#include <SmartFixbbSimAnnealer.hh>

Inheritance diagram for core::pack::annealer::SmartFixbbSimAnnealer:

Public Types
typedef interaction_graph::AnnealableGraphBaseOP	AnnealableGraphBaseOP

Public Types inherited from core::pack::annealer::RotamerAssigningAnnealer
typedef rotamer_set::FixbbRotamerSetsCOP	FixbbRotamerSetsCOP

Public Types inherited from core::pack::annealer::SimAnnealerBase
typedef pack_basic::RotamerSetsBaseCOP	RotamerSetsBaseCOP

Public Member Functions
	SmartFixbbSimAnnealer (utility::vector0< int > &rot_to_pack, ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy, bool start_with_current, AnnealableGraphBaseOP ig, FixbbRotamerSetsCOP rotamer_sets, ObjexxFCL::FArray1_int &current_rot_index, bool calc_rot_freq, ObjexxFCL::FArray1D< core::PackerEnergy > &rot_freq)

	SmartFixbbSimAnnealer (ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy, bool start_with_current, AnnealableGraphBaseOP ig, FixbbRotamerSetsCOP rotamer_sets, ObjexxFCL::FArray1_int &current_rot_index, bool calc_rot_freq, ObjexxFCL::FArray1D< core::PackerEnergy > &rot_freq)

	~SmartFixbbSimAnnealer () override
	virtual destructor More...

void	run () override
	sim_annealing for fixed backbone design mode More...

void	record_annealer_trajectory (bool setting)

void	trajectory_file_name (std::string const &setting)

void	perform_validation_test () const

void	initialize_from_task (core::pack::task::PackerTask const &task)

Public Member Functions inherited from core::pack::annealer::RotamerAssigningAnnealer
	RotamerAssigningAnnealer (int num_of_rot_to_pack, ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy, bool start_with_current, FixbbRotamerSetsCOP p_rotamer_set, ObjexxFCL::FArray1_int &current_rot_index, bool calc_rot_freq, ObjexxFCL::FArray1D< core::PackerEnergy > &rot_freq)

	RotamerAssigningAnnealer (utility::vector0< int > &rot_to_pack, int num_of_rot_to_pack, ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy, bool start_with_current, FixbbRotamerSetsCOP p_rotamer_set, ObjexxFCL::FArray1_int &current_rot_index, bool calc_rot_freq, ObjexxFCL::FArray1D< core::PackerEnergy > &rot_freq)

	~RotamerAssigningAnnealer () override

int	pick_a_rotamer (int cycle)
	pick a rotamer from a list More...

int	pick_a_rotamer_for_node (int node) const

void	set_assign_state_to_all_nodes_immediately (bool setting)

Public Member Functions inherited from core::pack::annealer::SimAnnealerBase
	SimAnnealerBase (int num_rots_to_pack, ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy, bool start_with_current, ObjexxFCL::FArray1_int &current_rot_index, bool calc_rot_freq, ObjexxFCL::FArray1D< core::PackerEnergy > &rot_freq)

	~SimAnnealerBase () override
	virtual destructor More...

bool	pass_metropolis (core::PackerEnergy delta_energy) const
	accept or reject movement based on Metropolis criterion if this is the first movement, accept by default. More...

bool	pass_metropolis (core::PackerEnergy previous_energy, core::PackerEnergy delta_energy) const

void	setup_iterations ()

void	setup_iterations (const int &num_of_state_changes)

int	get_outeriterations () const
	get the iterations number for simulation More...

int	get_inneriterations () const

void	setup_temperature (const int &nn)

void	setup_temperature (const ObjexxFCL::FArray1D< core::PackerEnergy > &loopenergy, int nn)

void	set_temperature (core::PackerEnergy new_temperature)

core::PackerEnergy	get_temperature () const

void	set_to_quench ()

void	set_not_to_quench ()

bool	quench () const

bool	get_start_with_current () const

bool	get_calc_rot_freq () const

void	set_disallow_quench (bool const &setting)

void	set_hightemp (core::PackerEnergy)

void	set_lowtemp (core::PackerEnergy)

void	scale_outeriterations (core::PackerEnergy const so)

void	scale_inneriterations (core::PackerEnergy const si)

AnnealerObserverOP	get_annealer_observer ()

AnnealerObserverCOP	get_annealer_observer () const

void	set_annealer_observer (AnnealerObserverOP obs)

Private Member Functions
	SmartFixbbSimAnnealer (const SmartFixbbSimAnnealer &rhs)

Private Attributes
AnnealableGraphBaseOP	ig_

bool	record_annealer_trajectory_

std::string	trajectory_file_name_

bool	has_been_initialized_from_task_ = false

std::string	model_ = "generation2"

core::Real	cutoff_ = 0.25

bool	pick_again_ = true

bool	disable_during_quench_ = true

Additional Inherited Members
Protected Member Functions inherited from core::pack::annealer::RotamerAssigningAnnealer
FixbbRotamerSetsCOP	rotamer_sets () const

utility::vector0< int > const &	rot_to_pack () const

Protected Member Functions inherited from core::pack::annealer::SimAnnealerBase
Size	num_rots_to_pack () const

void	num_rots_to_pack (Size setting)

