params_opt.cc File Reference

#include <devel/init.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <core/import_pose/import_pose.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AA.hh>
#include <core/optimization/Multifunc.hh>
#include <core/optimization/Minimizer.hh>
#include <core/optimization/NelderMeadSimplex.hh>
#include <core/optimization/CartesianMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreTypeManager.hh>
#include <core/energy_methods/FA_ElecEnergy.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/util/cryst_util.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/rtmin.hh>
#include <utility/graph/Graph.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <protocols/symmetry/SetupForSymmetryMover.hh>
#include <utility/vector1.hh>
#include <numeric/random/random.hh>
#include <boost/thread.hpp>
#include <functional>

Classes
class	RTminOptMultifunc

Functions
utility::vector1< core::pose::PoseOP >	load_models ()
utility::vector1< utility::vector1< bool > >	select_residues_for_evaluation (utility::vector1< core::pose::PoseOP > const &models)
void	sf2multivec (core::scoring::ScoreFunctionCOP scorefxn, Multivec &y, bool islow=false, bool ishigh=false)
void	multivec2sf (Multivec const &vars, core::scoring::ScoreFunctionOP scorefxn)
void	dump_multivec (Multivec const &vars)
void	do_rtmin (core::scoring::ScoreFunction const &sf, core::pack::task::PackerTask const &packer_task, core::pose::Pose const &pose, core::Real &rr_score, core::Real &abs_rr_score)
int	main (int argc, char *argv[])

Function Documentation

do_rtmin()

void do_rtmin	(	core::scoring::ScoreFunction const &	sf,
		core::pack::task::PackerTask const &	packer_task,
		core::pose::Pose const &	pose,
		core::Real &	rr_score,
		core::Real &	abs_rr_score
	)

References create_a3b_hbs::ii, option, demo.D050_Packer_task::packer_task(), beta_nonlocal::pose, basic::options::OptionKeys::rot_anl::rtmin, basic::options::OptionKeys::out::sf, and utility_exit_with_message.

Referenced by RTminOptMultifunc::operator()().

dump_multivec()

void dump_multivec

(

Multivec const &

vars

)

References utility::io::oc::cerr, and create_a3b_hbs::i.

Referenced by RTminOptMultifunc::operator()().

load_models()

utility::vector1<core::pose::PoseOP> load_models

(

)

References closure_error::models, option, and docking::s.

Referenced by main().

main()

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

References argv, pyrosetta::create_score_function, test.T009_Exceptions::e, create_a3b_hbs::f, hist2d::H, create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, load_models(), closure_error::models, NEW_OPT, option, options, numeric::random::random_range(), runtime_assert, docking::s, oop_conformations::scorefxn, select_residues_for_evaluation(), sf2multivec(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::sigma, and predPRE::y.

multivec2sf()

void multivec2sf	(	Multivec const &	vars,
		core::scoring::ScoreFunctionOP	scorefxn
	)

References demo.D060_Folding::counter, test.T220_AtomAtomPairEnergies::fa_elec, basic::options::OptionKeys::AnchoredDesign::filters::omega, option, basic::options::OptionKeys::remodel::rama, and oop_conformations::scorefxn.

Referenced by RTminOptMultifunc::operator()().

select_residues_for_evaluation()

utility::vector1< utility::vector1<bool> > select_residues_for_evaluation

(

utility::vector1< core::pose::PoseOP > const &

models

)

References utility::io::oc::cerr, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, closure_error::models, and subloop_histogram::size.

Referenced by main().

sf2multivec()

void sf2multivec	(	core::scoring::ScoreFunctionCOP	scorefxn,
		Multivec &	y,
		bool	islow = false,
		bool	ishigh = false
	)

References test.T220_AtomAtomPairEnergies::fa_elec, basic::options::OptionKeys::AnchoredDesign::filters::omega, option, basic::options::OptionKeys::remodel::rama, oop_conformations::scorefxn, and predPRE::y.

Referenced by main().