turner_two_chain.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/pose/rna/RNA_SuiteName.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/scoring/dna/base_geometry.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/StepWiseLegacyClusterer.hh>
#include <core/pose/rna/RNA_IdealCoord.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 <array>
#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 utility::vector1< float >	float_vec
typedef std::array< float, 5 >	Backbone_Torsion
typedef std::array< float, 2 >	Nucleoside_Torsion

Functions
std::pair< Backbone_Torsion, Nucleoside_Torsion >	ideal_A_form_torsions ()
void	apply_backbone (Backbone_Torsion const &backbone, pose::Pose &pose, Size const suite)
void	apply_nucleoside (Nucleoside_Torsion const &nucleoside, pose::Pose &pose, Size const residue)
void	apply_all (utility::vector1< Backbone_Torsion > const &backbones, utility::vector1< Nucleoside_Torsion > const &nucleosides, pose::Pose &pose)
void	get_backbone (Backbone_Torsion &backbone, pose::Pose const &pose, Size const suite)
void	get_nucleoside (Nucleoside_Torsion &nucleoside, pose::Pose const &pose, Size const residue)
void	get_all (utility::vector1< Backbone_Torsion > &backbones, utility::vector1< Nucleoside_Torsion > &nucleosides, pose::Pose const &pose)
void	get_all_tor_id (utility::vector1< id::TorsionID > &tor_id, utility::vector1< Real > &torsions, utility::vector1< Backbone_Torsion > const &backbones, utility::vector1< Nucleoside_Torsion > const &nucleosides, Size const skipped_backbone)
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 > const &moving_res, utility::vector1< Real > const &rbs)
void	setup_pose (pose::Pose &pose)
void	random_angle (float &angle, Real const lower_bound=-180, Real const upper_bound=180)
void	random_delta (float &angle)
void	gaussian_angle_move (float &angle, Real const stdev)
void	nucleoside_sampling (Nucleoside_Torsion &nucleoside, Real const sample_stdev, Real const lowerbound, Real const upperbound, Real const pucker_prob)
void	backbone_sampling (Backbone_Torsion &backbone, Real const sample_stdev, Real const lowerbound, Real const upperbound)
void	update_nucleoside (utility::vector1< Nucleoside_Torsion > &nucleosides, utility::vector1< Size > const &sample_modes, Real const stdev_bp, Real const stdev_free, Real const lowerbound_bp, Real const upperbound_bp, Real const pucker_prob)
void	update_backbone (utility::vector1< Backbone_Torsion > &backbones, utility::vector1< Size > const &sample_modes, Real const stdev_bp, Real const stdev_free, Real const lowerbound_bp, Real const upperbound_bp)
void	get_torsion_list (utility::vector1< float > &data, utility::vector1< Backbone_Torsion > const &backbones, utility::vector1< Nucleoside_Torsion > const &nucleosides, Real const missing_suite)
void	get_score_terms (utility::vector1< float > &data, pose::Pose &pose, utility::vector1< scoring::ScoreFunctionOP > const &scorefxns)
void	get_base_steps (utility::vector1< float > &data, pose::Pose &pose)
void	helix_minimize (core::pose::Pose &pose, scoring::ScoreFunctionOP scorefxn)
void	MC_run ()
void	torsion2pdb ()
void	hessian_estimate ()
void	bp_score_calibrate ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static const chemical::rna::RNA_FittedTorsionInfo	rna_fitted_torsion_info

Typedef Documentation

Backbone_Torsion

typedef std::array<float,5> Backbone_Torsion

float_vec

typedef utility::vector1<float> float_vec

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Nucleoside_Torsion

typedef std::array<float,2> Nucleoside_Torsion

Function Documentation

apply_all()

void apply_all	(	utility::vector1< Backbone_Torsion > const &	backbones,
		utility::vector1< Nucleoside_Torsion > const &	nucleosides,
		pose::Pose &	pose
	)

References apply_backbone(), apply_nucleoside(), internal_coordinates::backbones, create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by MC_run(), and torsion2pdb().

apply_backbone()

void apply_backbone	(	Backbone_Torsion const &	backbone,
		pose::Pose &	pose,
		Size const	suite
	)

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

Referenced by apply_all(), and setup_pose().

apply_nucleoside()

void apply_nucleoside	(	Nucleoside_Torsion const &	nucleoside,
		pose::Pose &	pose,
		Size const	residue
	)

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

Referenced by apply_all(), and setup_pose().

apply_rigid_body_settings()

void apply_rigid_body_settings	(	pose::Pose &	pose,
		pose::Pose const &	pose_start,
		utility::vector1< Size > const &	moving_res,
		utility::vector1< Real > const &	rbs
	)

References beta_nonlocal::pose, pyrosetta.bindings.pose::rotate(), and beta_nonlocal::translate.

