make_truecyclicpeptide.cc File Reference

#include <basic/options/option.hh>
#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/option_macros.hh>
#include <basic/Tracer.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <devel/init.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/import_pose/import_pose.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/conformation/util.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <stdio.h>
#include <protocols/simple_moves/MutateResidue.hh>
#include <protocols/relax/FastRelax.fwd.hh>
#include <protocols/relax/FastRelax.hh>
#include <core/kinematics/MoveMap.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/minimization_packing/RepackSidechainsMover.hh>
#include <numeric/random/random.hh>
#include <numeric/random/uniform.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/CartesianMinimizer.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/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <protocols/loops/loop_closure/kinematic_closure/KinematicMover.hh>
#include <protocols/loops/loop_closure/kinematic_closure/KinematicWrapper.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

Functions
void	register_options ()
void	copyresidueposition (core::pose::Pose &alteredpose, int alteredresidue, const core::pose::Pose &referencepose, int referenceresidue)
bool	inlist (core::Size number, utility::vector1< core::Size > list)
int	main (int argc, char *argv[])

Macro Definition Documentation

CaCN_ANGLE

#define CaCN_ANGLE   116.2

CNCa_ANGLE

#define CNCa_ANGLE   121.7

CNH_ANGLE

#define CNH_ANGLE   119.15

OCN_ANGLE

#define OCN_ANGLE   123.01

PI

#define PI   3.1415926535897932384626433832795

Function Documentation

copyresidueposition()

void copyresidueposition	(	core::pose::Pose &	alteredpose,
		int	alteredresidue,
		const core::pose::Pose &	referencepose,
		int	referenceresidue
	)

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

Referenced by main().

inlist()

bool inlist	(	core::Size	number,
		utility::vector1< core::Size >	list
	)

References create_a3b_hbs::i, and basic::options::OptionKeys::in::file::list.

Referenced by main().

main()

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

References alapose(), numeric::angle_degrees(), argv, CaCN_ANGLE, CNCa_ANGLE, CNH_ANGLE, basic::options::OptionKeys::constraints::constraints, copyresidueposition(), numeric::dihedral_degrees(), utility::options::OptionKeys::options::exit, create_a3b_hbs::i, basic::init(), inlist(), create_a3b_hbs::j, beta_nonlocal::mm, local::nstruct, out::nstruct(), out::file::o(), OCN_ANGLE, basic::options::option, lactamize::outfile, PI, beta_nonlocal::pose, ObjexxFCL::pow(), printf(), register_options(), test.T220_AtomAtomPairEnergies::rep, residue_types_from_sequence(), numeric::random::rg(), basic::options::OptionKeys::frags::scoring::scoring, test.T120_core::sfxn, subloop_histogram::size, build::stdout, numeric::random::uniform(), and basic::options::OptionKeys::inout::dbms::user.

register_options()

void register_options

(

)

References NEW_OPT.

Referenced by main().