turner_rules_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/ResidueTypeSet.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/rna/RNA_CentroidInfo.hh>
#include <core/scoring/rna/RNA_ScoringInfo.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/scoring/Energies.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.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/id/TorsionID.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/io/silent/RNA_SilentStruct.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.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/Pose.hh>
#include <basic/options/option.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/util.hh>
#include <basic/options/option_macros.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <protocols/stepwise/StepWiseLegacyClusterer.hh>
#include <protocols/stepwise/sample_generators/StepWisePoseSampleGenerator.hh>
#include <protocols/stepwise/sample_generators/StepWisePoseCombineSampleGenerator.hh>
#include <protocols/stepwise/RigidBodySampler.hh>
#include <protocols/stepwise/InputStreamWithResidueInfo.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_BaseSugarRotamer.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_Classes.hh>
#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_RotamerGeneratorWrapper.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_RotamerGeneratorWrapper.fwd.hh>
#include <protocols/stepwise/modeler/rna/RNA_AnalyticLoopCloser.hh>
#include <protocols/stepwise/modeler/rna/RNA_LoopCloseSampler.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/tools/make_vector1.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/file/gzip_util.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.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 <fstream>
#include <iostream>
#include <string>
#include <core/util/Tracer.hh>
#include <time.h>
#include <core/options/keys/out.OptionKeys.gen.hh>
#include <core/options/keys/score.OptionKeys.gen.hh>
#include <core/options/keys/in.OptionKeys.gen.hh>
#include <core/options/keys/cluster.OptionKeys.gen.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
utility::vector1< Real >	get_suite_ideal_A_form_torsions ()
void	apply_ideal_A_form_torsions (pose::Pose &pose)
void	apply_south_syn_to_dinucleotide_pose (pose::Pose &pose)
void	initialize_base_pair (pose::Pose &pose, utility::vector1< Size > &moving_res1, utility::vector1< Size > &moving_res2)
Matrix	cycle (Matrix const &M0)
protocols::stepwise::RigidBodySamplerOP	initialize_rigid_body_sampler (utility::vector1< Size > const &moving_res1, utility::vector1< Size > const &moving_res2)
void	output_stuff (protocols::stepwise::RigidBodySamplerOP rigid_body_sampler)
void	cluster_silent_file_data (io::silent::SilentFileDataOP &sfd)
void	adjust_pose_chi (core::pose::Pose &pose, Size const res, Real const delstd)
void	expand_chi_for_silent_structs (core::io::silent::SilentFileDataOP &sfd, core::scoring::ScoreFunctionOP scorefxn)
void	split_silent_file_data (core::io::silent::SilentFileDataOP &sfd, utility::vector1< core::io::silent::SilentFileDataOP > &split_sfds)
void	define_states_test ()
Real	msd_base_doublet (Matrix const &MA, Matrix const &MB, Vector const &vA, Vector const &vB, Matrix const &moments)
Real	rmsd_base_doublet (Matrix const &MA, Matrix const &MB, Vector const &vA, Vector const &vB, Matrix const &moments)
Real	msd_base_doublet_symmetric (Matrix const &MA, Matrix const &MB, Vector const &vA, Vector const &vB, Matrix const &moments1, Matrix const &moments2)
Real	rmsd_base_doublet_symmetric (Matrix const &MA, Matrix const &MB, Vector const &vA, Vector const &vB, Matrix const &moments1, Matrix const &moments2)
Real	rmsd_over_base (conformation::Residue const &rsd1, conformation::Residue const &rsd2)
Matrix	calculate_moments (conformation::Residue const &rsd)
void	base_doublet_rmsd_test ()
void	read_rigid_body_settings (std::string const infile, utility::vector1< utility::vector1< Real > > &input_rigid_body_settings)
void	cluster_rigid_body_settings_test ()
void	finely_sample_base_pair_test ()
void	fill_v_and_M (utility::vector1< utility::vector1< Real > > &rigid_body_settings, utility::vector1< Vector > &v_list, utility::vector1< Matrix > &M_list)
void	assign_rigid_body_settings_to_clusters_test ()
void	setup_two_base_pair_pose (pose::Pose &pose)
Real	initialize_fa_rep (pose::Pose const &pose, utility::vector1< Size > const &moving_suites, scoring::ScoreFunctionOP rep_scorefxn)
bool	check_clash (pose::Pose &pose, Real const &fa_rep_score_baseline, Real const &rep_cutoff_, scoring::ScoreFunctionOP rep_scorefxn)
void	save_torsions (pose::Pose const &pose, Size const &moving_suite, utility::vector1< utility::vector1< Real > > &torsion_list)
void	save_torsion_M_v (pose::Pose const &pose, Size const &moving_suite, Size const &moving_base, utility::vector1< utility::vector1< Real > > &torsion_list, utility::vector1< Matrix > &M_list, utility::vector1< Vector > &v_list)
