rna_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/chemical/ResidueType.hh>
#include <core/chemical/rna/RNA_Info.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/geometric_solvation/GeometricSolEnergyEvaluator.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/rna/RNA_ScoringInfo.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/etable/EtableOptions.hh>
#include <core/scoring/Energies.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/io/silent/RNA_SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.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/pose/variant_util.hh>
#include <core/pack/palette/CustomBaseTypePackerPalette.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/AtomTreeMultifunc.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/MinimizerMap.hh>
#include <core/optimization/types.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/rna/util.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/PDBInfo.fwd.hh>
#include <core/pose/rna/RNA_BasePairClassifier.hh>
#include <protocols/idealize/IdealizeMover.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/rna/denovo/RNA_DeNovoProtocol.hh>
#include <protocols/rna/denovo/movers/RNA_Minimizer.hh>
#include <protocols/rna/movers/RNA_LoopCloser.hh>
#include <core/io/rna/RNA_DataReader.hh>
#include <protocols/rna/denovo/util.hh>
#include <core/pose/rna/RNA_FilteredBaseBaseInfo.hh>
#include <core/scoring/EnergyGraph.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/file/file_sys_util.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/angle.functions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <ctime>
#include <core/pack/task/ResidueLevelTask.hh>

Namespaces
	benchmark_ns

Typedefs
using	Matrix = numeric::xyzMatrix< Real >
using	GaussianParameterSet = utility::vector1< GaussianParameter >

