turner_test_double_helix.cc File Reference

#include <devel/init.hh>
#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/ScoringManager.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 <core/pose/util.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/import_pose/import_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/sampling/rna/util.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/random/random.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 <math.h>
#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 <basic/options/keys/cluster.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix
typedef std::pair< unsigned int, float[4]>	RNA_scores
typedef std::pair< core::Size, utility::vector1< utility::vector1< Real > > >	Torsions

Functions
utility::vector1< Real >	get_suite_ideal_A_form_torsions ()
void	apply_suite_torsions (utility::vector1< Real > const &torsion_set, pose::Pose &pose, Size const moving_suite, bool const sample_3prime_pucker=true)
void	initialize_o2prime_pack (pose::Pose const &pose, scoring::ScoreFunctionOP const scorefxn, scoring::ScoreFunctionOP o2prime_pack_scorefxn, pack::task::PackerTaskOP o2prime_pack_task)
Real	create_random_angle_from_range (Real lower_bound=0, Real upper_bound=360)
Real	create_random_angle_from_range_list (utility::vector1< std::pair< Real, Real > > const &range_list)
void	create_random_torsions (utility::vector1< Real > &torsion_list, bool const modify_pucker=true)
void	sample_near_current_torsion (utility::vector1< Real > &torsion_list, Real const stddev, utility::vector1< Real > const &upper_bound, utility::vector1< Real > const &lower_bound, bool const modify_pucker=true, bool const cyclic=true)
void	output_torsion_list (std::string const &outfile, utility::vector1< utility::vector1< Real > > const &data_list, Real const volume_factor)
void	read_rigid_body_settings (std::string const infile, utility::vector1< utility::vector1< Real > > &input_rigid_body_settings)
void	apply_rigid_body_settings (pose::Pose &pose, pose::Pose const &pose_start, utility::vector1< Size > moving_res, Real const alpha, Real const beta, Real const gamma, Real const x, Real const y, Real const z)
void	setup_double_helix_pose (pose::Pose &pose)
Size	score2bin (Real const score, Real const min_score, Real const max_score, Real const bin_size)
void	update_system (utility::vector1< Real > &torsion_list, Real const sampling_range)
void	helix_minimize (core::pose::Pose &pose, scoring::ScoreFunctionOP scorefxn)
Real	rmsd_compute (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
bool	is_atom_clash (core::pose::Pose const &pose, Real const dist_cutoff=1.2)
Size	torsion2bin (Real const torsion, Size const total_bin)
bool	pose_list_compare (std::pair< pose::Pose, Real > const &i, std::pair< pose::Pose, Real > const &j)
void	double_helix_test ()
void	helix_ST ()
void	minimize_and_score ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static const chemical::rna::RNA_FittedTorsionInfo	rna_fitted_torsion_info

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

RNA_scores

typedef std::pair< unsigned int, float[4]> RNA_scores

Torsions

typedef std::pair< core::Size, utility::vector1< utility::vector1< Real > > > Torsions

Function Documentation

apply_rigid_body_settings()

void apply_rigid_body_settings	(	pose::Pose &	pose,
		pose::Pose const &	pose_start,
		utility::vector1< Size >	moving_res,
		Real const	alpha,
		Real const	beta,
		Real const	gamma,
		Real const	x,
		Real const	y,
		Real const	z
	)

References compute_difference::alpha, basic::options::OptionKeys::corrections::beta, loops::gamma, beta_nonlocal::pose, pyrosetta.bindings.pose::rotate(), beta_nonlocal::translate, x, predPRE::y, and predPRE::z.

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

apply_suite_torsions()

void apply_suite_torsions	(	utility::vector1< Real > const &	torsion_set,
		pose::Pose &	pose,
		Size const	moving_suite,
		bool const	sample_3prime_pucker = true
	)

References beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, and rna_fitted_torsion_info.

Referenced by double_helix_test(), helix_ST(), and setup_double_helix_pose().

create_random_angle_from_range()

Real create_random_angle_from_range	(	Real	lower_bound = 0,
		Real	upper_bound = 360
	)

References numeric::random::rg(), and numeric::random::RandomGenerator::uniform().