Size	get_bin_size ()
void	sample_new_base_in_two_base_pair_pose (pose::Pose &pose, Size const which_strand, utility::vector1< utility::vector1< Real > > &torsion_list, utility::vector1< Matrix > &M_list, utility::vector1< Vector > &v_list, scoring::ScoreFunctionOP rep_scorefxn)
void	input_torsion_M_v_lists (utility::vector1< utility::vector1< Real > > &torsion_list, utility::vector1< Matrix > &M_list, utility::vector1< Vector > &v_list, std::string const infile)
void	output_torsion_M_v_lists (utility::vector1< utility::vector1< Real > > const &torsion_list, utility::vector1< Matrix > const &M_list, utility::vector1< Vector > const &v_list, std::string const outfile)
void	apply_suite_torsions (utility::vector1< Real > const &torsion_set, pose::Pose &pose, Size const moving_suite)
void	do_the_match (utility::vector1< utility::vector1< utility::vector1< Real > > > &strand1_strand2_info_for_each_cluster, utility::vector1< Size > const &strand2_index, utility::vector1< Size > const &reference_index, pose::Pose &pose, Matrix const &moments1, Matrix const &moments2, utility::vector1< Real > strand1_torsion_set, Matrix const &M1, Vector const &v1, utility::vector1< utility::vector1< Real > > const &torsion_list, utility::vector1< Matrix > const &M_list, utility::vector1< Vector > const &v_list, utility::vector1< utility::vector1< Real > > const &reference_rigid_body_settings, pose::Pose const &ideal_pose, scoring::ScoreFunctionOP scorefxn, std::string const &silent_file, Real const rmsd_cutoff_, Real const rep_cutoff_, Real const fa_rep_score_baseline, scoring::ScoreFunctionOP rep_scorefxn)
void	brute_force_matcher (utility::vector1< utility::vector1< utility::vector1< Real > > > &strand1_strand2_info_for_each_cluster, pose::Pose &pose, utility::vector1< Real > strand1_torsion_set, utility::vector1< utility::vector1< Real > > const &torsion_list, utility::vector1< Matrix > const &M_list, utility::vector1< Vector > const &v_list, utility::vector1< utility::vector1< Real > > const &reference_rigid_body_settings, pose::Pose const &ideal_pose, scoring::ScoreFunctionOP scorefxn, scoring::ScoreFunctionOP rep_scorefxn, std::string const &silent_file)
void	initialize_for_grid_matcher (Real &box_size, Real &box_spacing, ObjexxFCL::FArray3D< utility::vector1< Size > > &grid_strand2_index, utility::vector1< Vector > const &v_list)
void	grid_matcher (utility::vector1< utility::vector1< utility::vector1< Real > > > &strand1_strand2_info_for_each_cluster, pose::Pose &pose, utility::vector1< Real > strand1_torsion_set, utility::vector1< utility::vector1< Real > > const &torsion_list, utility::vector1< Matrix > const &M_list, utility::vector1< Vector > const &v_list, utility::vector1< utility::vector1< Real > > const &reference_rigid_body_settings, pose::Pose const &ideal_pose, scoring::ScoreFunctionOP scorefxn, scoring::ScoreFunctionOP rep_scorefxn, std::string const &silent_file, Real const box_size, Real const box_spacing, ObjexxFCL::FArray3D< utility::vector1< Size > > const &grid_strand2_index)
void	output_strand1_strand2_info (std::string const &outfile_prefix, utility::vector1< utility::vector1< utility::vector1< Real > > > const &strand1_strand2_info_for_each_cluster)
void	two_base_pairs_test ()
void	setup_two_base_pair_pose_with_chainbreak (pose::Pose &pose, Size const chainbreak_suite=3)
void	minimize_poses (pose::Pose &pose, PoseList &minimize_pose_list, core::io::silent::SilentFileData &minimize_silent_file_data, core::scoring::ScoreFunctionOP scorefxn)
bool	check_filter_base_stack (pose::Pose const &pose)
void	assign_stack_faces (core::io::silent::SilentStructOP &s)
void	apply_filter_base_stack_direction (protocols::stepwise::PoseList &minimize_pose_list)
void	apply_filter_base_stack_direction (core::io::silent::SilentFileDataOP &sfd)
void	base_pair_to_base_pair_test ()
void	rna_close_loop_test ()
void	sample_state_to_state (pose::Pose &pose, Size const moving_suite, Size const chainbreak_suite, utility::vector1< Real > const &rbs_new_pair, utility::vector1< utility::vector1< Real > > &all_torsion_info)
void	two_base_pairs_via_loop_closure_test (utility::vector1< utility::vector1< Real > > const &reference_rigid_body_settings_fixed_pair, utility::vector1< utility::vector1< Real > > const &reference_rigid_body_settings_new_pair, utility::vector1< Size > const &which_rigid_body_settings_fixed_pair, utility::vector1< Size > const &which_rigid_body_settings_new_pair)
void	two_base_pairs_via_loop_closure_test ()
void	check_determinant_test ()
utility::vector1< Real >	reverse (utility::vector1< Real > const rbs)
void	reverse_rbs_test ()
void	setup_dinucleotide_pose (pose::Pose &pose)
void	output_torsion_list (std::string const &outfile, utility::vector1< utility::vector1< Real > > const &torsion_info, utility::vector1< Real > const &scores, Real const bin_size)
void	dinucleotide_test ()
void	delta_chi_correction_test ()
void	reverse_doublet_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