Functions
void	figure_out_icoord_test ()
void	rna_fullatom_score_test ()
void	add_coordinate_constraints (pose::Pose &pose)
void	pack_o2prime (core::pose::Pose &pose, core::scoring::ScoreFunction const &scorefxn)
void	setup_rna_chainbreak_constraints (pose::Pose &pose)
void	get_basepair_atoms (pose::Pose &pose, Size const &i, Size const &j, std::string &atom1, std::string &atom2)
void	setup_rna_base_pair_constraints (pose::Pose &pose)
void	rna_fullatom_multiscore_test ()
void	convert_to_native_test ()
void	rna_fullatom_minimize_silent_test ()
void	rna_o2prime_test ()
void	rna_lores_score_test ()
void	rna_lores_score_silent_test ()
void	output_struct_type (utility::io::ozstream &pymol_out, pose::Pose const &pose, ObjexxFCL::FArray1D_int &struct_type, int const &match_type)
void	pymol_struct_type_test ()
void	rna_design_gap_test ()
void	print_internal_coord_test ()
void	set_ideal_geometry (pose::Pose &pose, pose::Pose const &extended_pose, chemical::ResidueTypeSetCOP &rsd_set)
void	copy_rna_torsions (Size const new_pos, Size const src_pos, pose::Pose &new_pose, pose::Pose &src_pose)
void	rna_idealize_test ()
void	print_torsions_check (pose::Pose &pose)
void	rna_torsion_check_test ()
void	rna_close_chainbreaks_test ()
Size	is_regular_helix (pose::Pose const &pose, Size const &seqpos)
Size	benchmark_ns::num_domain (0)
void	figure_out_domain_neighbors (Size const &i, core::pose::Pose const &pose)
void	figure_out_domain_map (pose::Pose const &pose)
void	absorb_surrounded_canonicals ()
void	setup_domain_list ()
void	fill_hbond_neighbors (pose::Pose const &pose)
void	output_benchmark_stuff (pose::Pose const &pose, std::string const &tag, utility::vector1< Size > const &domain_res_list, std::list< Size > const &stem_res_list, Size const &n, utility::io::ozstream &pymol_out)
void	figure_out_stems (pose::Pose &pose, std::string const &infile, utility::io::ozstream &pymol_out)
void	initialize_pymol_colors ()
void	create_rna_benchmark_test ()
void	rna_chain_closure_test ()
Real	get_jump_distance (kinematics::Jump const &jump1, kinematics::Jump const &jump2)
void	setup_crazy_fold_tree (pose::Pose &pose, core::chemical::ResidueTypeSetCOP &rsd_set)
void	rna_backbone_rebuild_test ()
void	output_sasa (std::ostream &out, pose::Pose &pose, Size const rsdno, id::AtomID_Map< Real > &atom_sasa, utility::vector1< std::string > const &atom_names, bool const &output)
void	sasa_test ()
void	env_sugar_test ()
void	print_hbonds_test ()
void	create_dihedral_constraint (core::scoring::constraints::ConstraintSetOP &cst_set, core::pose::Pose &pose, core::id::TorsionID torsion_id)
void	get_backbone_rotamers (utility::vector1< utility::vector1< Real > > &backbone_rotamers, PuckerState const &pucker1, PuckerState const &pucker2)
void	apply_backbone_rotamer (pose::Pose &pose, Size const i, utility::vector1< Real > backbone_rotamer, bool const pucker1=true, bool const pucker2=true)
void	dinucleotide_test ()
void	vary_bond_length (pose::Pose &pose, core::id::TorsionID &tor_id, core::kinematics::MoveMap &mm, core::scoring::constraints::ConstraintSetOP &cst_set)
void	vary_geometry_RNA (pose::Pose &pose, kinematics::MoveMap &mm)
void	build_next_nucleotide_test ()
void	copy_rotamerized_torsions (pose::Pose &pose, pose::Pose &source_pose, Size const i, Size const rna_torsion_number, GaussianParameterSet const &gaussian_parameter_set)
void	rotamerize_structure (pose::Pose &pose, pose::Pose &source_pose)
void	rotamerize_rna_test ()
void	calc_rmsd_test ()
void	output_sugar_geometry_parameters (pose::Pose &pose, utility::vector1< utility::vector1< std::string > > &bond_length_atoms, utility::vector1< utility::vector1< std::string > > &bond_angle_atoms, utility::io::ozstream &out)
void	put_it_in_list (utility::vector1< utility::vector1< std::string > > &my_list, std::string const &a1, std::string const &a2)
void	put_it_in_list (utility::vector1< utility::vector1< std::string > > &my_list, std::string const &a1, std::string const &a2, std::string const &a3)
void	put_it_in_list (utility::vector1< utility::vector1< std::string > > &my_list, std::string const &a1, std::string const &a2, std::string const &a3, std::string const &a4)
void	fill_sugar_atom_list (utility::vector1< std::string > &sugar_atom_list)
void	fill_bond_atoms (utility::vector1< utility::vector1< std::string > > &bond_length_atoms, utility::vector1< utility::vector1< std::string > > &bond_angle_atoms)
void	output_sugar_internal_dof (pose::Pose &pose, utility::vector1< std::string > const &sugar_atom_list, utility::io::ozstream &out)
void	replace_torsion_angles (pose::Pose &extended_pose, pose::Pose &fixed_pose, pose::Pose &pose)
void	fix_sugar_bond_angles_EMPIRICAL (pose::Pose &pose)
void	fix_sugar_bond_angles_CLOSE_BOND (pose::Pose &pose)
void	sugar_geometry_RNA_test ()
void	sugar_frag_RNA_test ()
void	color_by_geom_sol_RNA_test ()
void	color_by_lj_base_RNA_test ()
void	rna_stats_test ()
void	files_for_openMM_test ()
void	print_secstruct_test ()
void	print_all_torsions_test ()
void	rna_denovo_test ()
void	rna_design_test ()
void	create_rna_vall_torsions_test ()
void	create_bp_jump_database_test ()
void	extract_pdbs_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
ObjexxFCL::FArray1D< Size >	benchmark_ns::vanilla_helix
ObjexxFCL::FArray1D< Size >	benchmark_ns::domain_map
utility::vector1< utility::vector1< Size > >	benchmark_ns::domain_residue_list
Size	benchmark_ns::nres
FArray2D< bool >	benchmark_ns::hbonded
utility::vector1< std::string >	benchmark_ns::colors

Typedef Documentation

GaussianParameterSet

using GaussianParameterSet = utility::vector1<GaussianParameter>

Matrix

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

absorb_surrounded_canonicals()

void absorb_surrounded_canonicals

(

)

References benchmark_ns::domain_map, create_a3b_hbs::i, benchmark_ns::nres, and benchmark_ns::vanilla_helix.

Referenced by create_rna_benchmark_test().

add_coordinate_constraints()

void add_coordinate_constraints

(

pose::Pose &

pose

)

References basic::options::OptionKeys::constraints::constraints, func, create_a3b_hbs::i, create_a3b_hbs::ii, benchmark_ns::nres, and beta_nonlocal::pose.

apply_backbone_rotamer()

void apply_backbone_rotamer	(	pose::Pose &	pose,
		Size const	i,
		utility::vector1< Real >	backbone_rotamer,
		bool const	pucker1 = true,
		bool const	pucker2 = true
	)

References create_a3b_hbs::i, beta_nonlocal::pose, erraser_analysis::pucker1, and erraser_analysis::pucker2.

