optE_test.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <devel/init.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/packer_neighbors.hh>
#include <protocols/optimize_weights/OptEData.fwd.hh>
#include <protocols/optimize_weights/OptEData.hh>
#include <protocols/optimize_weights/OptEMultifunc.hh>
#include <utility/graph/Graph.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/optimization/types.hh>
#include <core/optimization/Multifunc.hh>
#include <core/optimization/Minimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/Pose.hh>
#include <basic/options/util.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <utility/vector1.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/VirtualBase.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/string.functions.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <algorithm>
#include <sstream>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/Jump.hh>

Functions
utility::vector1< std::string >	get_native_pdb_names ()
void	simple_opte_test ()
void	optimize_weights (utility::vector1< std::string > const &filenames, utility::vector1< std::string > const &native_filenames, core::scoring::EnergyMap const &free_parameters, core::scoring::EnergyMap const &fixed_parameters, utility::vector1< Real > const &starting_reference_energies, core::scoring::EnergyMap &optimized_free_parameters, utility::vector1< Real > &optimized_reference_energies)
void	iterative_optE ()
Real	measure_sequence_recovery (utility::vector1< std::string > const &native_pdb_names, utility::vector1< std::string > const &names_for_output_pdbs, core::scoring::ScoreFunctionOP sfxn)
Size	opte_num_inner_iterations (Size outer_loop_counter)
Real	opte_weight_mixing_factor (Size outer_loop_counter, Size inner_loop_counter)
core::scoring::ScoreFunctionOP	create_score_function_from_weights_and_refEs (core::scoring::EnergyMap const &emap, utility::vector1< Real > const &reference_energies)
void	initialize_free_and_fixed (core::scoring::EnergyMap &free_parameters, core::scoring::EnergyMap &fixed_parameters)
bool	converged (core::scoring::EnergyMap &free_parameters_prev, core::scoring::EnergyMap &free_parameters_curr, utility::vector1< Real > const &reference_energies_prev, utility::vector1< Real > const &reference_energies_curr)
void	setup_pdbnames_next_round (Size const outer_loop_counter, utility::vector1< std::string > &pdbs_next_round, utility::vector1< std::string > const &native_pdb_names)
bool	accept_new_weight_set (Size outer_loop_counter, Size inner_loop_counter, Real latest_seq_recovery_rate, Real last_sequence_recovery_rate, Real inner_loop_scale_factor)
void	write_parameters_to_std_out (core::scoring::EnergyMap &free_parameters, utility::vector1< Real > const &reference_energies)
void	get_opte_data (pose::Pose &pose, pose::Pose &native_pose, ScoreFunction const &scorefxn, ScoreTypes &score_list, ScoreTypes &fixed_score_vec, OptEData &opte_data)
int	main (int argc, char *argv[])

Function Documentation

accept_new_weight_set()

bool accept_new_weight_set	(	Size	outer_loop_counter,
		Size	inner_loop_counter,
		Real	latest_seq_recovery_rate,
		Real	last_sequence_recovery_rate,
		Real	inner_loop_scale_factor
	)

Referenced by iterative_optE().

converged()

bool converged	(	core::scoring::EnergyMap &	free_parameters_prev,
		core::scoring::EnergyMap &	free_parameters_curr,
		utility::vector1< Real > const &	reference_energies_prev,
		utility::vector1< Real > const &	reference_energies_curr
	)

References ObjexxFCL::abs(), utility::io::oc::cout, create_a3b_hbs::ii, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by iterative_optE().

create_score_function_from_weights_and_refEs()

core::scoring::ScoreFunctionOP create_score_function_from_weights_and_refEs	(	core::scoring::EnergyMap const &	emap,
		utility::vector1< Real > const &	reference_energies
	)

References pyrosetta.io::create_score_function, test.T200_Scoring::emap, val2thr::fout, create_a3b_hbs::ii, basic::options::OptionKeys::frags::scoring::scoring, and test.T120_core::sfxn.

Referenced by iterative_optE().

get_native_pdb_names()

utility::vector1< std::string > get_native_pdb_names

(

)

References data, getline(), line, and basic::options::start_file().

Referenced by iterative_optE().

get_opte_data()

void get_opte_data	(	pose::Pose &	pose,
		pose::Pose &	native_pose,
		ScoreFunction const &	scorefxn,
		ScoreTypes &	score_list,
		ScoreTypes &	fixed_score_vec,
		OptEData &	opte_data
	)

References utility::io::oc::cout, create_a3b_hbs::ii, beta_nonlocal::jj, docking::native_pose, beta_nonlocal::pose, oop_conformations::scorefxn, and vancomycin::task.

