#include <protocols/simple_moves/ScoreMover.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/pose/util.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/cluster/cluster.hh>
#include <protocols/loops/loop_closure/kinematic_closure/KinematicMover.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <devel/init.hh>
#include <iostream>
#include <string>
#include <deque>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/relax.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <utility/vector1.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/Energies.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <protocols/minimization_packing/RepackSidechainsMover.hh>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <protocols/simple_moves/MutateResidue.hh>
#include <protocols/relax/FastRelax.hh>
#include <numeric/model_quality/rms.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/kinematics/Jump.hh>
#include <core/scoring/constraints/util.hh>
#include <numeric/random/random.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/Patch.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <core/chemical/AA.hh>

Macros
#define	PI 3.1415926535897932384626433832795

#define	CNCa_ANGLE 121.7

#define	CNH_ANGLE 119.15

#define	CaCN_ANGLE 116.2

#define	OCN_ANGLE 123.01

#define	PI 3.1415926535897932384626433832795

#define	CNCa_ANGLE 121.7

#define	CNH_ANGLE 119.15

#define	CaCN_ANGLE 116.2

#define	OCN_ANGLE 123.01

Functions
void	register_options ()

bool	do_initial_checks ()

bool	do_postload_checks (const core::pose::Pose &mypose)

bool	is_in_list (const core::Size val, const utility::vector1< core::Size > &vallist)

bool	is_in_list (const std::string str, const utility::vector1< std::string > &stringlist)

void	reset_sfxn (core::scoring::ScoreFunctionOP sfxn_constrained)

void	constrain_loop_ends (core::pose::Pose &mypose, const core::Size resC, const core::Size resN, core::scoring::ScoreFunctionOP sfxn_constrained)

void	append_pose_by_jump (core::pose::Pose &mypose, const core::pose::Pose &pose_to_append)

void	append_alanines (core::pose::Pose &mypose, const core::Size alacount, const bool append_D)

void	create_loop (core::pose::Pose &stubpose, const core::pose::Pose &masterpose, const core::Size stub_chain, const bool d_only)

void	set_up_pose (core::pose::Pose &masterpose, utility::vector1< core::Size > &no_repack_positions, core::Size &new_startpos, core::Size &new_endpos, const bool d_only)

void	set_sc_repacking (core::kinematics::MoveMapOP mm, utility::vector1< core::Size > &no_repack_positions)

void	copy_residue_position (const core::pose::Pose &refpose, const core::Size refposition, core::pose::Pose &modifiedpose, const core::Size modifiedposition)

core::Real	superimposebb (core::pose::Pose &mod_pose, core::pose::Pose const &ref_pose, core::Size ref_start, core::Size ref_end, core::Size target_start, core::Size, bool use_O)

bool	noclash (const core::Size position, const core::pose::Pose &mypose)

bool	good_geometry (const core::pose::Pose &mypose, const core::Size start, const core::Size end, const core::Size additional)

void	kinclose (core::pose::Pose &mypose, const core::Size startres, const core::Size endres, const core::Size loop_length, const bool is_cyclic, const bool close_random_subset, numeric::random::RandomGenerator &RG, core::scoring::ScoreFunctionOP sfxn, const bool allowL, const bool allowD, const bool allowGLY)

bool	near_chain (const core::pose::Pose &mypose, const core::Size position, const core::Size designchain, const core::Real radius)

void	designloop (core::pose::Pose &mypose, const core::Size startres, const core::Size endres, const core::Size loop_length, const bool is_cyclic, core::scoring::ScoreFunctionOP sfxn, const utility::vector1< core::Size > &no_repack_positions, utility::vector1< core::Size > &can_repack_positions, const utility::vector1< std::string > &allowed_L_aas, const utility::vector1< std::string > &allowed_D_aas, const bool allow_gly)

void	relaxloop (core::pose::Pose &mypose, const core::Size startres, const core::Size endres, const core::Size loop_length, protocols::relax::FastRelaxOP frlx, protocols::minimization_packing::MinMoverOP minmove, core::kinematics::MoveMapOP mm, const utility::vector1< core::Size > &no_repack_positions, const utility::vector1< core::Size > &can_repack_positions)

void	set_loop_conformation (core::pose::Pose &mypose, const core::pose::Pose &refpose, const core::Size startres, const core::Size endres, const core::Size loop_length)

bool	metropolis_criterion (const core::Real newval, const core::Real oldval, const core::Real MCtemperature, numeric::random::RandomGenerator &RG)

void	jitterloop (core::pose::Pose &mypose, const core::Size startres, const core::Size loop_length, const core::Real magnitude, numeric::random::RandomGenerator &RG)

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

Variables
static numeric::random::RandomGenerator	RG (847322)

Macro Definition Documentation

◆ CaCN_ANGLE [1/2]

#define CaCN_ANGLE 116.2

◆ CaCN_ANGLE [2/2]

#define CaCN_ANGLE 116.2

◆ CNCa_ANGLE [1/2]