Referenced by setup_pose().

backbone_sampling()

void backbone_sampling	(	Backbone_Torsion &	backbone,
		Real const	sample_stdev,
		Real const	lowerbound,
		Real const	upperbound
	)

References basic::options::OptionKeys::hotspot::angle, internal_coordinates::backbone, erraser_analysis::diff, gaussian_angle_move(), create_a3b_hbs::i, ideal_A_form_torsions(), and random_angle().

Referenced by update_backbone().

bp_score_calibrate()

void bp_score_calibrate

(

)

References pyrosetta::create_score_function, create_a3b_hbs::i, option, erraser_single_res_analysis::out, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::recces::seq1, basic::options::OptionKeys::recces::seq2, setup_pose(), and beta_nonlocal::translate.

Referenced by my_main().

gaussian_angle_move()

void gaussian_angle_move	(	float &	angle,
		Real const	stdev
	)

References basic::options::OptionKeys::hotspot::angle, numeric::random::RandomGenerator::gaussian(), numeric::random::rg(), and myspace::stdev().

Referenced by backbone_sampling(), and nucleoside_sampling().

get_all()

void get_all	(	utility::vector1< Backbone_Torsion > &	backbones,
		utility::vector1< Nucleoside_Torsion > &	nucleosides,
		pose::Pose const &	pose
	)

References internal_coordinates::backbones, get_backbone(), get_nucleoside(), create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by hessian_estimate().

get_all_tor_id()

void get_all_tor_id	(	utility::vector1< id::TorsionID > &	tor_id,
		utility::vector1< Real > &	torsions,
		utility::vector1< Backbone_Torsion > const &	backbones,
		utility::vector1< Nucleoside_Torsion > const &	nucleosides,
		Size const	skipped_backbone
	)

References internal_coordinates::backbones, create_a3b_hbs::i, create_a3b_hbs::j, and internal_coordinates::torsions.

Referenced by hessian_estimate().

get_backbone()

void get_backbone	(	Backbone_Torsion &	backbone,
		pose::Pose const &	pose,
		Size const	suite
	)

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

Referenced by get_all().

get_base_steps()

void get_base_steps	(	utility::vector1< float > &	data,
		pose::Pose &	pose
	)

References data, create_a3b_hbs::i, create_a3b_hbs::j, basic::options::OptionKeys::dna::specificity::params, and beta_nonlocal::pose.

Referenced by MC_run().

get_nucleoside()

void get_nucleoside	(	Nucleoside_Torsion &	nucleoside,
		pose::Pose const &	pose,
		Size const	residue
	)

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

Referenced by get_all().

get_score_terms()

void get_score_terms	(	utility::vector1< float > &	data,
		pose::Pose &	pose,
		utility::vector1< scoring::ScoreFunctionOP > const &	scorefxns
	)

References data, create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by MC_run().

get_torsion_list()

void get_torsion_list	(	utility::vector1< float > &	data,
		utility::vector1< Backbone_Torsion > const &	backbones,
		utility::vector1< Nucleoside_Torsion > const &	nucleosides,
		Real const	missing_suite
	)

References internal_coordinates::backbones, data, create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by MC_run().

helix_minimize()

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

References create_a3b_hbs::i, beta_nonlocal::mm, beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by hessian_estimate(), and MC_run().

hessian_estimate()

void hessian_estimate

(

)

References internal_coordinates::backbones, utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::optE::fixed, get_all(), get_all_tor_id(), helix_minimize(), create_a3b_hbs::i, ideal_A_form_torsions(), create_a3b_hbs::j, option, erraser_single_res_analysis::out, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::recces::seq1, basic::options::OptionKeys::recces::seq2, setup_pose(), and internal_coordinates::torsions.

Referenced by my_main().

ideal_A_form_torsions()

std::pair< Backbone_Torsion, Nucleoside_Torsion > ideal_A_form_torsions

(

)

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

Referenced by backbone_sampling(), get_suite_ideal_A_form_torsions(), hessian_estimate(), MC_run(), nucleoside_sampling(), setup_pose(), and torsion2pdb().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), my_main(), basic::options::OptionKeys::recces::n_cycle, NEW_OPT, basic::options::OptionKeys::recces::output_min_pose, basic::options::OptionKeys::coupled_moves::output_prefix, basic::options::OptionKeys::recces::save_score_terms, save_torsions(), basic::options::OptionKeys::recces::seq1, basic::options::OptionKeys::recces::seq2, and viewer_main().

