rb_entropy.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/ChemicalManager.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/Stub.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/rna/util.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <devel/init.hh>
#include <protocols/recces/RECCES_Mover.hh>
#include <protocols/recces/setup_util.hh>
#include <protocols/recces/options/RECCES_Options.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <numeric/xyzVector.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/toolbox/sample_around/util.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 <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/recces.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <numeric/random/random_xyz.hh>
#include <numeric/random/random.hh>
#include <numeric/constants.hh>
#include <iostream>
#include <string>
#include <utility/excn/Exceptions.hh>

Typedefs
using	Matrix = numeric::xyzMatrix< Real >

Functions
core::Real	calc_base_centroid_rmsd (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2)
void	print_base_centroid_atoms (core::conformation::Residue const &rsd, std::string filename_xyz)
void	rb_entropy_test ()
void	MC_run ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("rb_entropy")

Typedef Documentation

Matrix

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

calc_base_centroid_rmsd()

core::Real calc_base_centroid_rmsd	(	core::conformation::Residue const &	rsd1,
		core::conformation::Residue const &	rsd2
	)

References dist(), create_a3b_hbs::i, average_rmsds::rmsd, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by rb_entropy_test().

main()

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

References argv, basic::options::OptionKeys::matdes::dock::dump_pdb, test.T009_Exceptions::e, basic::init(), my_main(), NEW_OPT, option, basic::options::OptionKeys::recces::base_pair::recces, and viewer_main().

MC_run()

void MC_run

(

)

References pyrosetta::create_score_function, option, options, beta_nonlocal::pose, basic::options::OptionKeys::recces::base_pair::recces, basic::Tracer::Red, runtime_assert, basic::options::OptionKeys::frags::scoring::scoring, TR, basic::options::OptionKeys::inout::dbms::user, and score::weights().

Referenced by my_main().

my_main()

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, MC_run(), option, rb_entropy_test(), and basic::options::OptionKeys::recces::base_pair::recces.

Referenced by main().

print_base_centroid_atoms()

void print_base_centroid_atoms	(	core::conformation::Residue const &	rsd,
		std::string	filename_xyz
	)

References utility::io::ozstream::close(), create_a3b_hbs::i, utility::io::ozstream::open(), and TR.

Referenced by rb_entropy_test().

rb_entropy_test()

void rb_entropy_test

(

)

References add_virtual_res(), calc_base_centroid_rmsd(), basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::cycles, create_a3b_hbs::f, lactamize::filename, ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, erraser_single_res_analysis::out, basic::options::OptionKeys::recces::out_prefix, out::path::path(), numeric::constants::d::pi, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, out::prefix(), print_base_centroid_atoms(), numeric::random::random_rotation(), numeric::random::random_translation(), basic::options::OptionKeys::remodel::rg, numeric::random::rg(), average_rmsds::rmsd, rotate_into_nucleobase_frame(), numeric::rotation_matrix(), runtime_assert, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, TR, numeric::random::uniform(), basic::options::OptionKeys::inout::dbms::user, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

Referenced by my_main().

Variable Documentation

TR

basic::Tracer TR("rb_entropy") ( "rb_entropy"  )

static

Referenced by MC_run(), print_base_centroid_atoms(), and rb_entropy_test().