adjust_pose_chi()

void adjust_pose_chi	(	core::pose::Pose &	pose,
		Size const	res,
		Real const	delstd
	)

References beta_nonlocal::pose, numeric::principal_angle_degrees(), res, basic::options::OptionKeys::full_model::rna::rna, and rna_fitted_torsion_info.

Referenced by expand_chi_for_silent_structs().

apply_filter_base_stack_direction() [1/2]

void apply_filter_base_stack_direction

(

core::io::silent::SilentFileDataOP &

sfd

)

References check_filter_base_stack(), utility::io::oc::cout, end, subloop_histogram::iterator, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, sfd, and basic::options::OptionKeys::in::file::silent.

apply_filter_base_stack_direction() [2/2]

void apply_filter_base_stack_direction

(

protocols::stepwise::PoseList &

minimize_pose_list

)

References check_filter_base_stack(), subloop_histogram::iterator, and beta_nonlocal::pose.

apply_ideal_A_form_torsions()

void apply_ideal_A_form_torsions

(

pose::Pose &

pose

)

References numeric::crick_equations::ALPHA(), get_suite_ideal_A_form_torsions(), create_a3b_hbs::i, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, and rna_fitted_torsion_info.

Referenced by delta_chi_correction_test(), and initialize_base_pair().

apply_south_syn_to_dinucleotide_pose()

void apply_south_syn_to_dinucleotide_pose

(

pose::Pose &

pose

)

References utility::io::oc::cout, option, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, rna_fitted_torsion_info, and basic::options::OptionKeys::inout::dbms::user.

Referenced by initialize_base_pair(), and setup_dinucleotide_pose().

apply_suite_torsions()

void apply_suite_torsions	(	utility::vector1< Real > const &	torsion_set,
		pose::Pose &	pose,
		Size const	moving_suite
	)

References numeric::crick_equations::ALPHA(), beta_nonlocal::pose, and basic::options::OptionKeys::full_model::rna::rna.

Referenced by do_the_match(), setup_dinucleotide_pose(), setup_two_base_pair_pose_with_chainbreak(), and two_base_pairs_test().

assign_rigid_body_settings_to_clusters_test()

void assign_rigid_body_settings_to_clusters_test

(

)

References calculate_moments(), utility::io::oc::cout, fill_v_and_M(), create_a3b_hbs::i, initialize_base_pair(), create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, out::file::o(), option, erraser_single_res_analysis::out, lactamize::outfile, beta_nonlocal::pose, read_rigid_body_settings(), average_rmsds::rmsd, rmsd_base_doublet_symmetric(), basic::options::OptionKeys::recces::base_pair::rmsd_cutoff, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, oop_scan::v1, and oop_scan::v2.

Referenced by my_main().

assign_stack_faces()

void assign_stack_faces

(

core::io::silent::SilentStructOP &

s

)

References measure_params::dot(), beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, docking::s, basic::options::OptionKeys::stepwise::s1, and basic::options::OptionKeys::stepwise::s2.

Referenced by base_pair_to_base_pair_test().

base_doublet_rmsd_test()

void base_doublet_rmsd_test

(

)

References calculate_moments(), utility::io::oc::cout, initialize_base_pair(), initialize_rigid_body_sampler(), beta_nonlocal::pose, test.T008_Serialization::pose1, test.T008_Serialization::pose2, rmsd_base_doublet(), rmsd_over_base(), basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, y1, y2, basic::options::OptionKeys::motifs::z1, and basic::options::OptionKeys::motifs::z2.

Referenced by my_main().

base_pair_to_base_pair_test()

void base_pair_to_base_pair_test

(

)

References assign_stack_faces(), basic::options::OptionKeys::cluster::energy_based_clustering::cluster_radius, count, utility::io::oc::cout, pyrosetta::create_score_function, get_bin_size(), ObjexxFCL::lead_zero_string_of(), minimize_poses(), out::nstruct(), option, basic::options::OptionKeys::frags::contacts::output_all, beta_nonlocal::pose, basic::options::OptionKeys::cluster::radius, basic::options::OptionKeys::full_model::rna::rna, docking::s, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_two_base_pair_pose_with_chainbreak(), basic::options::OptionKeys::in::file::silent, out::file::silent(), tag, basic::options::OptionKeys::inout::dbms::user, and score::weights().

Referenced by my_main().

brute_force_matcher()

void brute_force_matcher	(	utility::vector1< utility::vector1< utility::vector1< Real > > > &	strand1_strand2_info_for_each_cluster,
		pose::Pose &	pose,
		utility::vector1< Real >	strand1_torsion_set,
		utility::vector1< utility::vector1< Real > > const &	torsion_list,
		utility::vector1< Matrix > const &	M_list,
		utility::vector1< Vector > const &	v_list,
		utility::vector1< utility::vector1< Real > > const &	reference_rigid_body_settings,
		pose::Pose const &	ideal_pose,
		scoring::ScoreFunctionOP	scorefxn,
		scoring::ScoreFunctionOP	rep_scorefxn,
		std::string const &	silent_file
	)

References calculate_moments(), do_the_match(), create_a3b_hbs::i, initialize_fa_rep(), utility::tools::make_vector1(), option, beta_nonlocal::pose, basic::options::OptionKeys::recces::base_pair::rmsd_cutoff, oop_conformations::scorefxn, and oop_scan::v1.

calculate_moments()

Matrix calculate_moments

(

conformation::Residue const &

rsd

)

References create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and natoms().

