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 <core/graph/UpperEdgeGraph.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/filters/Filter.fwd.hh>
#include <utility/vector0.hh>

Namespaces
	sequence_recovery

Functions
static THREAD_LOCAL basic::Tracer	TR ("sequence_recovery")

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
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
	)

return the set of residues that are designable based given pose

References pyrosetta::get_score_function, test.T200_Scoring::ii, option, sequence_recovery::parse_taskops_file, app.surface_docking.surface_docking::pose, PyMOL_demo::scorefxn, TR(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by measure_sequence_recovery().

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
	)

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

References basic::options::OptionKeys::remodel::core_cutoff, basic::options::OptionKeys::cutoutdomain::end, ObjexxFCL::format::F(), fill_designable_set(), fill_num_neighbors(), test.T200_Scoring::ii, test.Workshop7test::native_pose, usec::native_sequence, clean_pdb_keep_ligand::nres, option, sequence_recovery::se_cutoff, sequence_recovery::seq_recov_filename, setup_tf(), sequence_recovery::sub_matrix_filename, and value.

Referenced by main().

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, test.G204_Module_ScoreAnalysis::tops, and basic::options::OptionKeys::inout::dbms::user.

Referenced by measure_sequence_recovery().

static THREAD_LOCAL basic::Tracer TR ( "sequence_recovery" )

static

Referenced by fill_designable_set(), and main().

Variable Documentation

std::string usage_string

Referenced by init_usage_prompt(), and main().

Namespaces

Functions

Variables

Detailed Description

Function Documentation

Variable Documentation