make_a3b_bundle.cc File Reference

#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/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 <core/scoring/rms_util.tmpl.hh>
#include <ObjexxFCL/format.hh>
#include <cstdio>
#include <cstdlib>
#include <cmath>
#include <protocols/relax/FastRelax.hh>
#include <numeric/random/random.hh>
#include <numeric/random/uniform.hh>
#include <numeric/constants.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>
#include <core/chemical/ResidueType.hh>
#include <protocols/loops/loop_closure/kinematic_closure/KinematicMover.hh>
#include <protocols/loops/loop_closure/kinematic_closure/KinematicWrapper.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/CoordinateConstraint.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>

Functions
void	register_options ()
core::Real	Xpos (core::Size t, core::Real R0, core::Real omega0, core::Real phi0, core::Real R1, core::Real omega1, core::Real phi1, core::Real alpha, core::Real Dz)
core::Real	Ypos (core::Size t, core::Real R0, core::Real omega0, core::Real phi0, core::Real R1, core::Real omega1, core::Real phi1, core::Real alpha, core::Real Dz)
core::Real	Zpos (core::Size t, core::Real R0, core::Real omega0, core::Real R1, core::Real omega1, core::Real phi1, core::Real alpha, core::Real Dz)
void	betapeptide_setphi (core::pose::Pose &pose, core::Size resnumber, core::Real angle)
void	betapeptide_settheta (core::pose::Pose &pose, core::Size resnumber, core::Real angle)
void	betapeptide_setpsi (core::pose::Pose &pose, core::Size resnumber, core::Real angle)
void	betapeptide_setomega (core::pose::Pose &pose, core::Size resnumber, core::Real angle)
void	normalizevector (numeric::xyzVector< core::Real > &v)
core::Real	dotpdt (const numeric::xyzVector< core::Real > &v1, const numeric::xyzVector< core::Real > &v2)
bool	use_in_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Size resno, core::Size atomno)
void	align_poses (core::pose::Pose &mypose, core::pose::Pose const &target)
core::Real	get_distance_measure (const core::pose::Pose &pose1, const core::pose::Pose &pose2)
int	main (int argc, char *argv[])

Function Documentation

align_poses()

void align_poses	(	core::pose::Pose &	mypose,
		core::pose::Pose const &	target
	)

References enumerate_junctions::int, superimpose_pose(), basic::options::OptionKeys::hotspot::target, and use_in_rmsd().

Referenced by hermann_phase_two_minimize(), and main().

betapeptide_setomega()

void betapeptide_setomega	(	core::pose::Pose &	pose,
		core::Size	resnumber,
		core::Real	angle
	)

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

Referenced by main().

betapeptide_setphi()

void betapeptide_setphi	(	core::pose::Pose &	pose,
		core::Size	resnumber,
		core::Real	angle
	)

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

Referenced by main().

betapeptide_setpsi()

void betapeptide_setpsi	(	core::pose::Pose &	pose,
		core::Size	resnumber,
		core::Real	angle
	)

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

Referenced by main().

betapeptide_settheta()

void betapeptide_settheta	(	core::pose::Pose &	pose,
		core::Size	resnumber,
		core::Real	angle
	)

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

Referenced by main().

dotpdt()

core::Real dotpdt	(	const numeric::xyzVector< core::Real > &	v1,
		const numeric::xyzVector< core::Real > &	v2
	)

References oop_scan::v1, and oop_scan::v2.

get_distance_measure()

core::Real get_distance_measure	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)

References enumerate_junctions::int, test.T008_Serialization::pose1, test.T008_Serialization::pose2, and use_in_rmsd().

Referenced by main().

main()

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

References align_poses(), compute_difference::alpha, argv, betapeptide_setomega(), betapeptide_setphi(), betapeptide_setpsi(), betapeptide_settheta(), basic::options::OptionKeys::cluster::cluster, numeric::dihedral_degrees(), test.T009_Exceptions::e, get_distance_measure(), create_a3b_hbs::i, basic::init(), basic::options::OptionKeys::optimization::optimization, option, lactamize::outfile, numeric::constants::d::pi, 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, build::stdout, oop_scan::v1, oop_scan::v2, Xpos(), Ypos(), and Zpos().

normalizevector()

void normalizevector

(

numeric::xyzVector< core::Real > &

v

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

register_options()

void register_options

(

)

References NEW_OPT.

Referenced by main().

use_in_rmsd()

bool use_in_rmsd	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		core::Size	resno,
		core::Size	atomno
	)

References test.T008_Serialization::pose1, and test.T008_Serialization::pose2.

Referenced by align_poses(), and get_distance_measure().

Xpos()

core::Real Xpos	(	core::Size	t,
		core::Real	R0,
		core::Real	omega0,
		core::Real	phi0,
		core::Real	R1,
		core::Real	omega1,
		core::Real	phi1,
		core::Real	alpha,
		core::Real	Dz
	)

References compute_difference::alpha, basic::options::OptionKeys::stepwise::s1, predPRE::t, and tan.

Referenced by main().

Ypos()

core::Real Ypos	(	core::Size	t,
		core::Real	R0,
		core::Real	omega0,
		core::Real	phi0,
		core::Real	R1,
		core::Real	omega1,
		core::Real	phi1,
		core::Real	alpha,
		core::Real	Dz
	)

References compute_difference::alpha, basic::options::OptionKeys::stepwise::s1, predPRE::t, and tan.

Referenced by main().

Zpos()

core::Real Zpos	(	core::Size	t,
		core::Real	R0,
		core::Real	omega0,
		core::Real	R1,
		core::Real	omega1,
		core::Real	phi1,
		core::Real	alpha,
		core::Real	Dz
	)

References compute_difference::alpha, predPRE::t, and tan.

Referenced by main().