Referenced by assign_rigid_body_settings_to_clusters_test(), base_doublet_rmsd_test(), brute_force_matcher(), cluster_rigid_body_settings_test(), and grid_matcher().

check_clash()

bool check_clash	(	pose::Pose &	pose,
		Real const &	fa_rep_score_baseline,
		Real const &	rep_cutoff_,
		scoring::ScoreFunctionOP	rep_scorefxn
	)

References utility::io::oc::cout, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::loops::ccd::tolerance.

Referenced by dinucleotide_test(), do_the_match(), double_helix_test(), gen_pep_bb_sequential(), helix_ST(), main(), one_chain_MC_sampling(), one_chain_ST_MC(), run_pep_prep(), RunPepSpec(), and sample_new_base_in_two_base_pair_pose().

check_determinant_test()

void check_determinant_test

(

)

Referenced by my_main().

check_filter_base_stack()

bool check_filter_base_stack

(

pose::Pose const &

pose

)

References measure_params::dot(), beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::stepwise::s1, and basic::options::OptionKeys::stepwise::s2.

Referenced by apply_filter_base_stack_direction().

cluster_rigid_body_settings_test()

void cluster_rigid_body_settings_test

(

)

References calculate_moments(), utility::io::oc::cout, oop_conformations::energy, create_a3b_hbs::i, initialize_base_pair(), initialize_rigid_body_sampler(), subloop_histogram::iterator, create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), basic::options::OptionKeys::in::file::list, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, out::file::o(), option, erraser_single_res_analysis::out, lactamize::outfile, beta_nonlocal::pose, read_rigid_body_settings(), average_rmsds::rmsd, rmsd_base_doublet_symmetric(), basic::options::OptionKeys::recces::base_pair::rmsd_cutoff, basic::options::OptionKeys::full_model::rna::rna, docking::s, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, sfd, basic::options::OptionKeys::in::file::silent, out::file::silent(), tag, oop_scan::v1, and oop_scan::v2.

Referenced by my_main().

cluster_silent_file_data()

void cluster_silent_file_data

(

io::silent::SilentFileDataOP &

sfd

)

References basic::options::OptionKeys::cluster::energy_based_clustering::cluster_radius, utility::io::oc::cout, utility::tools::make_vector1(), out::nstruct(), option, beta_nonlocal::pose, basic::options::OptionKeys::cluster::radius, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::cluster::score_diff_cut, basic::options::OptionKeys::frags::scoring::scoring, sfd, basic::options::OptionKeys::in::file::silent, out::file::silent(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by define_states_test().

cycle()

Matrix cycle

(

Matrix const &

M0

)

References create_a3b_hbs::k.

define_states_test()

void define_states_test

(

)

References cluster_silent_file_data(), expand_chi_for_silent_structs(), lactamize::filename, initialize_base_pair(), initialize_rigid_body_sampler(), ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, out::file::o(), option, output_stuff(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::frags::scoring::scoring, sfd, basic::options::OptionKeys::in::file::silent, out::file::silent(), split_silent_file_data(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

delta_chi_correction_test()

void delta_chi_correction_test

(

)

References apply_ideal_A_form_torsions(), utility::io::oc::cout, pyrosetta::create_score_function, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, out::file::o(), option, erraser_single_res_analysis::out, lactamize::outfile, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, basic::options::OptionKeys::in::file::silent, basic::options::OptionKeys::inout::dbms::user, and score::weights().

Referenced by my_main().

dinucleotide_test()

void dinucleotide_test

(

)

References a3b_test::bin_size, check_clash(), count, utility::io::oc::cout, pyrosetta::create_score_function, get_bin_size(), create_a3b_hbs::i, initialize_fa_rep(), basic::options::OptionKeys::hydrate::just_score, ObjexxFCL::lead_zero_string_of(), numeric::log(), utility::tools::make_vector1(), out::file::o(), option, output_torsion_list(), vancomycin::pack, beta_nonlocal::pose, numeric::conversions::radians(), basic::options::OptionKeys::full_model::rna::rna, test.T500_Packing::rotamer_trials, docking::s, save_torsions(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_dinucleotide_pose(), sfd, basic::options::OptionKeys::in::file::silent, out::file::silent(), tag, vancomycin::task, basic::options::OptionKeys::inout::dbms::user, and score::weights().