Referenced by create_random_torsions(), and update_system().

create_random_angle_from_range_list()

Real create_random_angle_from_range_list

(

utility::vector1< std::pair< Real, Real > > const &

range_list

)

References basic::options::OptionKeys::hotspot::angle, create_a3b_hbs::i, numeric::random::rg(), and numeric::random::RandomGenerator::uniform().

create_random_torsions()

void create_random_torsions	(	utility::vector1< Real > &	torsion_list,
		bool const	modify_pucker = true
	)

References compute_difference::alpha, basic::options::OptionKeys::corrections::beta, create_random_angle_from_range(), loops::gamma, numeric::random::rg(), rna_fitted_torsion_info, and numeric::random::RandomGenerator::uniform().

Referenced by update_system().

double_helix_test()

void double_helix_test

(

)

References apply_suite_torsions(), create_a3b_hbs::bin, a3b_test::bin_size, check_clash(), utility::io::oc::cout, pyrosetta::create_score_function, cycle(), basic::options::OptionKeys::optE::fixed, get_suite_ideal_A_form_torsions(), 3d_histogram::hist, create_a3b_hbs::i, initialize_o2prime_pack(), create_a3b_hbs::j, create_a3b_hbs::k, basic::options::OptionKeys::relax::range::kT, SmotifHasher::min_score, basic::options::OptionKeys::recces::n_cycle, out::file::o(), option, test.T008_Serialization::oss, erraser_single_res_analysis::out, rna_rosetta_ready_set::out_pdb, lactamize::outfile, output_pdb(), vancomycin::pack, beta_nonlocal::pose, numeric::random::rg(), basic::options::OptionKeys::full_model::rna::rna, local::sampling_range, save_torsions(), create_a3b_hbs::score, score2bin(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, basic::options::OptionKeys::relax::sequence, setup_double_helix_pose(), show(), vancomycin::task, numeric::random::RandomGenerator::uniform(), and update_system().

Referenced by my_main().

get_suite_ideal_A_form_torsions()

utility::vector1< Real > get_suite_ideal_A_form_torsions

(

)

References create_a3b_hbs::i, ideal_A_form_torsions(), basic::options::OptionKeys::full_model::rna::rna, and rna_fitted_torsion_info.

Referenced by double_helix_test(), helix_ST(), setup_double_helix_pose(), and update_system().

helix_minimize()

void helix_minimize	(	core::pose::Pose &	pose,
		scoring::ScoreFunctionOP	scorefxn
	)

References beta_nonlocal::mm, beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by minimize_and_score().

helix_ST()

void helix_ST

(

)

References apply_suite_torsions(), create_a3b_hbs::bin, a3b_test::bin_size, check_clash(), utility::io::oc::cout, pyrosetta::create_score_function, cycle(), basic::options::OptionKeys::optE::fixed, get_suite_ideal_A_form_torsions(), 3d_histogram::hist, create_a3b_hbs::i, initialize_o2prime_pack(), create_a3b_hbs::j, basic::options::OptionKeys::relax::range::kT, SmotifHasher::min_score, basic::options::OptionKeys::recces::n_cycle, out::file::o(), option, test.T008_Serialization::oss, erraser_single_res_analysis::out, rna_rosetta_ready_set::out_pdb, lactamize::outfile, output_pdb(), vancomycin::pack, beta_nonlocal::pose, numeric::random::rg(), basic::options::OptionKeys::full_model::rna::rna, local::sampling_range, create_a3b_hbs::score, score2bin(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, basic::options::OptionKeys::relax::sequence, setup_double_helix_pose(), show(), vancomycin::task, numeric::random::uniform(), numeric::random::RandomGenerator::uniform(), update_system(), and utility_exit_with_message.

Referenced by my_main().

initialize_o2prime_pack()

void initialize_o2prime_pack	(	pose::Pose const &	pose,
		scoring::ScoreFunctionOP const	scorefxn,
		scoring::ScoreFunctionOP	o2prime_pack_scorefxn,
		pack::task::PackerTaskOP	o2prime_pack_task
	)

References create_a3b_hbs::i, vancomycin::pack, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and vancomycin::task.

