adenosine_stack_test.cc File Reference

#include <core/scoring/rms_util.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/chemical/rna/util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <utility/io/ozstream.hh>
#include <protocols/idealize/idealize.hh>
#include <protocols/stepwise/StepWiseUtil.hh>
#include <core/pose/util.hh>
#include <core/pose/Pose.hh>
#include <devel/init.hh>
#include <utility/vector1.hh>
#include <utility/io/izstream.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/import_pose/import_pose.hh>
#include <protocols/viewer/viewers.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <utility/excn/Exceptions.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
void	add_virtual_res (core::pose::Pose &pose, bool set_res_as_root=true)
void	rotate_into_nucleobase_frame (core::pose::Pose &pose)
void	methane_pair_score_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

add_virtual_res()

void add_virtual_res	(	core::pose::Pose &	pose,
		bool	set_res_as_root = true
	)

References utility::io::oc::cout, basic::options::OptionKeys::in::file::fullatom, create_a3b_hbs::nres, and beta_nonlocal::pose.

Referenced by nucleobase_probe_score_test(), and rb_entropy_test().

main()

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

References basic::options::OptionKeys::sample_around::alpha_increment, argv, basic::options::OptionKeys::sample_around::cosbeta_increment, test.T009_Exceptions::e, basic::options::OptionKeys::sample_around::gamma_increment, basic::init(), my_main(), NEW_OPT, and viewer_main().

methane_pair_score_test()

void methane_pair_score_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, pyrosetta::create_score_function, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, rotate_into_nucleobase_frame(), docking::s, oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().

my_main()

void* my_main

(

void *

)

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

Referenced by main().

rotate_into_nucleobase_frame()

void rotate_into_nucleobase_frame

(

core::pose::Pose &

pose

)

References basic::options::OptionKeys::in::file::centroid, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, res, basic::options::OptionKeys::full_model::rna::rna, and stub().

Referenced by methane_pair_score_test(), nucleobase_probe_score_test(), and rb_entropy_test().