Referenced by build_next_nucleotide_test(), and dinucleotide_test().

build_next_nucleotide_test()

void build_next_nucleotide_test

(

)

References apply_backbone_rotamer(), basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, count, utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::rna::denovo::denovo, basic::options::OptionKeys::matdes::dock::dump_pdb, get_backbone_rotamers(), ObjexxFCL::lead_zero_string_of(), beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), benchmark_ns::nres, basic::options::OptionKeys::optimization::optimization, option, options, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::sc::quick, average_rmsds::rmsd, basic::options::OptionKeys::recces::base_pair::rmsd_cutoff, basic::options::OptionKeys::full_model::rna::rna, rna_fitted_torsion_info, docking::s, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, out::file::silent(), tag, basic::options::OptionKeys::inout::dbms::user, basic::options::OptionKeys::rna::vary_geometry, vary_geometry_RNA(), and score::weights().

Referenced by my_main().

calc_rmsd_test()

void calc_rmsd_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), docking::native_pose, basic::options::OptionKeys::optimization::optimization, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, average_rmsds::rmsd, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

color_by_geom_sol_RNA_test()

void color_by_geom_sol_RNA_test

(

)

References basic::options::OptionKeys::chemical::chemical, pyrosetta::create_score_function, basic::options::OptionKeys::rna::denovo::denovo, create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, lactamize::outfile, create_a3b_hbs::pdb_info, make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().

color_by_lj_base_RNA_test()

void color_by_lj_base_RNA_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::rna::denovo::denovo, create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, lactamize::outfile, create_a3b_hbs::pdb_info, make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().

convert_to_native_test()

void convert_to_native_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, pyrosetta.toolbox.load_ligand::fa_standard, create_a3b_hbs::i, basic::options::OptionKeys::optimization::optimization, option, basic::options::OptionKeys::motifs::output_file, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

copy_rna_torsions()

void copy_rna_torsions	(	Size const	new_pos,
		Size const	src_pos,
		pose::Pose &	new_pose,
		pose::Pose &	src_pose
	)

References create_a3b_hbs::j.

Referenced by rna_torsion_check_test().

copy_rotamerized_torsions()

void copy_rotamerized_torsions	(	pose::Pose &	pose,
		pose::Pose &	source_pose,
		Size const	i,
		Size const	rna_torsion_number,
		GaussianParameterSet const &	gaussian_parameter_set
	)

References center, utility::io::oc::cout, ObjexxFCL::format::F(), create_a3b_hbs::i, create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, numeric::principal_angle_degrees(), basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::sc::weight, and basic::options::OptionKeys::mp::visualize::width.

Referenced by rotamerize_structure().

create_bp_jump_database_test()

void create_bp_jump_database_test

(

)

References utility::io::oc::cout.

Referenced by my_main().

create_dihedral_constraint()

void create_dihedral_constraint	(	core::scoring::constraints::ConstraintSetOP &	cst_set,
		core::pose::Pose &	pose,
		core::id::TorsionID	torsion_id
	)

References basic::options::OptionKeys::constraints::constraints, func, beta_nonlocal::pose, numeric::conversions::radians(), and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by dinucleotide_test(), and rotamerize_rna_test().

create_rna_benchmark_test()

void create_rna_benchmark_test

(

)

References absorb_surrounded_canonicals(), basic::options::OptionKeys::chemical::chemical, utility::io::ozstream::close(), utility::io::oc::cout, figure_out_domain_map(), figure_out_stems(), fill_hbond_neighbors(), create_a3b_hbs::i, initialize_pymol_colors(), is_regular_helix(), benchmark_ns::nres, option, make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_domain_list(), basic::options::OptionKeys::loops::vall_file, and benchmark_ns::vanilla_helix.

Referenced by my_main().

create_rna_vall_torsions_test()

void create_rna_vall_torsions_test

(

)

References utility::io::oc::cout.

