turner_test_one_chain.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/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/util.hh>
#include <basic/options/option_macros.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/stepwise/sampling/util.hh>
#include <protocols/rna/denovo/RNA_SuiteAssign.hh>
#include <protocols/stepwise/StepWiseLegacyClusterer.hh>
#include <protocols/stepwise/sampling/rna/util.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/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 <utility/excn/Exceptions.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <math.h>
#include <time.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>

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

Functions
utility::vector1< Real >	get_suite_ideal_A_form_torsions ()
void	apply_nucleoside_torsion (utility::vector1< Real > const &torsion_set, pose::Pose &pose, Size const moving_res)
void	apply_suite_torsion (utility::vector1< Real > const &torsion_set, pose::Pose &pose, Size const moving_suite, bool const sample_3prime_pucker=true)
void	setup_one_chain_pose (pose::Pose &pose, bool is_virtualize=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_suite_torsion (utility::vector1< Real > &torsion_list)
void	create_random_nucleoside_torsion (utility::vector1< Real > &torsion_list)
void	sample_near_suite_torsion (utility::vector1< Real > &torsion_list, Real const stddev)
void	sample_near_nucleoside_torsion (utility::vector1< Real > &torsion_list, Real const stddev)
Size	score2bin (Real const score, Real const min_score, Real const max_score, Real const bin_size)
Real	rmsd_compute (core::pose::Pose const &pose, core::pose::Pose const &ref_pose)
void	one_chain_MC_sampling ()
void	one_chain_ST_MC ()
utility::vector1< Real >	id2torsion (Size torsion_id)
Size	torsion2id (utility::vector1< Real > const &nucleoside_torsion, utility::vector1< Real > const &suite_torsion)
utility::vector1< Real >	torsion_convert (utility::vector1< Real > const &nucleoside_torsion, utility::vector1< Real > const &suite_torsion)
bool	sort_mine (std::pair< Size, Size > const i, std::pair< Size, Size > const j)
void	torsion2decoy ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static const chemical::rna::RNA_FittedTorsionInfo	rna_fitted_torsion_info

Typedef Documentation

RNA_scores

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

Function Documentation

apply_nucleoside_torsion()

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

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

Referenced by one_chain_MC_sampling(), one_chain_ST_MC(), setup_one_chain_pose(), and torsion2decoy().

apply_suite_torsion()

void apply_suite_torsion	(	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 one_chain_MC_sampling(), one_chain_ST_MC(), setup_one_chain_pose(), and torsion2decoy().

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_nucleoside_torsion(), and create_random_suite_torsion().

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_nucleoside_torsion()

void create_random_nucleoside_torsion

(

utility::vector1< Real > &

torsion_list

)

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

Referenced by one_chain_MC_sampling(), and one_chain_ST_MC().

create_random_suite_torsion()

void create_random_suite_torsion

(

utility::vector1< Real > &

torsion_list

)

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 one_chain_MC_sampling(), and one_chain_ST_MC().

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 id2torsion(), one_chain_MC_sampling(), one_chain_ST_MC(), setup_one_chain_pose(), and torsion2id().

id2torsion()

utility::vector1< Real > id2torsion

(

Size

torsion_id

)

References basic::options::OptionKeys::hotspot::angle, get_suite_ideal_A_form_torsions(), create_a3b_hbs::i, numeric::remainder(), and rna_fitted_torsion_info.

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 one_chain_MC_sampling(), and one_chain_ST_MC().

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::stepwise::protein::n_sample, NEW_OPT, basic::options::OptionKeys::ddg::score_cutoff, beta_sc_scan::seq, and viewer_main().

my_main()

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, one_chain_MC_sampling(), one_chain_ST_MC(), and option.