Referenced by optimize_weights(), and simple_opte_test().

initialize_free_and_fixed()

void initialize_free_and_fixed	(	core::scoring::EnergyMap &	free_parameters,
		core::scoring::EnergyMap &	fixed_parameters
	)

References cenpack, utility::io::oc::cout, env, create_a3b_hbs::ii, basic::options::OptionKeys::corrections::score::p_aa_pp, pair, basic::options::OptionKeys::remodel::rama, numeric::random::rg(), numeric::random::RandomGenerator::uniform(), and basic::options::OptionKeys::remodel::vdw.

Referenced by iterative_optE().

iterative_optE()

void iterative_optE

(

)

References accept_new_weight_set(), converged(), utility::io::oc::cout, create_score_function_from_weights_and_refEs(), get_native_pdb_names(), create_a3b_hbs::ii, initialize_free_and_fixed(), beta_nonlocal::jj, kk, measure_sequence_recovery(), opte_num_inner_iterations(), opte_weight_mixing_factor(), optimize_weights(), basic::options::OptionKeys::frags::scoring::scoring, setup_pdbnames_next_round(), and write_parameters_to_std_out().

Referenced by main().

main()

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

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

measure_sequence_recovery()

Real measure_sequence_recovery	(	utility::vector1< std::string > const &	native_pdb_names,
		utility::vector1< std::string > const &	names_for_output_pdbs,
		core::scoring::ScoreFunctionOP	sfxn
	)

References in::file::centroid_input(), utility::io::oc::cout, create_a3b_hbs::ii, beta_nonlocal::jj, create_a3b_hbs::nres, option, test.Workshop6test::pack_mover, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), and test.T120_core::sfxn.

Referenced by iterative_optE().

opte_num_inner_iterations()

Size opte_num_inner_iterations

(

Size

outer_loop_counter

)

Referenced by iterative_optE().

opte_weight_mixing_factor()

Real opte_weight_mixing_factor	(	Size	outer_loop_counter,
		Size	inner_loop_counter
	)

Referenced by iterative_optE().

optimize_weights()

void optimize_weights	(	utility::vector1< std::string > const &	filenames,
		utility::vector1< std::string > const &	native_filenames,
		core::scoring::EnergyMap const &	free_parameters,
		core::scoring::EnergyMap const &	fixed_parameters,
		utility::vector1< Real > const &	starting_reference_energies,
		core::scoring::EnergyMap &	optimized_free_parameters,
		utility::vector1< Real > &	optimized_reference_energies
	)

References basic::options::OptionKeys::optE::component_weights, utility::io::oc::cout, lactamize::filename, get_opte_data(), create_a3b_hbs::i, create_a3b_hbs::ii, subloop_histogram::iterator, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, docking::native_pose, options, beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by iterative_optE().

setup_pdbnames_next_round()

void setup_pdbnames_next_round	(	Size const	outer_loop_counter,
		utility::vector1< std::string > &	pdbs_next_round,
		utility::vector1< std::string > const &	native_pdb_names
	)

References create_a3b_hbs::ii, and subloop_histogram::size.

Referenced by iterative_optE().

simple_opte_test()

void simple_opte_test

(

)

References basic::options::OptionKeys::remodel::cbeta, cenpack, basic::options::OptionKeys::optE::component_weights, utility::io::oc::cout, data, env, lactamize::filename, detail::find(), get_opte_data(), getline(), create_a3b_hbs::i, create_a3b_hbs::ii, subloop_histogram::iterator, line, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, docking::native_pose, options, basic::options::OptionKeys::corrections::score::p_aa_pp, pair, kic_runner::pdb, beta_nonlocal::pose, basic::options::OptionKeys::remodel::rama, basic::options::OptionKeys::remodel::rg, numeric::random::rg(), basic::options::OptionKeys::remodel::rsigma, oop_conformations::scorefxn, basic::options::OptionKeys::remodel::ss_pair, basic::options::start_file(), numeric::random::RandomGenerator::uniform(), utility_exit_with_message, and basic::options::OptionKeys::remodel::vdw.

write_parameters_to_std_out()

void write_parameters_to_std_out	(	core::scoring::EnergyMap &	free_parameters,
		utility::vector1< Real > const &	reference_energies
	)

References utility::io::oc::cout, and create_a3b_hbs::ii.

Referenced by iterative_optE().