myspace::Scheduler Class Reference

#include <NMsearch.hh>

Public Member Functions
	Scheduler ()
	~Scheduler ()
	Scheduler (pose::Pose &pose, pose::Pose const &native, std::string const mode, Size const maxiter=100)
void	run_NM (pose::Pose &pose, std::string const mode)
void	run_NM_evalmodes (pose::Pose &pose, Size const maxmode)
void	set_maxiter (Size const value)
void	run_LH (pose::Pose &pose, std::string const mode)
void	run_LHeval (pose::Pose &pose)
void	run_combine (pose::Pose &pose, bool const report_full)
	Combined. More...
void	run_md (pose::Pose &pose)

Private Member Functions
void	set_default_parameters ()
void	set_pertscale (Real const scale)
pose::Pose	NM_linesearch (pose::Pose const &pose, Real &gdtmin, Real &pert_best, std::vector< io::silent::SilentStructOP > &ss)
	NormalMode methods. More...
void	control_schedule (pose::Pose const &pose, pose::Pose &pose_ref, Real const gdt_to_ref)
void	setup_LHsampler (pose::Pose const &pose, Size const max_struct=20)
pose::Pose	loophash_search (pose::Pose const &pose, Real &gdt, Size const ires, std::vector< io::silent::SilentStructOP > &ss)
Size	pick_hashing_res (pose::Pose const &pose, std::string const mode, Size &Lcount)
void	put_coordinate_constraints (pose::Pose &pose)
void	accept_and_report (pose::Pose &pose_tmp, pose::Pose &pose, Size const iter, Size const arg1, Real const arg2, Real const gdt, Real const gdt_to_ref, bool const is_lh, Real const pdb_dump_cut=0.005)

Private Attributes
myspace::Evaluator	evaluator_
protocols::loophash::LoopHashSamplerOP	LHsampler_
protocols::normalmode::NormalModeRelaxMoverOP	NMmover_
Real	gdtmax_
Size	iter_updated_last_
Size	iter_added_last_
Size	maxmode_
Size	maxiter_
Real	max_scale_
Real	min_scale_
Size	loopcut_
Real	gdt_refresh_cut_
Size	looplen_
utility::vector1< Real >	pert_scales_

Constructor & Destructor Documentation

Scheduler() [1/2]

myspace::Scheduler::Scheduler ( )

inline

~Scheduler()

myspace::Scheduler::~Scheduler ( )

inline

Scheduler() [2/2]

myspace::Scheduler::Scheduler	(	pose::Pose &	pose,
		pose::Pose const &	native,
		std::string const	mode,
		Size const	maxiter = 100
	)

References pyrosetta::create_score_function, SmotifHasher::mode, surface_app::native, option, beta_nonlocal::pose, setup_LHsampler(), test.T120_core::sfxn, internal_coordinates::torsion(), and score::weights().

Member Function Documentation

accept_and_report()

void myspace::Scheduler::accept_and_report ( pose::Pose &  pose_tmp, pose::Pose &  pose, Size const  iter, Size const  arg1, Real const  arg2, Real const  gdt, Real const  gdt_to_ref, bool const  is_lh, Real const  pdb_dump_cut = 0.005  )

private

References option, predPRE::pdbname, beta_nonlocal::pose, out::prefix(), and printf().

control_schedule()

void myspace::Scheduler::control_schedule ( pose::Pose const &  pose, pose::Pose &  pose_ref, Real const  gdt_to_ref  )

private

References utility::io::oc::cout, and beta_nonlocal::pose.

loophash_search()

pose::Pose myspace::Scheduler::loophash_search ( pose::Pose const &  pose, Real &  gdt, Size const  ires, std::vector< io::silent::SilentStructOP > &  ss  )

private

References beta_nonlocal::pose, and challenge::ss.

NM_linesearch()

pose::Pose myspace::Scheduler::NM_linesearch ( pose::Pose const &  pose, Real &  gdtmin, Real &  pert_best, std::vector< io::silent::SilentStructOP > &  ss  )

private

NormalMode methods.