#define CNCa_ANGLE 121.7

◆ CNCa_ANGLE [2/2]

#define CNCa_ANGLE 121.7

◆ CNH_ANGLE [1/2]

#define CNH_ANGLE 119.15

◆ CNH_ANGLE [2/2]

#define CNH_ANGLE 119.15

◆ OCN_ANGLE [1/2]

#define OCN_ANGLE 123.01

◆ OCN_ANGLE [2/2]

#define OCN_ANGLE 123.01

◆ PI [1/2]

#define PI 3.1415926535897932384626433832795

◆ PI [2/2]

#define PI 3.1415926535897932384626433832795

Function Documentation

◆ append_alanines()

void append_alanines	(	core::pose::Pose &	mypose,
		const core::Size	alacount,
		const bool	append_D
	)

References create_a3b_hbs::i, residue_types_from_sequence(), and beta_sc_scan::seq.

Referenced by create_loop().

◆ append_pose_by_jump()

void append_pose_by_jump	(	core::pose::Pose &	mypose,
		const core::pose::Pose &	pose_to_append
	)

References create_a3b_hbs::nres.

Referenced by set_up_pose().

◆ constrain_loop_ends()

void constrain_loop_ends	(	core::pose::Pose &	mypose,
		const core::Size	resC,
		const core::Size	resN,
		core::scoring::ScoreFunctionOP	sfxn_constrained
	)

References CaCN_ANGLE, CNCa_ANGLE, CNH_ANGLE, basic::options::OptionKeys::constraints::constraints, func, OCN_ANGLE, PI, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by main().

◆ copy_residue_position()

void copy_residue_position	(	const core::pose::Pose &	refpose,
		const core::Size	refposition,
		core::pose::Pose &	modifiedpose,
		const core::Size	modifiedposition
	)

Referenced by kinclose(), and set_loop_conformation().

◆ create_loop()

void create_loop	(	core::pose::Pose &	stubpose,
		const core::pose::Pose &	masterpose,
		const core::Size	stub_chain,
		const bool	d_only
	)

References append_alanines(), cyclic, create_a3b_hbs::nres, and option.

Referenced by set_up_pose().

◆ designloop()

void designloop	(	core::pose::Pose &	mypose,
		const core::Size	startres,
		const core::Size	endres,
		const core::Size	loop_length,
		const bool	is_cyclic,
		core::scoring::ScoreFunctionOP	sfxn,
		const utility::vector1< core::Size > &	no_repack_positions,
		utility::vector1< core::Size > &	can_repack_positions,
		const utility::vector1< std::string > &	allowed_L_aas,
		const utility::vector1< std::string > &	allowed_D_aas,
		const bool	allow_gly
	)

References basic::options::OptionKeys::hotspot::allow_gly, create_a3b_hbs::i, is_in_list(), indel::loop_length, near_chain(), create_a3b_hbs::nres, option, printf(), basic::options::OptionKeys::casp::repack, test.T120_core::sfxn, build::stdout, vancomycin::task, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

◆ do_initial_checks()

bool do_initial_checks ( )

References cyclic, test.T009_Exceptions::e, option, printf(), in::file::s(), basic::options::OptionKeys::relax::script, ObjexxFCL::size(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

◆ do_postload_checks()

bool do_postload_checks ( const core::pose::Pose & mypose )

References option, and printf().

Referenced by main().

◆ good_geometry()

bool good_geometry	(	const core::pose::Pose &	mypose,
		const core::Size	start,
		const core::Size	end,
		const core::Size	additional
	)

References dist(), ObjexxFCL::end(), oop_conformations::length, printf(), basic::options::OptionKeys::cutoutdomain::start, and build::stdout.

Referenced by kinclose().

◆ is_in_list() [1/2]

bool is_in_list	(	const core::Size	val,
		const utility::vector1< core::Size > &	vallist
	)

References create_a3b_hbs::i.

Referenced by designloop(), main(), and relaxloop().

◆ is_in_list() [2/2]

bool is_in_list	(	const std::string	str,
		const utility::vector1< std::string > &	stringlist
	)

References create_a3b_hbs::i, and str().

◆ jitterloop()

void jitterloop	(	core::pose::Pose &	mypose,
		const core::Size	startres,
		const core::Size	loop_length,
		const core::Real	magnitude,
		numeric::random::RandomGenerator &	RG
	)

References demo.D060_Folding::counter, numeric::random::RandomGenerator::gaussian(), create_a3b_hbs::i, indel::loop_length, lactamize::nr, printf(), RG, and build::stdout.

Referenced by main().

◆ kinclose()

void kinclose	(	core::pose::Pose &	mypose,
		const core::Size	startres,
		const core::Size	endres,
		const core::Size	loop_length,
		const bool	is_cyclic,
		const bool	close_random_subset,
		numeric::random::RandomGenerator &	RG,
		core::scoring::ScoreFunctionOP	sfxn,
		const bool	allowL,
		const bool	allowD,
		const bool	allowGLY
	)

References copy_residue_position(), ObjexxFCL::end(), good_geometry(), indel::loop_length, noclash(), create_a3b_hbs::nres, option, printf(), numeric::random::RandomGenerator::random_range(), RG, test.T120_core::sfxn, basic::options::OptionKeys::cutoutdomain::start, build::stdout, superimposebb(), and numeric::random::RandomGenerator::uniform().