ObjexxFCL::FArray1D_int &	bestrotamer_at_seqpos ()

ObjexxFCL::FArray1D_int const &	bestrotamer_at_seqpos () const

core::PackerEnergy &	bestenergy ()

bool	start_with_current () const

ObjexxFCL::FArray1_int &	current_rot_index ()

ObjexxFCL::FArray1_int const &	current_rot_index () const

bool	calc_rot_freq () const

ObjexxFCL::FArray1D < core::PackerEnergy > &	rot_freq ()

ObjexxFCL::FArray1D < core::PackerEnergy > const &	rot_freq () const

core::PackerEnergy	get_hightemp () const

core::PackerEnergy	get_lowtemp () const

void	clear ()

Static Protected Attributes inherited from core::pack::annealer::SimAnnealerBase
static const core::PackerEnergy	hightemp = 100.0

static const core::PackerEnergy	lowtemp = 0.3

static const int	maxouteriterations = 500

static const core::PackerEnergy	calc_freq_temp = 1.0

Member Typedef Documentation

typedef interaction_graph::AnnealableGraphBaseOP core::pack::annealer::SmartFixbbSimAnnealer::AnnealableGraphBaseOP

Constructor & Destructor Documentation

core::pack::annealer::SmartFixbbSimAnnealer::SmartFixbbSimAnnealer	(	utility::vector0< int > &	rot_to_pack,
		ObjexxFCL::FArray1D_int &	bestrotamer_at_seqpos,
		core::PackerEnergy &	bestenergy,
		bool	start_with_current,
		AnnealableGraphBaseOP	ig,
		FixbbRotamerSetsCOP	rotamer_sets,
		ObjexxFCL::FArray1_int &	current_rot_index,
		bool	calc_rot_freq,
		ObjexxFCL::FArray1D< core::PackerEnergy > &	rot_freq
	)

core::pack::annealer::SmartFixbbSimAnnealer::SmartFixbbSimAnnealer	(	ObjexxFCL::FArray1D_int &	bestrotamer_at_seqpos,
		core::PackerEnergy &	bestenergy,
		bool	start_with_current,
		AnnealableGraphBaseOP	ig,
		FixbbRotamerSetsCOP	rotamer_sets,
		ObjexxFCL::FArray1_int &	current_rot_index,
		bool	calc_rot_freq,
		ObjexxFCL::FArray1D< core::PackerEnergy > &	rot_freq
	)

core::pack::annealer::SmartFixbbSimAnnealer::~SmartFixbbSimAnnealer ( )

overridedefault

virtual destructor

core::pack::annealer::SmartFixbbSimAnnealer::SmartFixbbSimAnnealer ( const SmartFixbbSimAnnealer & rhs )

private

Member Function Documentation

void core::pack::annealer::SmartFixbbSimAnnealer::initialize_from_task ( core::pack::task::PackerTask const & task )

References core::pack::task::PackerTask::smart_annealer_cutoff(), core::pack::task::PackerTask::smart_annealer_disable_during_quench(), core::pack::task::PackerTask::smart_annealer_model(), and core::pack::task::PackerTask::smart_annealer_pick_again().

void core::pack::annealer::SmartFixbbSimAnnealer::perform_validation_test ( ) const

References core::pack::annealer::expected_output_for_model_name(), and core::pack::TR().

void core::pack::annealer::SmartFixbbSimAnnealer::record_annealer_trajectory ( bool setting )

void core::pack::annealer::SmartFixbbSimAnnealer::run ( )

overridevirtual

sim_annealing for fixed backbone design mode

Implements core::pack::annealer::SimAnnealerBase.

References core::pack::annealer::Key::AA, core::pack::annealer::Key::mres, core::pack::annealer::Value::num_accept_from_AA, core::pack::annealer::Value::num_accept_intra_AA, core::pack::annealer::Value::num_accept_to_AA, core::pack::annealer::Value::num_total_from_AA, core::pack::annealer::Value::num_total_intra_AA, core::pack::annealer::Value::num_total_to_AA, core::pack::pass_metropolis(), core::scoring::rg, and core::pack::TR().

void core::pack::annealer::SmartFixbbSimAnnealer::trajectory_file_name ( std::string const & setting )

Member Data Documentation

core::Real core::pack::annealer::SmartFixbbSimAnnealer::cutoff_ = 0.25

private

bool core::pack::annealer::SmartFixbbSimAnnealer::disable_during_quench_ = true

private

bool core::pack::annealer::SmartFixbbSimAnnealer::has_been_initialized_from_task_ = false

private

AnnealableGraphBaseOP core::pack::annealer::SmartFixbbSimAnnealer::ig_

private

std::string core::pack::annealer::SmartFixbbSimAnnealer::model_ = "generation2"

private

bool core::pack::annealer::SmartFixbbSimAnnealer::pick_again_ = true

private

bool core::pack::annealer::SmartFixbbSimAnnealer::record_annealer_trajectory_

private

std::string core::pack::annealer::SmartFixbbSimAnnealer::trajectory_file_name_

private

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

src/core/pack/annealer/SmartFixbbSimAnnealer.hh
src/core/pack/annealer/SmartFixbbSimAnnealer.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation