make_ideal_betapeptide.cc File Reference

#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/Loops.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/relax.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <utility/vector1.hh>
#include <core/scoring/rms_util.hh>
#include <ObjexxFCL/format.hh>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <protocols/relax/FastRelax.hh>
#include <numeric/random/random.hh>
#include <numeric/random/uniform.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/id/TorsionID.hh>
#include <core/scoring/Energies.hh>
#include <protocols/minimization_packing/RepackSidechainsMover.hh>
#include <core/kinematics/MoveMap.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <protocols/simple_moves/MutateResidue.hh>

Functions
	OPT_KEY (Real, v_MCtemperature) OPT_KEY(Integer
v_MCrounds	OPT_KEY (Integer, v_MCsteps_per_round) OPT_KEY(Real
v_MCrounds v_MCanglepert void	register_options ()
void	betapeptide_setphi (core::pose::Pose &pose, int resnumber, double angle)
void	betapeptide_settheta (core::pose::Pose &pose, int resnumber, double angle)
void	betapeptide_setpsi (core::pose::Pose &pose, int resnumber, double angle)
void	betapeptide_setomega (core::pose::Pose &pose, int resnumber, double angle)
double	randangle (numeric::random::RandomGenerator &RG)
void	perturb_bb (core::pose::Pose &pose, numeric::random::RandomGenerator &RG)
void	jitter_and_minimize (core::pose::Pose &pose, numeric::random::RandomGenerator &RG, protocols::relax::FastRelax &frlx, core::scoring::ScoreFunctionOP &sfxn, int MCrounds, int MCsteps_per_round, double anglepertsize, double MCtemperature)
int	main (int argc, char *argv[])

Variables
static numeric::random::RandomGenerator	RG (923749)

Function Documentation

betapeptide_setomega()

void betapeptide_setomega	(	core::pose::Pose &	pose,
		int	resnumber,
		double	angle
	)

References basic::options::OptionKeys::hotspot::angle, and beta_nonlocal::pose.

Referenced by main().

betapeptide_setphi()

void betapeptide_setphi	(	core::pose::Pose &	pose,
		int	resnumber,
		double	angle
	)

References basic::options::OptionKeys::hotspot::angle, and beta_nonlocal::pose.

Referenced by jitter_and_minimize(), main(), and perturb_bb().

betapeptide_setpsi()

void betapeptide_setpsi	(	core::pose::Pose &	pose,
		int	resnumber,
		double	angle
	)

References basic::options::OptionKeys::hotspot::angle, and beta_nonlocal::pose.

Referenced by jitter_and_minimize(), main(), and perturb_bb().

betapeptide_settheta()

void betapeptide_settheta	(	core::pose::Pose &	pose,
		int	resnumber,
		double	angle
	)

References basic::options::OptionKeys::hotspot::angle, and beta_nonlocal::pose.

Referenced by jitter_and_minimize(), main(), and perturb_bb().

jitter_and_minimize()

void jitter_and_minimize	(	core::pose::Pose &	pose,
		numeric::random::RandomGenerator &	RG,
		protocols::relax::FastRelax &	frlx,
		core::scoring::ScoreFunctionOP &	sfxn,
		int	MCrounds,
		int	MCsteps_per_round,
		double	anglepertsize,
		double	MCtemperature
	)

References betapeptide_setphi(), betapeptide_setpsi(), betapeptide_settheta(), numeric::random::RandomGenerator::gaussian(), beta_nonlocal::pose, RG, and numeric::random::RandomGenerator::uniform().

main()

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

References argv, betapeptide_setomega(), betapeptide_setphi(), betapeptide_setpsi(), betapeptide_settheta(), basic::options::OptionKeys::cluster::cluster, create_a3b_hbs::i, basic::init(), out::nstruct(), out::file::o(), basic::options::OptionKeys::optimization::optimization, option, lactamize::outfile, beta_nonlocal::pose, printf(), register_options(), basic::options::OptionKeys::in::file::residue_type_set, residue_types_from_sequence(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, test.T120_core::sfxn, build::stdout, and basic::options::OptionKeys::inout::dbms::user.

OPT_KEY() [1/2]

v_MCrounds OPT_KEY	(	Integer	,
		v_MCsteps_per_round
	)

OPT_KEY() [2/2]

OPT_KEY	(	Real	,
		v_MCtemperature
	)

perturb_bb()

void perturb_bb	(	core::pose::Pose &	pose,
		numeric::random::RandomGenerator &	RG
	)

References betapeptide_setphi(), betapeptide_setpsi(), betapeptide_settheta(), beta_nonlocal::pose, randangle(), and RG.

randangle()

double randangle

(

numeric::random::RandomGenerator &

RG

)

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

Referenced by perturb_bb().

register_options()

v_MCrounds v_MCanglepert void register_options

(

)

References NEW_OPT.

Referenced by main().

Variable Documentation

RG

numeric::random::RandomGenerator RG(923749) ( 923749  )

static

Referenced by jitter_and_minimize(), perturb_bb(), and randangle().