Referenced by main().

◆ main()

◆ metropolis_criterion()

bool metropolis_criterion	(	const core::Real	newval,
		const core::Real	oldval,
		const core::Real	MCtemperature,
		numeric::random::RandomGenerator &	RG
	)

References RG, and numeric::random::RandomGenerator::uniform().

Referenced by main().

◆ near_chain()

bool near_chain	(	const core::pose::Pose &	mypose,
		const core::Size	position,
		const core::Size	designchain,
		const core::Real	radius
	)

References create_a3b_hbs::nres, and basic::options::OptionKeys::cluster::radius.

Referenced by designloop().

◆ noclash()

bool noclash	(	const core::Size	position,
		const core::pose::Pose &	mypose
	)

References create_a3b_hbs::nres, printf(), and build::stdout.

Referenced by kinclose().

◆ register_options()

void register_options ( )

References cyclic, and NEW_OPT.

Referenced by main().

◆ relaxloop()

void relaxloop	(	core::pose::Pose &	mypose,
		const core::Size	startres,
		const core::Size	endres,
		const core::Size	loop_length,
		protocols::relax::FastRelaxOP	frlx,
		protocols::minimization_packing::MinMoverOP	minmove,
		core::kinematics::MoveMapOP	mm,
		const utility::vector1< core::Size > &	no_repack_positions,
		const utility::vector1< core::Size > &	can_repack_positions
	)

References create_a3b_hbs::i, is_in_list(), indel::loop_length, beta_nonlocal::mm, create_a3b_hbs::nres, option, printf(), build::stdout, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

◆ reset_sfxn()

void reset_sfxn ( core::scoring::ScoreFunctionOP sfxn_constrained )

References basic::options::OptionKeys::constraints::constraints, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by main().

◆ set_loop_conformation()

void set_loop_conformation	(	core::pose::Pose &	mypose,
		const core::pose::Pose &	refpose,
		const core::Size	startres,
		const core::Size	endres,
		const core::Size	loop_length
	)

References copy_residue_position(), numeric::dihedral_radians(), indel::loop_length, option, and superimposebb().

◆ set_sc_repacking()

void set_sc_repacking	(	core::kinematics::MoveMapOP	mm,
		utility::vector1< core::Size > &	no_repack_positions
	)

References create_a3b_hbs::i, and beta_nonlocal::mm.

Referenced by main().

◆ set_up_pose()

void set_up_pose	(	core::pose::Pose &	masterpose,
		utility::vector1< core::Size > &	no_repack_positions,
		core::Size &	new_startpos,
		core::Size &	new_endpos,
		const bool	d_only
	)

References append_pose_by_jump(), create_loop(), cyclic, create_a3b_hbs::i, option, pyrosetta.distributed.io::pose_from_file, printf(), residue, in::file::s(), ObjexxFCL::size(), and build::stdout.

Referenced by main().

◆ superimposebb()

core::Real superimposebb	(	core::pose::Pose &	mod_pose,
		core::pose::Pose const &	ref_pose,
		core::Size	ref_start,
		core::Size	ref_end,
		core::Size	target_start,
		core::Size	,
		bool	use_O
	)

References utility::options::OptionKeys::options::exit, printf(), build::stdout, and superimpose_pose().

Referenced by kinclose(), and set_loop_conformation().

Variable Documentation

◆ RG

numeric::random::RandomGenerator RG(847322) ( 847322 )

static

Referenced by jitterloop(), kinclose(), main(), and metropolis_criterion().

Macros

Functions

Variables

Macro Definition Documentation

◆ CaCN_ANGLE [1/2]

◆ CaCN_ANGLE [2/2]

◆ CNCa_ANGLE [1/2]

◆ CNCa_ANGLE [2/2]

◆ CNH_ANGLE [1/2]

◆ CNH_ANGLE [2/2]

◆ OCN_ANGLE [1/2]

◆ OCN_ANGLE [2/2]

◆ PI [1/2]

◆ PI [2/2]

Function Documentation

◆ append_alanines()

◆ append_pose_by_jump()

◆ constrain_loop_ends()

◆ copy_residue_position()

◆ create_loop()

◆ designloop()

◆ do_initial_checks()

◆ do_postload_checks()

◆ good_geometry()

◆ is_in_list() [1/2]

◆ is_in_list() [2/2]

◆ jitterloop()

◆ kinclose()

◆ main()

◆ metropolis_criterion()

◆ near_chain()

◆ noclash()

◆ register_options()

◆ relaxloop()

◆ reset_sfxn()

◆ set_loop_conformation()

◆ set_sc_repacking()

◆ set_up_pose()

◆ superimposebb()

Variable Documentation

◆ RG