Referenced by my_main().

dinucleotide_test()

void dinucleotide_test

(

)

References apply_backbone_rotamer(), basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, count, create_dihedral_constraint(), pyrosetta::create_score_function, basic::options::OptionKeys::rna::denovo::denovo, basic::options::OptionKeys::matdes::dock::dump_pdb, get_backbone_rotamers(), create_a3b_hbs::i, ObjexxFCL::lead_zero_string_of(), beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::optimization::optimization, option, options, beta_nonlocal::pose, rna_fitted_torsion_info, docking::s, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::in::file::silent, out::file::silent(), and tag.

Referenced by my_main().

env_sugar_test()

void env_sugar_test

(

)

References create_a3b_hbs::bin, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, dist(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, oop_conformations::length, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::optimization::optimization, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

extract_pdbs_test()

void extract_pdbs_test

(

)

References utility::io::oc::cout.

Referenced by my_main().

figure_out_domain_map()

void figure_out_domain_map

(

pose::Pose const &

pose

)

References benchmark_ns::domain_map, figure_out_domain_neighbors(), create_a3b_hbs::i, benchmark_ns::nres, benchmark_ns::num_domain(), beta_nonlocal::pose, and benchmark_ns::vanilla_helix.

Referenced by create_rna_benchmark_test().

figure_out_domain_neighbors()

void figure_out_domain_neighbors	(	Size const &	i,
		core::pose::Pose const &	pose
	)

References utility::graph::Node::const_edge_list_end(), benchmark_ns::domain_map, utility::graph::Edge::get_node(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, benchmark_ns::nres, benchmark_ns::num_domain(), beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, utility_exit_with_message, and benchmark_ns::vanilla_helix.

Referenced by figure_out_domain_map().

figure_out_icoord_test()

void figure_out_icoord_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::OptionKeys::in::file::extended_pose, create_a3b_hbs::j, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, cal_NBR_radius::res_num, docking::s, basic::options::OptionKeys::relax::sequence, and ObjexxFCL::string_of().

Referenced by my_main().

figure_out_stems()

void figure_out_stems	(	pose::Pose &	pose,
		std::string const &	infile,
		utility::io::ozstream &	pymol_out
	)

References utility::io::oc::cout, benchmark_ns::domain_map, benchmark_ns::domain_residue_list, benchmark_ns::hbonded, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, benchmark_ns::nres, benchmark_ns::num_domain(), output_benchmark_stuff(), beta_nonlocal::pose, subloop_histogram::size, tag, and benchmark_ns::vanilla_helix.

Referenced by create_rna_benchmark_test().

files_for_openMM_test()

void files_for_openMM_test

(

)

References basic::options::OptionKeys::hotspot::angle, numeric::angle_radians(), basic::options::OptionKeys::chemical::chemical, utility::io::ozstream::close(), count, basic::options::OptionKeys::rna::denovo::denovo, create_a3b_hbs::i, create_a3b_hbs::j, oop_conformations::length, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, natoms(), option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, enumerate_junctions::q, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by my_main().

fill_bond_atoms()

void fill_bond_atoms	(	utility::vector1< utility::vector1< std::string > > &	bond_length_atoms,
		utility::vector1< utility::vector1< std::string > > &	bond_angle_atoms
	)

References put_it_in_list().

Referenced by sugar_geometry_RNA_test().

fill_hbond_neighbors()

void fill_hbond_neighbors

(

pose::Pose const &

pose

)

References utility::graph::Node::const_edge_list_end(), utility::graph::Edge::get_node(), benchmark_ns::hbonded, create_a3b_hbs::i, create_a3b_hbs::j, benchmark_ns::nres, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by create_rna_benchmark_test().

fill_sugar_atom_list()

void fill_sugar_atom_list

(

utility::vector1< std::string > &

sugar_atom_list

)

Referenced by sugar_geometry_RNA_test().

fix_sugar_bond_angles_CLOSE_BOND()

void fix_sugar_bond_angles_CLOSE_BOND

(

pose::Pose &

pose

)

References a, compute_difference::alpha, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, create_a3b_hbs::i, create_a3b_hbs::j, oop_conformations::length, oop_conformations::phi, PHI, beta_nonlocal::pose, THETA, oop_scan::v1, and oop_scan::v2.

fix_sugar_bond_angles_EMPIRICAL()

void fix_sugar_bond_angles_EMPIRICAL

(

pose::Pose &

pose

)

References create_a3b_hbs::i, create_a3b_hbs::j, oop_conformations::phi, PHI, beta_nonlocal::pose, numeric::conversions::radians(), and THETA.

get_backbone_rotamers()

void get_backbone_rotamers	(	utility::vector1< utility::vector1< Real > > &	backbone_rotamers,
		PuckerState const &	pucker1,
		PuckerState const &	pucker2
	)

References docking::a2, docking::b2, erraser_analysis::delta1, erraser_analysis::delta2, option, erraser_analysis::pucker1, erraser_analysis::pucker2, rna_fitted_torsion_info, and basic::options::OptionKeys::motifs::z1.

