#include <basic/database/open.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/datacache/CacheableString.hh>
#include <basic/options/keys/holes.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/matdes.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/parser.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/id/AtomID_Map.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/make_symmetric_task.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/init_id_map.hh>
#include <core/pose/symmetry/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/scoring/packing/HolesParams.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/types.hh>
#include <fstream>
#include <iostream>
#include <math.h>
#include <numeric/random/random.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <protocols/docking/util.hh>
#include <protocols/jobdist/not_universal_main.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/viewer/viewers.hh>
#include <sstream>
#include <string>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/mpistream.hh>
#include <utility/string_util.hh>
#include <core/scoring/sc/ShapeComplementarityCalculator.hh>
#include <protocols/relax/FastRelax.hh>
#include <core/scoring/constraints/ResidueTypeConstraint.hh>
#include <protocols/simple_ddg/ddG.hh>
#include <protocols/pose_metric_calculators/RotamerBoltzCalculator.hh>
#include <protocols/calc_taskop_filters/RotamerBoltzmannWeight.hh>
#include <core/pack/task/ResfileReader.hh>
#include <protocols/simple_pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/pose/metrics/PoseMetricCalculatorBase.hh>
#include <protocols/simple_pose_metric_calculators/NumberHBondsCalculator.hh>
#include <core/pose/metrics/simple_calculators/SasaCalculatorLegacy.hh>
#include <basic/MetricValue.hh>
#include <protocols/task_operations/LimitAromaChi2Operation.hh>

Typedefs
typedef numeric::xyzVector< Real >	Vec

typedef numeric::xyzMatrix< Real >	Mat

typedef vector1< Size >	Sizes

Functions
void	design (Pose &pose, ScoreFunctionOP sf, utility::vector1< Size > revert_pos, utility::vector1< string > revert_ids)

void	design_using_resfile (Pose &pose, ScoreFunctionOP sf, std::string resfile, utility::vector1< Size > &mutalyze_pos)

void	repack (Pose &pose, ScoreFunctionOP sf, utility::vector1< Size > design_pos)

void	minimize (Pose &pose, ScoreFunctionOP sf, utility::vector1< Size > design_pos, bool move_bb, bool move_sc, bool move_rb)

utility::vector1< Real >	sidechain_sasa (Pose const &pose, Real probe_radius)

void	new_sc (Pose &pose, utility::vector1< Size > intra_subs, Real &int_area, Real &sc)

void	newer_sc (Pose &pose, utility::vector1< Size > intra_subs, Real &int_area, Real &sc)

Pose	get_neighbor_subs (Pose const &pose, vector1< Size > intra_subs)

Real	get_atom_packing_score (Pose const &pose, vector1< Size > intra_subs, Real cutoff=9.0)

Real	average_degree (Pose const &pose, vector1< Size > mutalyze_pos, Size intra_subs, Real distance_threshold=10.0)

Real	get_unsat_polars (Pose const &bound, Pose const &unbound, Size nres_monomer)

void *	dostuff (void *)

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

Variables
static basic::Tracer	TR ("matdes::mutalyze")

Typedef Documentation

◆ Mat

typedef numeric::xyzMatrix<Real> Mat

◆ Sizes

typedef vector1<Size> Sizes

◆ Vec

typedef numeric::xyzVector<Real> Vec

Function Documentation

◆ average_degree()

Real average_degree	(	Pose const &	pose,
		vector1< Size >	mutalyze_pos,
		Size	intra_subs,
		Real	distance_threshold = `10.0`
	)

References count_neighbors(), build_jacobian::distance, create_a3b_hbs::i, beta_nonlocal::pose, pna::resi, basic::options::OptionKeys::cmiles::jumping::resj, and TR.

Referenced by dostuff().

◆ design()

void design	(	Pose &	pose,
		ScoreFunctionOP	sf,
		utility::vector1< Size >	revert_pos,
		utility::vector1< string >	revert_ids
	)

References detail::find(), create_a3b_hbs::i, vancomycin::pack, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, and vancomycin::task.

Referenced by dostuff().

◆ design_using_resfile()

void design_using_resfile	(	Pose &	pose,
		ScoreFunctionOP	sf,
		std::string	resfile,
		utility::vector1< Size > &	mutalyze_pos
	)

References create_a3b_hbs::i, vancomycin::pack, parse_resfile(), beta_nonlocal::pose, basic::options::OptionKeys::packing::resfile, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, and vancomycin::task.

Referenced by dostuff().