Referenced by my_main().

do_the_match()

void do_the_match	(	utility::vector1< utility::vector1< utility::vector1< Real > > > &	strand1_strand2_info_for_each_cluster,
		utility::vector1< Size > const &	strand2_index,
		utility::vector1< Size > const &	reference_index,
		pose::Pose &	pose,
		Matrix const &	moments1,
		Matrix const &	moments2,
		utility::vector1< Real >	strand1_torsion_set,
		Matrix const &	M1,
		Vector const &	v1,
		utility::vector1< utility::vector1< Real > > const &	torsion_list,
		utility::vector1< Matrix > const &	M_list,
		utility::vector1< Vector > const &	v_list,
		utility::vector1< utility::vector1< Real > > const &	reference_rigid_body_settings,
		pose::Pose const &	ideal_pose,
		scoring::ScoreFunctionOP	scorefxn,
		std::string const &	silent_file,
		Real const	rmsd_cutoff_,
		Real const	rep_cutoff_,
		Real const	fa_rep_score_baseline,
		scoring::ScoreFunctionOP	rep_scorefxn
	)

References apply_suite_torsions(), check_clash(), utility::io::oc::cout, get_bin_size(), create_a3b_hbs::i, create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), numeric::log(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, numeric::conversions::radians(), average_rmsds::rmsd, rmsd_base_doublet_symmetric(), basic::options::OptionKeys::full_model::rna::rna, docking::s, basic::options::OptionKeys::frags::scoring::scoring, sfd, basic::options::OptionKeys::in::file::silent, tag, oop_scan::v1, and oop_scan::v2.

Referenced by brute_force_matcher(), and grid_matcher().

expand_chi_for_silent_structs()

void expand_chi_for_silent_structs	(	core::io::silent::SilentFileDataOP &	sfd,
		core::scoring::ScoreFunctionOP	scorefxn
	)

References adjust_pose_chi(), count, end, create_a3b_hbs::i, subloop_histogram::iterator, create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), beta_nonlocal::pose, docking::s, sfd, basic::options::OptionKeys::in::file::silent, and tag.

Referenced by define_states_test().

fill_v_and_M()

void fill_v_and_M	(	utility::vector1< utility::vector1< Real > > &	rigid_body_settings,
		utility::vector1< Vector > &	v_list,
		utility::vector1< Matrix > &	M_list
	)

References create_a3b_hbs::i.

Referenced by assign_rigid_body_settings_to_clusters_test().

finely_sample_base_pair_test()

void finely_sample_base_pair_test

(

)

References basic::options::OptionKeys::sample_around::cosbeta_increment, utility::io::oc::cout, initialize_base_pair(), initialize_rigid_body_sampler(), docking::native_pose, option, beta_nonlocal::pose, numeric::conversions::radians(), read_rigid_body_settings(), basic::options::OptionKeys::recces::base_pair::rmsd_cutoff, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, and out::file::silent().

Referenced by my_main().

get_bin_size()

Size get_bin_size

(

)

References a3b_test::bin_size, option, and basic::options::OptionKeys::inout::dbms::user.

Referenced by base_pair_to_base_pair_test(), dinucleotide_test(), do_the_match(), sample_new_base_in_two_base_pair_pose(), and sample_state_to_state().

get_suite_ideal_A_form_torsions()

utility::vector1< Real > get_suite_ideal_A_form_torsions

(

)

References ideal_A_form_torsions(), basic::options::OptionKeys::full_model::rna::rna, and rna_fitted_torsion_info.

Referenced by apply_ideal_A_form_torsions(), setup_dinucleotide_pose(), setup_two_base_pair_pose_with_chainbreak(), and two_base_pairs_test().

grid_matcher()

void grid_matcher	(	utility::vector1< utility::vector1< utility::vector1< Real > > > &	strand1_strand2_info_for_each_cluster,
		pose::Pose &	pose,
		utility::vector1< Real >	strand1_torsion_set,
		utility::vector1< utility::vector1< Real > > const &	torsion_list,
		utility::vector1< Matrix > const &	M_list,
		utility::vector1< Vector > const &	v_list,
		utility::vector1< utility::vector1< Real > > const &	reference_rigid_body_settings,
		pose::Pose const &	ideal_pose,
		scoring::ScoreFunctionOP	scorefxn,
		scoring::ScoreFunctionOP	rep_scorefxn,
		std::string const &	silent_file,
		Real const	box_size,
		Real const	box_spacing,
		ObjexxFCL::FArray3D< utility::vector1< Size > > const &	grid_strand2_index
	)

References ObjexxFCL::abs(), calculate_moments(), utility::io::oc::cout, do_the_match(), create_a3b_hbs::i, initialize_fa_rep(), create_a3b_hbs::j, create_a3b_hbs::k, utility::tools::make_vector1(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, basic::options::OptionKeys::recces::base_pair::rmsd_cutoff, basic::options::OptionKeys::full_model::rna::rna, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, oop_scan::v1, x, predPRE::y, and predPRE::z.

Referenced by two_base_pairs_test().

initialize_base_pair()

void initialize_base_pair	(	pose::Pose &	pose,
		utility::vector1< Size > &	moving_res1,
		utility::vector1< Size > &	moving_res2
	)

References apply_ideal_A_form_torsions(), apply_south_syn_to_dinucleotide_pose(), create_a3b_hbs::f, utility::tools::make_vector1(), option, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::frags::scoring::scoring, and beta_sc_scan::seq.