Referenced by build_next_nucleotide_test(), and dinucleotide_test().

get_basepair_atoms()

void get_basepair_atoms	(	pose::Pose &	pose,
		Size const &	i,
		Size const &	j,
		std::string &	atom1,
		std::string &	atom2
	)

References basic::options::OptionKeys::mh::match::aa1, basic::options::OptionKeys::mh::match::aa2, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, create_a3b_hbs::i, create_a3b_hbs::j, and beta_nonlocal::pose.

Referenced by setup_rna_base_pair_constraints().

get_jump_distance()

Real get_jump_distance	(	kinematics::Jump const &	jump1,
		kinematics::Jump const &	jump2
	)

References dist().

Referenced by rna_backbone_rebuild_test().

initialize_pymol_colors()

void initialize_pymol_colors

(

)

References benchmark_ns::colors.

Referenced by create_rna_benchmark_test().

is_regular_helix()

Size is_regular_helix	(	pose::Pose const &	pose,
		Size const &	seqpos
	)

References basic::options::OptionKeys::recces::base_pair::base_pair, basic::options::OptionKeys::chemical::chemical, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, beta_nonlocal::pose, and basic::options::OptionKeys::full_model::rna::rna.

Referenced by create_rna_benchmark_test().

main()

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

References argv, close_loops(), basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, basic::options::OptionKeys::cycles, basic::options::OptionKeys::motifs::data_file, basic::options::OptionKeys::magnesium::montecarlo::dump, test.T009_Exceptions::e, extract_by_sidechain_sasa_score::extract, pyrosetta.toolbox.load_ligand::fa_standard, basic::options::OptionKeys::rna::denovo::filter_lores_base_pairs, basic::options::OptionKeys::rna::denovo::heat, basic::options::OptionKeys::rna::denovo::ignore_secstruct, basic::init(), basic::options::OptionKeys::rna::denovo::jump_change_frequency, basic::options::OptionKeys::rna::denovo::jump_library_file, basic::options::OptionKeys::rna::denovo::minimize_rna, my_main(), NEW_OPT, basic::options::OptionKeys::rna::denovo::out::output_lores_silent_file, basic::options::OptionKeys::flexPepDocking::params_file, basic::options::OptionKeys::rna::denovo::relax_rna, basic::options::OptionKeys::recces::base_pair::rmsd_cutoff, simple_relax(), basic::options::OptionKeys::rna::denovo::minimize::skip_coord_constraints, local::temperature, basic::options::OptionKeys::rna::denovo::vall_torsions, basic::options::OptionKeys::rna::vary_geometry, and viewer_main().

my_main()

void* my_main

(

void *

)

References build_next_nucleotide_test(), calc_rmsd_test(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), convert_to_native_test(), create_bp_jump_database_test(), create_rna_benchmark_test(), create_rna_vall_torsions_test(), dinucleotide_test(), env_sugar_test(), utility::options::OptionKeys::options::exit, extract_by_sidechain_sasa_score::extract, extract_pdbs_test(), figure_out_icoord_test(), files_for_openMM_test(), option, print_all_torsions_test(), print_hbonds_test(), print_internal_coord_test(), print_secstruct_test(), pymol_struct_type_test(), rna_backbone_rebuild_test(), rna_chain_closure_test(), rna_close_chainbreaks_test(), rna_denovo_test(), rna_design_gap_test(), rna_design_test(), rna_fullatom_minimize_silent_test(), rna_fullatom_multiscore_test(), rna_fullatom_score_test(), rna_idealize_test(), rna_lores_score_silent_test(), rna_lores_score_test(), rna_o2prime_test(), rna_stats_test(), rna_torsion_check_test(), rotamerize_rna_test(), sasa_test(), sugar_frag_RNA_test(), and sugar_geometry_RNA_test().