Referenced by double_helix_test(), and helix_ST().

is_atom_clash()

bool is_atom_clash	(	core::pose::Pose const &	pose,
		Real const	dist_cutoff = 1.2
	)

References dist_cutoff, create_a3b_hbs::i, create_a3b_hbs::j, natoms(), and beta_nonlocal::pose.

main()

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

References argv, check_clash(), test.T009_Exceptions::e, basic::init(), basic::options::OptionKeys::relax::range::kT, my_main(), basic::options::OptionKeys::recces::n_cycle, NEW_OPT, rna_rosetta_ready_set::out_pdb, save_torsions(), beta_sc_scan::seq, and viewer_main().

minimize_and_score()

void minimize_and_score

(

)

References utility::io::oc::cout, pyrosetta::create_score_function, helix_minimize(), option, rna_rosetta_ready_set::out_pdb, output_pdb(), vancomycin::pack, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_double_helix_pose(), show(), and vancomycin::task.

Referenced by my_main().

my_main()

void* my_main

(

void *

)

References double_helix_test(), utility::options::OptionKeys::options::exit, helix_ST(), minimize_and_score(), and option.

Referenced by main().

output_torsion_list()

void output_torsion_list	(	std::string const &	outfile,
		utility::vector1< utility::vector1< Real > > const &	data_list,
		Real const	volume_factor
	)

References create_a3b_hbs::i, info(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, erraser_single_res_analysis::out, and lactamize::outfile.

pose_list_compare()

bool pose_list_compare	(	std::pair< pose::Pose, Real > const &	i,
		std::pair< pose::Pose, Real > const &	j
	)

References create_a3b_hbs::i, and create_a3b_hbs::j.

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 setup_double_helix_pose().

rmsd_compute()

Real rmsd_compute	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

References create_a3b_hbs::i, create_a3b_hbs::j, test.T008_Serialization::pose1, test.T008_Serialization::pose2, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

sample_near_current_torsion()

void sample_near_current_torsion	(	utility::vector1< Real > &	torsion_list,
		Real const	stddev,
		utility::vector1< Real > const &	upper_bound,
		utility::vector1< Real > const &	lower_bound,
		bool const	modify_pucker = true,
		bool const	cyclic = true
	)

References cyclic, numeric::random::RandomGenerator::gaussian(), create_a3b_hbs::i, numeric::random::rg(), rna_fitted_torsion_info, numeric::random::uniform(), and numeric::random::RandomGenerator::uniform().

Referenced by update_system().

score2bin()

Size score2bin	(	Real const	score,
		Real const	min_score,
		Real const	max_score,
		Real const	bin_size
	)

References a3b_test::bin_size, SmotifHasher::min_score, and utility_exit_with_message.

Referenced by double_helix_test(), and helix_ST().

setup_double_helix_pose()

void setup_double_helix_pose

(

pose::Pose &

pose

)

References apply_rigid_body_settings(), 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, read_rigid_body_settings(), basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::in::file::silent, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by double_helix_test(), helix_ST(), and minimize_and_score().

torsion2bin()

Size torsion2bin	(	Real const	torsion,
		Size const	total_bin
	)

References internal_coordinates::torsion().

update_system()

void update_system	(	utility::vector1< Real > &	torsion_list,
		Real const	sampling_range
	)

References create_random_angle_from_range(), create_random_torsions(), get_suite_ideal_A_form_torsions(), create_a3b_hbs::i, option, sample_near_current_torsion(), and local::sampling_range.

Referenced by double_helix_test(), and helix_ST().

Variable Documentation

rna_fitted_torsion_info

const chemical::rna::RNA_FittedTorsionInfo rna_fitted_torsion_info

static

Referenced by adjust_pose_chi(), apply_ideal_A_form_torsions(), apply_south_syn_to_dinucleotide_pose(), apply_suite_torsions(), build_next_nucleotide_test(), create_random_torsions(), dinucleotide_test(), get_backbone_rotamers(), get_suite_ideal_A_form_torsions(), rotamerize_structure(), sample_near_current_torsion(), setup_dinucleotide_pose(), setup_two_base_pair_pose(), and setup_two_base_pair_pose_with_chainbreak().