Referenced by assign_rigid_body_settings_to_clusters_test(), base_doublet_rmsd_test(), cluster_rigid_body_settings_test(), define_states_test(), and finely_sample_base_pair_test().

initialize_fa_rep()

Real initialize_fa_rep	(	pose::Pose const &	pose,
		utility::vector1< Size > const &	moving_suites,
		scoring::ScoreFunctionOP	rep_scorefxn
	)

References create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by brute_force_matcher(), dinucleotide_test(), grid_matcher(), and sample_new_base_in_two_base_pair_pose().

initialize_for_grid_matcher()

void initialize_for_grid_matcher	(	Real &	box_size,
		Real &	box_spacing,
		ObjexxFCL::FArray3D< utility::vector1< Size > > &	grid_strand2_index,
		utility::vector1< Vector > const &	v_list
	)

References utility::io::oc::cout, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, x, predPRE::y, and predPRE::z.

Referenced by two_base_pairs_test().

initialize_rigid_body_sampler()

protocols::stepwise::RigidBodySamplerOP initialize_rigid_body_sampler	(	utility::vector1< Size > const &	moving_res1,
		utility::vector1< Size > const &	moving_res2
	)

References basic::options::OptionKeys::sample_around::alpha_increment, basic::options::OptionKeys::sample_around::cosbeta_increment, hbscan::fa_rep_cutoff, basic::options::OptionKeys::sample_around::gamma_increment, basic::options::OptionKeys::stepwise::protein::n_sample, option, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::ddg::score_cutoff, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, sfd, basic::options::OptionKeys::in::file::silent, out::file::silent(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by base_doublet_rmsd_test(), cluster_rigid_body_settings_test(), define_states_test(), finely_sample_base_pair_test(), and setup_two_base_pair_pose().

input_torsion_M_v_lists()

void input_torsion_M_v_lists	(	utility::vector1< utility::vector1< Real > > &	torsion_list,
		utility::vector1< Matrix > &	M_list,
		utility::vector1< Vector > &	v_list,
		std::string const	infile
	)

References utility::io::ocstream::clear(), utility::io::oc::cout, create_a3b_hbs::i, create_a3b_hbs::k, utility::tools::make_vector1(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, skip(), and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by two_base_pairs_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, hbscan::fa_rep_cutoff, basic::options::OptionKeys::sample_around::gamma_increment, basic::init(), my_main(), basic::options::OptionKeys::stepwise::protein::n_sample, NEW_OPT, basic::options::OptionKeys::frags::contacts::output_all, basic::options::OptionKeys::recces::base_pair::rmsd_cutoff, basic::options::OptionKeys::ddg::score_cutoff, basic::options::OptionKeys::cluster::score_diff_cut, beta_sc_scan::seq, local::temperature, and viewer_main().

minimize_poses()

void minimize_poses	(	pose::Pose &	pose,
		PoseList &	minimize_pose_list,
		core::io::silent::SilentFileData &	minimize_silent_file_data,
		core::scoring::ScoreFunctionOP	scorefxn
	)

References numeric::crick_equations::ALPHA(), utility::io::oc::cout, subloop_histogram::iterator, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::optimization::optimization, option, options, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, docking::s, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, and tag.

Referenced by base_pair_to_base_pair_test().

msd_base_doublet()

Real msd_base_doublet	(	Matrix const &	MA,
		Matrix const &	MB,
		Vector const &	vA,
		Vector const &	vB,
		Matrix const &	moments
	)

References trace.

Referenced by msd_base_doublet_symmetric(), and rmsd_base_doublet().

msd_base_doublet_symmetric()

Real msd_base_doublet_symmetric	(	Matrix const &	MA,
		Matrix const &	MB,
		Vector const &	vA,
		Vector const &	vB,
		Matrix const &	moments1,
		Matrix const &	moments2
	)

References msd_base_doublet().

Referenced by rmsd_base_doublet_symmetric().

my_main()

void* my_main

(

void *

)

References assign_rigid_body_settings_to_clusters_test(), base_doublet_rmsd_test(), base_pair_to_base_pair_test(), check_determinant_test(), cluster_rigid_body_settings_test(), define_states_test(), delta_chi_correction_test(), dinucleotide_test(), utility::options::OptionKeys::options::exit, finely_sample_base_pair_test(), option, reverse_doublet_test(), reverse_rbs_test(), rna_close_loop_test(), two_base_pairs_test(), and two_base_pairs_via_loop_closure_test().

Referenced by main().

output_strand1_strand2_info()

void output_strand1_strand2_info	(	std::string const &	outfile_prefix,
		utility::vector1< utility::vector1< utility::vector1< Real > > > const &	strand1_strand2_info_for_each_cluster
	)

References utility::io::oc::cout, utility::file::gzip(), create_a3b_hbs::i, info(), create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, erraser_single_res_analysis::out, and lactamize::outfile.