Referenced by main().

output_benchmark_stuff()

void output_benchmark_stuff	(	pose::Pose const &	pose,
		std::string const &	tag,
		utility::vector1< Size > const &	domain_res_list,
		std::list< Size > const &	stem_res_list,
		Size const &	n,
		utility::io::ozstream &	pymol_out
	)

References utility::io::ozstream::close(), benchmark_ns::colors, count, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, benchmark_ns::nres, make_symmdef_file_denovo::pos, beta_nonlocal::pose, tag, and benchmark_ns::vanilla_helix.

Referenced by figure_out_stems().

output_sasa()

void output_sasa	(	std::ostream &	out,
		pose::Pose &	pose,
		Size const	rsdno,
		id::AtomID_Map< Real > &	atom_sasa,
		utility::vector1< std::string > const &	atom_names,
		bool const &	output
	)

References basic::options::OptionKeys::james::atom_names, ObjexxFCL::format::F(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, bin_torsions::output, and beta_nonlocal::pose.

Referenced by sasa_test().

output_struct_type()

void output_struct_type	(	utility::io::ozstream &	pymol_out,
		pose::Pose const &	pose,
		ObjexxFCL::FArray1D_int &	struct_type,
		int const &	match_type
	)

References create_a3b_hbs::i, benchmark_ns::nres, and beta_nonlocal::pose.

Referenced by pymol_struct_type_test().

output_sugar_geometry_parameters()

void output_sugar_geometry_parameters	(	pose::Pose &	pose,
		utility::vector1< utility::vector1< std::string > > &	bond_length_atoms,
		utility::vector1< utility::vector1< std::string > > &	bond_angle_atoms,
		utility::io::ozstream &	out
	)

References a, docking::a1, docking::a2, docking::a3, numeric::angle_radians(), compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, numeric::conversions::degrees(), create_a3b_hbs::i, oop_conformations::length, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, benchmark_ns::nres, beta_nonlocal::pose, and basic::options::OptionKeys::full_model::rna::rna.

Referenced by sugar_geometry_RNA_test().

output_sugar_internal_dof()

void output_sugar_internal_dof	(	pose::Pose &	pose,
		utility::vector1< std::string > const &	sugar_atom_list,
		utility::io::ozstream &	out
	)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, utility::io::oc::cout, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, numeric::conversions::degrees(), ObjexxFCL::format::F(), create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, PHI, beta_nonlocal::pose, and THETA.

Referenced by sugar_geometry_RNA_test().

pack_o2prime()

void pack_o2prime	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	scorefxn
	)

References utility::io::oc::cout, create_a3b_hbs::i, beta_nonlocal::pose, oop_conformations::scorefxn, and vancomycin::task.

Referenced by rna_o2prime_test().

print_all_torsions_test()

void print_all_torsions_test

(

)

References numeric::crick_equations::ALPHA(), basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, ObjexxFCL::format::F(), test.T110_numeric::I, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::full_model::rna::rna, and docking::s.

Referenced by my_main().

print_hbonds_test()

void print_hbonds_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, basic::options::OptionKeys::mp::scoring::hbond, test.T200_Scoring::hbond_set, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::optimization::optimization, basic::options::option, option, create_a3b_hbs::pdb_info, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

print_internal_coord_test()

void print_internal_coord_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, numeric::conversions::degrees(), numeric::dihedral_radians(), end, create_a3b_hbs::f, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by my_main().

print_secstruct_test()

void print_secstruct_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and docking::s.

Referenced by my_main().

print_torsions_check()

void print_torsions_check

(

pose::Pose &

pose

)

References utility::io::oc::cout, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, and beta_nonlocal::pose.

Referenced by rna_torsion_check_test().

put_it_in_list() [1/3]

void put_it_in_list	(	utility::vector1< utility::vector1< std::string > > &	my_list,
		std::string const &	a1,
		std::string const &	a2
	)

References docking::a1, docking::a2, and vec().