Referenced by main().

one_chain_MC_sampling()

void one_chain_MC_sampling

(

)

References apply_nucleoside_torsion(), apply_suite_torsion(), create_a3b_hbs::bin, a3b_test::bin_size, check_clash(), count, utility::io::oc::cout, create_random_nucleoside_torsion(), create_random_suite_torsion(), pyrosetta::create_score_function, 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::stepwise::protein::n_sample, out::file::o(), option, test.T008_Serialization::oss, erraser_single_res_analysis::out, lactamize::outfile, vancomycin::pack, beta_nonlocal::pose, numeric::random::rg(), basic::options::OptionKeys::full_model::rna::rna, sample_near_nucleoside_torsion(), sample_near_suite_torsion(), create_a3b_hbs::score, score2bin(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_one_chain_pose(), show(), vancomycin::task, numeric::random::RandomGenerator::uniform(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

one_chain_ST_MC()

void one_chain_ST_MC

(

)

References apply_nucleoside_torsion(), apply_suite_torsion(), create_a3b_hbs::bin, a3b_test::bin_size, check_clash(), count, utility::io::oc::cout, create_random_nucleoside_torsion(), create_random_suite_torsion(), pyrosetta::create_score_function, get_suite_ideal_A_form_torsions(), 3d_histogram::hist, create_a3b_hbs::i, initialize_o2prime_pack(), SmotifHasher::min_score, basic::options::OptionKeys::stepwise::protein::n_sample, out::file::o(), utility::io::ozstream::open(), option, erraser_single_res_analysis::out, lactamize::outfile, vancomycin::pack, beta_nonlocal::pose, numeric::random::rg(), basic::options::OptionKeys::full_model::rna::rna, sample_near_nucleoside_torsion(), sample_near_suite_torsion(), create_a3b_hbs::score, score2bin(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_one_chain_pose(), show(), vancomycin::task, numeric::random::uniform(), numeric::random::RandomGenerator::uniform(), and utility_exit_with_message.

Referenced by my_main().

rmsd_compute()

Real rmsd_compute	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	ref_pose
	)

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

sample_near_nucleoside_torsion()

void sample_near_nucleoside_torsion	(	utility::vector1< Real > &	torsion_list,
		Real const	stddev
	)

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

Referenced by one_chain_MC_sampling(), and one_chain_ST_MC().

sample_near_suite_torsion()

void sample_near_suite_torsion	(	utility::vector1< Real > &	torsion_list,
		Real const	stddev
	)

References 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 one_chain_MC_sampling(), and one_chain_ST_MC().

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 one_chain_MC_sampling(), and one_chain_ST_MC().

setup_one_chain_pose()

void setup_one_chain_pose	(	pose::Pose &	pose,
		bool	is_virtualize = true
	)

References apply_nucleoside_torsion(), apply_suite_torsion(), get_suite_ideal_A_form_torsions(), create_a3b_hbs::i, option, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, beta_sc_scan::seq, basic::options::OptionKeys::relax::sequence, and basic::options::OptionKeys::in::file::silent.

Referenced by one_chain_MC_sampling(), one_chain_ST_MC(), and torsion2decoy().

sort_mine()

bool sort_mine	(	std::pair< Size, Size > const	i,
		std::pair< Size, Size > const	j
	)

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

torsion2decoy()

void torsion2decoy

(

)

References apply_nucleoside_torsion(), apply_suite_torsion(), utility::io::oc::cout, create_a3b_hbs::i, option, beta_nonlocal::pose, setup_one_chain_pose(), and internal_coordinates::torsion().

torsion2id()

Size torsion2id	(	utility::vector1< Real > const &	nucleoside_torsion,
		utility::vector1< Real > const &	suite_torsion
	)

References ObjexxFCL::abs(), angle_diff(), get_suite_ideal_A_form_torsions(), create_a3b_hbs::i, basic::options::OptionKeys::mh::harvest::multiplier, and rna_fitted_torsion_info.

torsion_convert()

utility::vector1< Real > torsion_convert	(	utility::vector1< Real > const &	nucleoside_torsion,
		utility::vector1< Real > const &	suite_torsion
	)

References create_a3b_hbs::i.

Variable Documentation

rna_fitted_torsion_info

const chemical::rna::RNA_FittedTorsionInfo rna_fitted_torsion_info

static

Referenced by apply_nucleoside_torsion(), apply_suite_torsion(), create_random_nucleoside_torsion(), create_random_suite_torsion(), get_suite_ideal_A_form_torsions(), id2torsion(), sample_near_nucleoside_torsion(), sample_near_suite_torsion(), and torsion2id().