Referenced by two_base_pairs_test().

output_stuff()

void output_stuff

(

protocols::stepwise::RigidBodySamplerOP

rigid_body_sampler

)

References utility::io::ozstream::close(), utility::io::oc::cout, out::file::o(), option, erraser_single_res_analysis::out, and lactamize::outfile.

Referenced by define_states_test().

output_torsion_list()

void output_torsion_list	(	std::string const &	outfile,
		utility::vector1< utility::vector1< Real > > const &	torsion_info,
		utility::vector1< Real > const &	scores,
		Real const	bin_size
	)

References a3b_test::bin_size, create_a3b_hbs::i, info(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, erraser_single_res_analysis::out, lactamize::outfile, numeric::conversions::radians(), and legacy_score_vs_rmsd::scores.

Referenced by dinucleotide_test().

output_torsion_M_v_lists()

void output_torsion_M_v_lists	(	utility::vector1< utility::vector1< Real > > const &	torsion_list,
		utility::vector1< Matrix > const &	M_list,
		utility::vector1< Vector > const &	v_list,
		std::string const	outfile
	)

References create_a3b_hbs::i, create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, erraser_single_res_analysis::out, lactamize::outfile, and utility_exit_with_message.

Referenced by two_base_pairs_test().

read_rigid_body_settings()

void read_rigid_body_settings	(	std::string const	infile,
		utility::vector1< utility::vector1< Real > > &	input_rigid_body_settings
	)

References utility::io::oc::cerr, create_a3b_hbs::i, gaussian-sampling::input, basic::options::OptionKeys::in::file::silent, skip(), and utility_exit_with_message.

Referenced by assign_rigid_body_settings_to_clusters_test(), cluster_rigid_body_settings_test(), finely_sample_base_pair_test(), reverse_rbs_test(), rna_close_loop_test(), setup_two_base_pair_pose(), two_base_pairs_test(), and two_base_pairs_via_loop_closure_test().

reverse()

utility::vector1< Real > reverse

(

utility::vector1< Real > const

rbs

)

References compute_difference::alpha, basic::options::OptionKeys::corrections::beta, loops::gamma, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and numeric::xyzMatrix< T >::transposed().

Referenced by CrystFFTDock::apply(), compare_gpu_result_against_cpu(), DomainDescription::compatible_sheet(), design_test(), TCDock::dump_pdb(), TCDock::gather_hits(), binder::getQualifiedNameAsStringLLVM5Fix(), TCDock::init(), TCDock::justone(), register_options(), apps::pilot::frankdt::reverse_motif(), reverse_rbs_test(), TCDock::run(), CapriTotalEnergy::score_experimental_constraints(), and TCDock::TCDock().

reverse_doublet_test()

void reverse_doublet_test

(

)

References end, create_a3b_hbs::f, subloop_histogram::iterator, option, beta_nonlocal::pose, docking::s, basic::options::OptionKeys::in::file::silent, in::file::silent(), out::file::silent(), and tag.

Referenced by my_main().

reverse_rbs_test()

void reverse_rbs_test

(

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, out::file::o(), option, erraser_single_res_analysis::out, lactamize::outfile, read_rigid_body_settings(), and reverse().

Referenced by my_main().

rmsd_base_doublet()

Real rmsd_base_doublet	(	Matrix const &	MA,
		Matrix const &	MB,
		Vector const &	vA,
		Vector const &	vB,
		Matrix const &	moments
	)

References msd_base_doublet().

Referenced by base_doublet_rmsd_test().

rmsd_base_doublet_symmetric()

Real rmsd_base_doublet_symmetric	(	Matrix const &	MA,
		Matrix const &	MB,
		Vector const &	vA,
		Vector const &	vB,
		Matrix const &	moments1,
		Matrix const &	moments2
	)

References msd_base_doublet_symmetric().

Referenced by assign_rigid_body_settings_to_clusters_test(), cluster_rigid_body_settings_test(), and do_the_match().

rmsd_over_base()

Real rmsd_over_base	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)

References create_a3b_hbs::i, natoms(), test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by base_doublet_rmsd_test().

rna_close_loop_test()

void rna_close_loop_test

(

)

References apply_rigid_body_settings(), option, beta_nonlocal::pose, read_rigid_body_settings(), basic::options::OptionKeys::full_model::rna::rna, and setup_two_base_pair_pose_with_chainbreak().

Referenced by my_main().

sample_new_base_in_two_base_pair_pose()

void sample_new_base_in_two_base_pair_pose	(	pose::Pose &	pose,
		Size const	which_strand,
		utility::vector1< utility::vector1< Real > > &	torsion_list,
		utility::vector1< Matrix > &	M_list,
		utility::vector1< Vector > &	v_list,
		scoring::ScoreFunctionOP	rep_scorefxn
	)

References a3b_test::bin_size, check_clash(), count, utility::io::oc::cout, get_bin_size(), initialize_fa_rep(), utility::tools::make_vector1(), option, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, save_torsion_M_v(), and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by two_base_pairs_test().

sample_state_to_state()

void sample_state_to_state	(	pose::Pose &	pose,
		Size const	moving_suite,
		Size const	chainbreak_suite,
		utility::vector1< Real > const &	rbs_new_pair,
		utility::vector1< utility::vector1< Real > > &	all_torsion_info
	)

References pyrosetta::create_score_function, get_bin_size(), in::file::native(), docking::native_pose, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, out::file::silent(), basic::options::OptionKeys::inout::dbms::user, and score::weights().

