lariat_modeling.cc File Reference

#include <devel/init.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.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 <protocols/rna/denovo/RNA_SuiteAssign.hh>
#include <core/chemical/rna/util.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/id/TorsionID.hh>
#include <core/id/AtomID.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.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 <protocols/rna/denovo/RNA_IdealCoord.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/stepwise/sampling/rna/util.hh>
#include <utility/vector1.hh>
#include <utility/tools/make_vector1.hh>
#include <numeric/random/random.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/conversions.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <utility/excn/Exceptions.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>

Functions
utility::vector1< utility::vector1< Real > >	get_torsion_set (Pose const &pose)
void	apply_torsion_set (Pose &pose, utility::vector1< utility::vector1< Real > > const &torsion_set)
void	update_torsion_set (utility::vector1< utility::vector1< Real > > &torsion_set, Real const stdev)
bool	pose_list_compare (std::pair< Real, Pose > const &i, std::pair< Real, Pose > const &j)
void	lariat_modeling ()
int	main (int argc, char *argv[])

Function Documentation

apply_torsion_set()

void apply_torsion_set	(	Pose &	pose,
		utility::vector1< utility::vector1< Real > > const &	torsion_set
	)

References create_a3b_hbs::i, beta_nonlocal::pose, internal_coordinates::torsion(), and rna_decompose::total_res.

Referenced by lariat_modeling().

get_torsion_set()

utility::vector1< utility::vector1 < Real > > get_torsion_set

(

Pose const &

pose

)

References create_a3b_hbs::i, beta_nonlocal::pose, internal_coordinates::torsion(), and rna_decompose::total_res.

Referenced by lariat_modeling().

lariat_modeling()

void lariat_modeling

(

)

References apply_torsion_set(), basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::constraints::cst_weight, get_torsion_set(), create_a3b_hbs::i, create_a3b_hbs::j, basic::options::OptionKeys::relax::range::kT, beta_nonlocal::mm, in::file::native(), basic::options::OptionKeys::ProQ::normalize, option, test.T008_Serialization::oss, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, pose_list_compare(), basic::options::OptionKeys::in::file::residue_type_set, numeric::random::rg(), basic::options::OptionKeys::full_model::rna::rna, docking::s, create_a3b_hbs::score, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, out::file::silent(), myspace::stdev(), rna_decompose::total_res, numeric::random::RandomGenerator::uniform(), update_torsion_set(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::options::OptionKeys::score::weights.

Referenced by main().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), and lariat_modeling().

pose_list_compare()

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

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

Referenced by lariat_modeling().

update_torsion_set()

void update_torsion_set	(	utility::vector1< utility::vector1< Real > > &	torsion_set,
		Real const	stdev
	)

References numeric::random::RandomGenerator::gaussian(), create_a3b_hbs::i, create_a3b_hbs::j, numeric::random::rg(), myspace::stdev(), numeric::random::uniform(), and numeric::random::RandomGenerator::uniform().

Referenced by lariat_modeling().