MC_run()

void MC_run

(

)

References apply_all(), internal_coordinates::backbones, utility::io::oc::cout, pyrosetta::create_score_function, cycle(), basic::options::OptionKeys::optE::fixed, get_base_steps(), get_score_terms(), get_torsion_list(), helix_minimize(), create_a3b_hbs::i, ideal_A_form_torsions(), basic::options::OptionKeys::relax::range::kT, min(), SmotifHasher::min_score, basic::options::OptionKeys::recces::n_cycle, option, test.T008_Serialization::oss, erraser_single_res_analysis::out, basic::options::OptionKeys::recces::out_prefix, basic::options::OptionKeys::recces::output_min_pose, basic::options::OptionKeys::coupled_moves::output_prefix, beta_nonlocal::pose, numeric::random::rg(), basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::recces::save_score_terms, save_torsions(), create_a3b_hbs::score, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::recces::seq1, basic::options::OptionKeys::recces::seq2, setup_pose(), show(), subloop_histogram::size, numeric::random::uniform(), numeric::random::RandomGenerator::uniform(), update_backbone(), update_nucleoside(), utility_exit_with_message, and weights().

Referenced by my_main().

my_main()

void* my_main

(

void *

)

References bp_score_calibrate(), utility::options::OptionKeys::options::exit, hessian_estimate(), MC_run(), option, and torsion2pdb().

Referenced by main().

nucleoside_sampling()

void nucleoside_sampling	(	Nucleoside_Torsion &	nucleoside,
		Real const	sample_stdev,
		Real const	lowerbound,
		Real const	upperbound,
		Real const	pucker_prob
	)

References erraser_analysis::diff, gaussian_angle_move(), ideal_A_form_torsions(), random_angle(), random_delta(), numeric::random::rg(), and numeric::random::uniform().

Referenced by update_nucleoside().

random_angle()

void random_angle	(	float &	angle,
		Real const	lower_bound = -180,
		Real const	upper_bound = 180
	)

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

Referenced by backbone_sampling(), and nucleoside_sampling().

random_delta()

void random_delta

(

float &

angle

)

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

Referenced by nucleoside_sampling().

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_pose().

setup_pose()

void setup_pose

(

pose::Pose &

pose

)

References apply_backbone(), apply_nucleoside(), apply_rigid_body_settings(), create_a3b_hbs::f, create_a3b_hbs::i, ideal_A_form_torsions(), option, beta_nonlocal::pose, read_rigid_body_settings(), basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::recces::seq1, basic::options::OptionKeys::recces::seq2, basic::options::OptionKeys::in::file::silent, and utility_exit_with_message.

Referenced by bp_score_calibrate(), hessian_estimate(), MC_run(), torsion2pdb(), and TryScoreFilter::TryScoreFilter().

torsion2pdb()

void torsion2pdb

(

)

References apply_all(), internal_coordinates::backbone, internal_coordinates::backbones, create_a3b_hbs::i, ideal_A_form_torsions(), create_a3b_hbs::j, option, beta_nonlocal::pose, basic::options::OptionKeys::recces::seq1, basic::options::OptionKeys::recces::seq2, setup_pose(), and utility_exit_with_message.

Referenced by my_main().

update_backbone()

void update_backbone	(	utility::vector1< Backbone_Torsion > &	backbones,
		utility::vector1< Size > const &	sample_modes,
		Real const	stdev_bp,
		Real const	stdev_free,
		Real const	lowerbound_bp,
		Real const	upperbound_bp
	)

References backbone_sampling(), internal_coordinates::backbones, and create_a3b_hbs::i.

Referenced by MC_run().

update_nucleoside()

void update_nucleoside	(	utility::vector1< Nucleoside_Torsion > &	nucleosides,
		utility::vector1< Size > const &	sample_modes,
		Real const	stdev_bp,
		Real const	stdev_free,
		Real const	lowerbound_bp,
		Real const	upperbound_bp,
		Real const	pucker_prob
	)

References create_a3b_hbs::i, and nucleoside_sampling().

Referenced by MC_run().

Variable Documentation

rna_fitted_torsion_info

const chemical::rna::RNA_FittedTorsionInfo rna_fitted_torsion_info

static

Referenced by ideal_A_form_torsions(), and random_delta().