Referenced by two_base_pairs_via_loop_closure_test().

save_torsion_M_v()

void save_torsion_M_v	(	pose::Pose const &	pose,
		Size const &	moving_suite,
		Size const &	moving_base,
		utility::vector1< utility::vector1< Real > > &	torsion_list,
		utility::vector1< Matrix > &	M_list,
		utility::vector1< Vector > &	v_list
	)

References basic::options::OptionKeys::in::file::centroid, beta_nonlocal::pose, and save_torsions().

Referenced by sample_new_base_in_two_base_pair_pose().

save_torsions()

void save_torsions	(	pose::Pose const &	pose,
		Size const &	moving_suite,
		utility::vector1< utility::vector1< Real > > &	torsion_list
	)

References numeric::crick_equations::ALPHA(), beta_nonlocal::pose, and basic::options::OptionKeys::full_model::rna::rna.

Referenced by dinucleotide_test(), double_helix_test(), main(), MC_run(), and save_torsion_M_v().

setup_dinucleotide_pose()

void setup_dinucleotide_pose

(

pose::Pose &

pose

)

References apply_south_syn_to_dinucleotide_pose(), apply_suite_torsions(), utility::io::oc::cout, get_suite_ideal_A_form_torsions(), create_a3b_hbs::i, option, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, rna_fitted_torsion_info, beta_sc_scan::seq, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::in::file::silent, and basic::options::OptionKeys::inout::dbms::user.

Referenced by dinucleotide_test().

setup_two_base_pair_pose()

void setup_two_base_pair_pose

(

pose::Pose &

pose

)

References utility::io::oc::cout, create_a3b_hbs::f, create_a3b_hbs::i, initialize_rigid_body_sampler(), utility::tools::make_vector1(), option, beta_nonlocal::pose, read_rigid_body_settings(), basic::options::OptionKeys::full_model::rna::rna, rna_fitted_torsion_info, and basic::options::OptionKeys::in::file::silent.

Referenced by two_base_pairs_test().

setup_two_base_pair_pose_with_chainbreak()

void setup_two_base_pair_pose_with_chainbreak	(	pose::Pose &	pose,
		Size const	chainbreak_suite = 3
	)

References apply_suite_torsions(), utility::io::oc::cout, create_a3b_hbs::f, get_suite_ideal_A_form_torsions(), create_a3b_hbs::i, option, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, rna_fitted_torsion_info, basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::in::file::silent, and basic::options::OptionKeys::inout::dbms::user.

Referenced by base_pair_to_base_pair_test(), rna_close_loop_test(), and two_base_pairs_via_loop_closure_test().

split_silent_file_data()

void split_silent_file_data	(	core::io::silent::SilentFileDataOP &	sfd,
		utility::vector1< core::io::silent::SilentFileDataOP > &	split_sfds
	)

References end, subloop_histogram::iterator, sfd, and basic::options::OptionKeys::in::file::silent.

Referenced by define_states_test().

two_base_pairs_test()

void two_base_pairs_test

(

)

References apply_suite_torsions(), utility::io::oc::cout, pyrosetta::create_score_function, get_suite_ideal_A_form_torsions(), grid_matcher(), initialize_for_grid_matcher(), input_torsion_M_v_lists(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, out::file::o(), option, output_strand1_strand2_info(), output_torsion_M_v_lists(), beta_nonlocal::pose, read_rigid_body_settings(), basic::options::OptionKeys::full_model::rna::rna, sample_new_base_in_two_base_pair_pose(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_two_base_pair_pose(), basic::options::OptionKeys::in::file::silent, out::file::silent(), basic::options::OptionKeys::inout::dbms::user, and score::weights().

Referenced by my_main().

two_base_pairs_via_loop_closure_test() [1/2]

void two_base_pairs_via_loop_closure_test

(

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, read_rigid_body_settings(), two_base_pairs_via_loop_closure_test(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

two_base_pairs_via_loop_closure_test() [2/2]

void two_base_pairs_via_loop_closure_test	(	utility::vector1< utility::vector1< Real > > const &	reference_rigid_body_settings_fixed_pair,
		utility::vector1< utility::vector1< Real > > const &	reference_rigid_body_settings_new_pair,
		utility::vector1< Size > const &	which_rigid_body_settings_fixed_pair,
		utility::vector1< Size > const &	which_rigid_body_settings_new_pair
	)

References apply_rigid_body_settings(), utility::io::oc::cout, create_a3b_hbs::i, info(), create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, out::file::o(), option, erraser_single_res_analysis::out, lactamize::outfile, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, sample_state_to_state(), and setup_two_base_pair_pose_with_chainbreak().

Referenced by my_main(), and two_base_pairs_via_loop_closure_test().