OLD_TRIAL_protein_helix_assemble.cc File Reference

#include <core/scoring/rms_util.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/RNA_SilentStruct.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/options/option.hh>
#include <core/options/after_opts.hh>
#include <core/options/util.hh>
#include <core/options/option_macros.hh>
#include <protocols/idealize/idealize.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/rna/denovo/setup/RNA_DeNovoPoseInitializer.fwd.hh>
#include <protocols/rna/denovo/setup/RNA_DeNovoPoseInitializer.hh>
#include <protocols/rna/denovo/libraries/RNA_ChunkLibrary.hh>
#include <protocols/rna/denovo/libraries/RNA_ChunkLibrary.fwd.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/rna/movers/RNA_HelixAssembler.hh>
#include <protocols/rna/movers/RNA_LoopCloser.hh>
#include <protocols/rna/denovo/movers/RNA_Minimizer.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/util/basic.hh>
#include <core/io/database/open.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <utility/exit.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/scoring/Energies.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <core/util/Tracer.hh>
#include <core/options/keys/out.OptionKeys.gen.hh>
#include <core/options/keys/score.OptionKeys.gen.hh>
#include <core/options/keys/in.OptionKeys.gen.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
void	set_helix_torsions (pose::Pose &pose, Size const &n)
void	build_on_helix (pose::Pose &pose, Size const n, char const &seq1)
void	put_constraints_on_helix (pose::Pose &pose, Size const n)
void	minimize_helix (pose::Pose &pose, Size const n)
void	pack_sidechains (pose::Pose &pose)
void	protein_helix_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

build_on_helix()

void build_on_helix	(	pose::Pose &	pose,
		Size const	n,
		char const &	seq1
	)

References basic::options::OptionKeys::chemical::chemical, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, test.T200_Scoring::rsd1, basic::options::OptionKeys::recces::seq1, and set_helix_torsions().

Referenced by protein_helix_test().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), my_main(), NEW_OPT, beta_sc_scan::seq, and viewer_main().

minimize_helix()

void minimize_helix	(	pose::Pose &	pose,
		Size const	n
	)

References utility::io::oc::cout, pyrosetta.distributed.io::get_score_function(), beta_nonlocal::mm, basic::options::OptionKeys::optimization::optimization, options, beta_nonlocal::pose, oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by protein_helix_test().

my_main()

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, and protein_helix_test().

Referenced by main().

pack_sidechains()

void pack_sidechains

(

pose::Pose &

pose

)

References pyrosetta.distributed.io::get_score_function(), create_a3b_hbs::i, beta_nonlocal::pose, test.T500_Packing::rotamer_trials, basic::options::OptionKeys::frags::scoring::scoring, and vancomycin::task.

Referenced by protein_helix_test().

protein_helix_test()

void protein_helix_test

(

)

References build_on_helix(), basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, minimize_helix(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, pack_sidechains(), beta_nonlocal::pose, put_constraints_on_helix(), basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, set_helix_torsions(), and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

put_constraints_on_helix()

void put_constraints_on_helix	(	pose::Pose &	pose,
		Size const	n
	)

References basic::options::OptionKeys::constraints::constraints, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and beta_nonlocal::pose.

Referenced by protein_helix_test().

set_helix_torsions()

void set_helix_torsions	(	pose::Pose &	pose,
		Size const &	n
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and beta_nonlocal::pose.

Referenced by build_on_helix(), and protein_helix_test().