◆ dostuff()

void* dostuff ( void * )

References matdes::mutalyze::ala_scan(), matdes::angle(), oop_conformations::angles, average_degree(), matdes::mutalyze::calc_rot_boltz(), utility::io::oc::cout, design(), design_using_resfile(), extract_scores(), evaluate_beta_mutants::file, basic::options::OptionKeys::optE::fixed, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, get_atom_packing_score(), get_unsat_polars(), create_a3b_hbs::i, subloop_histogram::iterator, create_a3b_hbs::j, make_symmdef_file_denovo::jump_num, basic::options::OptionKeys::matdes::mutalyze::min_rb, matdes::mutalyze::min_rb(), newer_sc(), matdes::num_subs_building_block(), matdes::num_subs_total(), out::file::o(), basic::options::option, option, erraser_single_res_analysis::out, matdes::pdbID(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, matdes::prefix(), matdes::radial_disp(), basic::options::OptionKeys::packing::resfile, matdes::mutalyze::revert_scan(), runtime_assert, in::file::s(), basic::options::OptionKeys::canonical_sampling::probabilities::sc, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, sfd, out::file::silent(), ObjexxFCL::string_of(), basic::options::OptionKeys::symmetry::symmetry, matdes::tag(), TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and numeric::x_rotation_matrix_degrees().

Referenced by main().

◆ get_atom_packing_score()

Real get_atom_packing_score	(	Pose const &	pose,
		vector1< Size >	intra_subs,
		Real	cutoff = `9.0`
	)

References count, extract_by_sidechain_sasa_score::cutoff, basic::database::full_name(), get_neighbor_subs(), and beta_nonlocal::pose.

Referenced by dostuff().

◆ get_neighbor_subs()

Pose get_neighbor_subs	(	Pose const &	pose,
		vector1< Size >	intra_subs
	)

References detail::find(), create_a3b_hbs::i, beta_nonlocal::pose, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by get_atom_packing_score().

◆ get_unsat_polars()

Real get_unsat_polars	(	Pose const &	bound,
		Pose const &	unbound,
		Size	nres_monomer
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::flag, TR, and basic::MetricValue< T >::value().

Referenced by dostuff().

◆ main()

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

References argv, dostuff(), test.T009_Exceptions::e, func, and basic::init().

◆ minimize()

void minimize	(	Pose &	pose,
		ScoreFunctionOP	sf,
		utility::vector1< Size >	design_pos,
		bool	move_bb,
		bool	move_sc,
		bool	move_rb
	)

References test.T009_Exceptions::e, create_a3b_hbs::i, basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, and basic::options::OptionKeys::out::sf.

◆ new_sc()

void new_sc	(	Pose &	pose,
		utility::vector1< Size >	intra_subs,
		Real &	int_area,
		Real &	sc
	)

References detail::find(), create_a3b_hbs::i, beta_nonlocal::pose, basic::options::OptionKeys::canonical_sampling::probabilities::sc, and basic::options::OptionKeys::cutoutdomain::start.

◆ newer_sc()

void newer_sc	(	Pose &	pose,
		utility::vector1< Size >	intra_subs,
		Real &	int_area,
		Real &	sc
	)

References detail::find(), create_a3b_hbs::i, beta_nonlocal::pose, basic::options::OptionKeys::canonical_sampling::probabilities::sc, basic::options::OptionKeys::cutoutdomain::start, and TR.

Referenced by dostuff().

◆ repack()

void repack	(	Pose &	pose,
		ScoreFunctionOP	sf,
		utility::vector1< Size >	design_pos
	)

References detail::find(), create_a3b_hbs::i, vancomycin::pack, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, and vancomycin::task.

◆ sidechain_sasa()

utility::vector1<Real> sidechain_sasa	(	Pose const &	pose,
		Real	probe_radius
	)

References basic::options::OptionKeys::edensity::atom_mask, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, and bur_nodon_tyr::probe_radius.

Variable Documentation

◆ TR

basic::Tracer TR("matdes::mutalyze") ( "matdes::mutalyze" )

static

Referenced by average_degree(), dostuff(), get_unsat_polars(), and newer_sc().

Typedefs

Functions

Variables

Typedef Documentation

◆ Mat

◆ Sizes

◆ Vec

Function Documentation

◆ average_degree()

◆ design()

◆ design_using_resfile()

◆ dostuff()

◆ get_atom_packing_score()

◆ get_neighbor_subs()

◆ get_unsat_polars()

◆ main()

◆ minimize()

◆ new_sc()

◆ newer_sc()

◆ repack()

◆ sidechain_sasa()

Variable Documentation

◆ TR