries to file.

References end, fill_designable_set(), basic::Tracer::flush(), test.T200_Scoring::hbond_set, bur_nodon_tyr::layered_sasa, create_a3b_hbs::nres, basic::options::option, beta_nonlocal::pose, pna::resi, bur_nodon_tyr::sasa_bur_cutoff, oop_conformations::scorefxn, basic::options::OptionKeys::relax::sequence, setup_tf(), TR, and basic::MetricValue< T >::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, bur_nodon_tyr::parse_taskops_file, test.G204_Module_ScoreAnalysis::tops, and basic::options::OptionKeys::inout::dbms::user.

Referenced by measure_sequence_recovery().

Variable Documentation

TR

basic::Tracer TR("bur_nodon_tyr") ( "bur_nodon_tyr"  )

static

Referenced by main(), and measure_sequence_recovery().