Referenced by fill_bond_atoms().

put_it_in_list() [2/3]

void put_it_in_list	(	utility::vector1< utility::vector1< std::string > > &	my_list,
		std::string const &	a1,
		std::string const &	a2,
		std::string const &	a3
	)

References docking::a1, docking::a2, docking::a3, and vec().

put_it_in_list() [3/3]

void put_it_in_list	(	utility::vector1< utility::vector1< std::string > > &	my_list,
		std::string const &	a1,
		std::string const &	a2,
		std::string const &	a3,
		std::string const &	a4
	)

References docking::a1, docking::a2, docking::a3, and vec().

pymol_struct_type_test()

void pymol_struct_type_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::ozstream::close(), benchmark_ns::nres, option, output_struct_type(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().

replace_torsion_angles()

void replace_torsion_angles	(	pose::Pose &	extended_pose,
		pose::Pose &	fixed_pose,
		pose::Pose &	pose
	)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, basic::options::OptionKeys::in::file::extended_pose, create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, PHI, beta_nonlocal::pose, THETA, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, oop_scan::v1, and oop_scan::v2.

Referenced by sugar_geometry_RNA_test().

rna_backbone_rebuild_test()

void rna_backbone_rebuild_test

(

)

References utility::io::oc::cout, get_jump_distance(), getline(), create_a3b_hbs::i, create_a3b_hbs::j, line, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_crazy_fold_tree(), tag, and basic::options::OptionKeys::rna::denovo::vall_torsions.

Referenced by my_main().

rna_chain_closure_test()

void rna_chain_closure_test

(

)

References utility::io::oc::cout, loops::cutpoint, create_a3b_hbs::f, create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().

rna_close_chainbreaks_test()

void rna_close_chainbreaks_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, pyrosetta::create_score_function, create_a3b_hbs::f, create_a3b_hbs::i, create_a3b_hbs::j, basic::options::OptionKeys::rna::denovo::lores_scorefxn, beta_nonlocal::mm, basic::options::OptionKeys::optimization::optimization, option, options, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().

rna_denovo_test()

void rna_denovo_test

(

)

References utility::io::oc::cout.

Referenced by my_main().

rna_design_gap_test()

void rna_design_gap_test

(

)

References basic::options::OptionKeys::chemical::chemical, create_a3b_hbs::i, create_a3b_hbs::ii, local::nstruct, out::nstruct(), option, options, lactamize::outfile, in::path::path(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, runtime_assert, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, vancomycin::task, test.T500_Packing::task_design, and local::temperature.

Referenced by my_main().

rna_design_test()

void rna_design_test

(

)

References utility::io::oc::cout.

Referenced by my_main().

rna_fullatom_minimize_silent_test()

void rna_fullatom_minimize_silent_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, pyrosetta::create_score_function, end, utility::file::file_exists(), create_a3b_hbs::i, subloop_histogram::iterator, basic::options::OptionKeys::rna::denovo::lores_scorefxn, in::file::native(), docking::native_pose, basic::options::OptionKeys::optimization::optimization, option, lactamize::outfile, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, average_rmsds::rmsd, docking::s, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, in::file::silent(), out::file::silent(), predPRE::t, and tag.

Referenced by my_main().

rna_fullatom_multiscore_test()

void rna_fullatom_multiscore_test

(

)

References basic::options::OptionKeys::chemical::chemical, count, utility::io::oc::cout, create_a3b_hbs::f, pyrosetta.toolbox.load_ligand::fa_standard, pyrosetta.distributed.cluster.base::G, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::mm, natoms(), out::nstruct(), basic::options::OptionKeys::optimization::optimization, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

rna_fullatom_score_test()

void rna_fullatom_score_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::motifs::data_file, pyrosetta.toolbox.load_ligand::fa_standard, create_a3b_hbs::i, option, options, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, docking::s, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, out::file::silent(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

rna_idealize_test()

void rna_idealize_test

(

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

rna_lores_score_silent_test()

void rna_lores_score_silent_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, pyrosetta::create_score_function, end, subloop_histogram::iterator, in::file::native(), docking::native_pose, option, lactamize::outfile, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, average_rmsds::rmsd, docking::s, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, in::file::silent(), out::file::silent(), and tag.

Referenced by my_main().

rna_lores_score_test()

void rna_lores_score_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, pyrosetta::create_score_function, create_a3b_hbs::i, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().

rna_o2prime_test()

void rna_o2prime_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, create_a3b_hbs::i, basic::options::OptionKeys::optimization::optimization, option, pack_o2prime(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, docking::s, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, and out::file::silent().

Referenced by my_main().

rna_stats_test()

void rna_stats_test

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::rna::denovo::denovo, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), docking::native_pose, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and out::file::silent().