References create_a3b_hbs::k, beta_nonlocal::pose, basic::options::OptionKeys::in::file::silent, and challenge::ss.

pick_hashing_res()

Size myspace::Scheduler::pick_hashing_res ( pose::Pose const &  pose, std::string const  mode, Size &  Lcount  )

private

References SmotifHasher::mode, create_a3b_hbs::nres, beta_nonlocal::pose, numeric::random::rg(), shift, and numeric::random::RandomGenerator::uniform().

put_coordinate_constraints()

void myspace::Scheduler::put_coordinate_constraints ( pose::Pose &  pose )

private

run_combine()

void myspace::Scheduler::run_combine	(	pose::Pose &	pose,
		bool const	report_full
	)

Combined.

References loophash_search(), option, beta_nonlocal::pose, out::prefix(), numeric::random::rg(), RG, sfd, challenge::ss, tag, numeric::random::uniform(), and numeric::random::RandomGenerator::uniform().

Referenced by main().

run_LH()

void myspace::Scheduler::run_LH	(	pose::Pose &	pose,
		std::string const	mode
	)

References loophash_search(), SmotifHasher::mode, beta_nonlocal::pose, and challenge::ss.

Referenced by main().

run_LHeval()

void myspace::Scheduler::run_LHeval

(

pose::Pose &

pose

)

References option, predPRE::pdbname, beta_nonlocal::pose, out::prefix(), printf(), and shift.

Referenced by main().

run_md()

void myspace::Scheduler::run_md

(

pose::Pose &

pose

)

References utility::io::oc::cout, pyrosetta::create_score_function, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, test.T009_Exceptions::e, basic::options::OptionKeys::in::file::movemap, option, beta_nonlocal::pose, printf(), test.T120_core::sfxn, THETA, and score::weights().

Referenced by main().

run_NM()

void myspace::Scheduler::run_NM	(	pose::Pose &	pose,
		std::string const	mode
	)

References SmotifHasher::mode, beta_nonlocal::pose, numeric::random::rg(), RG, challenge::ss, and numeric::random::RandomGenerator::uniform().

Referenced by main().

run_NM_evalmodes()

void myspace::Scheduler::run_NM_evalmodes	(	pose::Pose &	pose,
		Size const	maxmode
	)

References create_a3b_hbs::k, option, predPRE::pdbname, beta_nonlocal::pose, out::prefix(), and printf().

Referenced by main().

set_default_parameters()

void myspace::Scheduler::set_default_parameters ( )

private

References option.

set_maxiter()

void myspace::Scheduler::set_maxiter ( Size const  value )

inline

References value.

set_pertscale()

void myspace::Scheduler::set_pertscale ( Real const  scale )

private

References create_a3b_hbs::i, and spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::scale.

setup_LHsampler()

void myspace::Scheduler::setup_LHsampler ( pose::Pose const &  pose, Size const  max_struct = 20  )

private

References loop_hash_library, basic::options::OptionKeys::lh::max_struct, and option.

Member Data Documentation

evaluator_

myspace::Evaluator myspace::Scheduler::evaluator_

private

gdt_refresh_cut_

Real myspace::Scheduler::gdt_refresh_cut_

private

gdtmax_

Real myspace::Scheduler::gdtmax_

private

iter_added_last_

Size myspace::Scheduler::iter_added_last_

private

iter_updated_last_

Size myspace::Scheduler::iter_updated_last_

private

LHsampler_

protocols::loophash::LoopHashSamplerOP myspace::Scheduler::LHsampler_

private

loopcut_

Size myspace::Scheduler::loopcut_

private

looplen_

Size myspace::Scheduler::looplen_

private

max_scale_

Real myspace::Scheduler::max_scale_

private

maxiter_

Size myspace::Scheduler::maxiter_

private

maxmode_

Size myspace::Scheduler::maxmode_

private

min_scale_

Real myspace::Scheduler::min_scale_

private

NMmover_

protocols::normalmode::NormalModeRelaxMoverOP myspace::Scheduler::NMmover_

private

pert_scales_

utility::vector1< Real > myspace::Scheduler::pert_scales_

private

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The documentation for this class was generated from the following files:

• src/apps/pilot/hpark/NMsearch.hh
• src/apps/pilot/hpark/NMsearch.cc