Referenced by my_main().

rna_torsion_check_test()

void rna_torsion_check_test

(

)

References basic::options::OptionKeys::chemical::chemical, copy_rna_torsions(), utility::io::oc::cout, pyrosetta::create_score_function, create_a3b_hbs::f, in::file::fasta(), create_a3b_hbs::i, basic::options::OptionKeys::rna::denovo::lores_scorefxn, benchmark_ns::nres, option, beta_nonlocal::pose, test.T008_Serialization::pose2, print_torsions_check(), and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().

rotamerize_rna_test()

void rotamerize_rna_test

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, create_dihedral_constraint(), pyrosetta::create_score_function, basic::options::OptionKeys::rna::denovo::denovo, basic::options::OptionKeys::matdes::dock::dump_pdb, func, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, beta_nonlocal::mm, basic::options::OptionKeys::optimization::optimization, option, options, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, test.T500_Packing::rotamer_trials, rotamerize_structure(), docking::s, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::in::file::silent, vancomycin::task, basic::options::OptionKeys::inout::dbms::user, basic::options::OptionKeys::rna::vary_geometry, vary_geometry_RNA(), and score::weights().

Referenced by my_main().

rotamerize_structure()

void rotamerize_structure	(	pose::Pose &	pose,
		pose::Pose &	source_pose
	)

References numeric::crick_equations::ALPHA(), copy_rotamerized_torsions(), create_a3b_hbs::i, benchmark_ns::nres, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, rna_fitted_torsion_info, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by rotamerize_rna_test().

sasa_test()

void sasa_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, ObjexxFCL::format::F(), test.T110_numeric::I, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::optimization::optimization, option, output_sasa(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, bur_nodon_tyr::probe_radius, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

set_ideal_geometry()

void set_ideal_geometry	(	pose::Pose &	pose,
		pose::Pose const &	extended_pose,
		chemical::ResidueTypeSetCOP &	rsd_set
	)

References basic::options::OptionKeys::in::file::extended_pose, create_a3b_hbs::i, create_a3b_hbs::j, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and in::file::s().

setup_crazy_fold_tree()

void setup_crazy_fold_tree	(	pose::Pose &	pose,
		core::chemical::ResidueTypeSetCOP &	rsd_set
	)

References create_a3b_hbs::f, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by rna_backbone_rebuild_test().

setup_domain_list()

void setup_domain_list

(

)

References benchmark_ns::domain_map, benchmark_ns::domain_residue_list, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, benchmark_ns::nres, and benchmark_ns::num_domain().

Referenced by create_rna_benchmark_test().

setup_rna_base_pair_constraints()

void setup_rna_base_pair_constraints

(

pose::Pose &

pose

)

References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, dist(), func, get_basepair_atoms(), getline(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, oop_conformations::length, line, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, and beta_nonlocal::pose.

setup_rna_chainbreak_constraints()

void setup_rna_chainbreak_constraints

(

pose::Pose &

pose

)

References basic::options::OptionKeys::constraints::constraints, func, create_a3b_hbs::i, beta_nonlocal::pose, numeric::conversions::radians(), test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

sugar_frag_RNA_test()

void sugar_frag_RNA_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, create_a3b_hbs::f, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::optimization::optimization, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

sugar_geometry_RNA_test()

void sugar_geometry_RNA_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, basic::options::OptionKeys::in::file::extended_pose, fill_bond_atoms(), fill_sugar_atom_list(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::optimization::optimization, option, erraser_single_res_analysis::out, output_sugar_geometry_parameters(), output_sugar_internal_dof(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, replace_torsion_angles(), in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

vary_bond_length()

void vary_bond_length	(	pose::Pose &	pose,
		core::id::TorsionID &	tor_id,
		core::kinematics::MoveMap &	mm,
		core::scoring::constraints::ConstraintSetOP &	cst_set
	)

References basic::options::OptionKeys::constraints::constraints, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, func, beta_nonlocal::mm, PHI, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, THETA, and utility_exit_with_message.

Referenced by vary_geometry_RNA().

vary_geometry_RNA()

void vary_geometry_RNA	(	pose::Pose &	pose,
		kinematics::MoveMap &	mm
	)

References basic::options::OptionKeys::constraints::constraints, create_a3b_hbs::i, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::frags::scoring::scoring, and vary_bond_length().

Referenced by build_next_nucleotide_test(), and rotamerize_rna_test().