core::pack::annealer::FASTERAnnealer Class Reference

#include <FASTERAnnealer.hh>

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

Public Member Functions
	FASTERAnnealer (ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy, bool start_with_current, interaction_graph::FASTERInteractionGraphOP ig, FixbbRotamerSetsCOP rotamer_sets, ObjexxFCL::FArray1_int &current_rot_index, bool calc_rot_freq, ObjexxFCL::FArray1D< core::PackerEnergy > &rot_freq)
virtual	~FASTERAnnealer ()
void	run ()
void	set_ciBR_only (bool setting)
void	set_num_sa_trajectories (int setting)
void	set_sa_length_scale (Real setting)
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)
virtual	~RotamerAssigningAnnealer ()
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)
virtual	~SimAnnealerBase ()
	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)

Private Member Functions
void	iBR ()
void	trySeveral_ciBRs ()
void	ciBR ()
void	sBR ()
void	dBR ()
void	finalize_output ()
void	run_quench_cycles ()
void	reset_recent_network_state_history ()
void	note_current_network_state (ObjexxFCL::FArray1_int const &netstate)
bool	stuck_in_network_state_loop ()
int	pick_rotamer_for_node (int node)
int	pick_a_rotamer_for_sBR ()
void	shuffle_sBR_rotamers ()
int	hash_recent_history (int history_index)

Private Attributes
interaction_graph::FASTERInteractionGraphOP	ig_
FixbbRotamerSetsCOP	rotamer_sets_
int const	num_nodes_
ObjexxFCL::FArray2D_int	recent_network_state_history_
ObjexxFCL::FArray1D_int	recent_history_hash_values_
ObjexxFCL::FArray1D_int	recent_history_hash_count_
int	recent_history_head_
int	curr_in_recent_history_
bool	netstate_duplicated_
int	progress_through_sBR_
utility::vector0< int >	sBR_rotamers_
bool	ciBR_only_
int	num_sa_trajectories_
Real	sa_inner_iterations_length_scale_
int	sBR_limit_

Static Private Attributes
static int const	recent_history_size_ = 100
static int const	hash_size_ = 2017

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 ()
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 rotamer_set::FixbbRotamerSetsCOP core::pack::annealer::FASTERAnnealer::FixbbRotamerSetsCOP

typedef RotamerAssigningAnnealer core::pack::annealer::FASTERAnnealer::parent

Constructor & Destructor Documentation

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

References sBR_rotamers_.

core::pack::annealer::FASTERAnnealer::~FASTERAnnealer ( )

virtual

Member Function Documentation

void core::pack::annealer::FASTERAnnealer::ciBR ( )

private

References ig_, note_current_network_state(), num_nodes_, reset_recent_network_state_history(), and stuck_in_network_state_loop().

Referenced by trySeveral_ciBRs().

void core::pack::annealer::FASTERAnnealer::dBR ( )

private

References ig_, num_nodes_, pick_rotamer_for_node(), core::pack::annealer::RG, and numeric::random::RandomGenerator::uniform().

void core::pack::annealer::FASTERAnnealer::finalize_output ( )

private

References core::pack::annealer::SimAnnealerBase::bestrotamer_at_seqpos(), ig_, num_nodes_, and rotamer_sets_.

Referenced by run().

int core::pack::annealer::FASTERAnnealer::hash_recent_history ( int  history_index )

private

References hash_size_, num_nodes_, and recent_network_state_history_.

Referenced by note_current_network_state().

void core::pack::annealer::FASTERAnnealer::iBR ( )

private

References ig_, note_current_network_state(), num_nodes_, reset_recent_network_state_history(), and stuck_in_network_state_loop().

void core::pack::annealer::FASTERAnnealer::note_current_network_state ( ObjexxFCL::FArray1_int const &  netstate )

private

References curr_in_recent_history_, hash_recent_history(), netstate_duplicated_, num_nodes_, recent_history_hash_count_, recent_history_hash_values_, recent_history_head_, recent_history_size_, and recent_network_state_history_.

Referenced by ciBR(), and iBR().

int core::pack::annealer::FASTERAnnealer::pick_a_rotamer_for_sBR ( )

private

References progress_through_sBR_, and sBR_rotamers_.

Referenced by sBR().

int core::pack::annealer::FASTERAnnealer::pick_rotamer_for_node ( int  node )

private

References ig_, core::pack::annealer::RG, and numeric::random::RandomGenerator::uniform().

Referenced by dBR().

void core::pack::annealer::FASTERAnnealer::reset_recent_network_state_history ( )

private

References curr_in_recent_history_, netstate_duplicated_, recent_history_hash_count_, recent_history_hash_values_, recent_history_head_, and recent_network_state_history_.

Referenced by ciBR(), and iBR().

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

virtual

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

References core::pack::annealer::SimAnnealerBase::bestenergy(), core::pack::annealer::SimAnnealerBase::bestrotamer_at_seqpos(), core::pack::annealer::SimAnnealerBase::calc_rot_freq(), ciBR_only_, finalize_output(), ig_, num_nodes_, num_sa_trajectories_, core::pack::annealer::SimAnnealerBase::rot_freq(), rotamer_sets_, core::pack::annealer::FixbbSimAnnealer::run(), run_quench_cycles(), sa_inner_iterations_length_scale_, sBR(), core::pack::annealer::SimAnnealerBase::scale_inneriterations(), and core::pack::annealer::RotamerAssigningAnnealer::set_assign_state_to_all_nodes_immediately().

void core::pack::annealer::FASTERAnnealer::run_quench_cycles ( )

private

References ig_, core::pack::annealer::RotamerAssigningAnnealer::pick_a_rotamer(), rotamer_sets_, sBR_rotamers_, core::pack::annealer::SimAnnealerBase::set_not_to_quench(), and core::pack::annealer::SimAnnealerBase::set_to_quench().

Referenced by run().

void core::pack::annealer::FASTERAnnealer::sBR ( )

private

References ig_, pick_a_rotamer_for_sBR(), rotamer_sets_, sBR_limit_, sBR_rotamers_, and shuffle_sBR_rotamers().

Referenced by run().

void core::pack::annealer::FASTERAnnealer::set_ciBR_only

(

bool

setting

)

References ciBR_only_.

void core::pack::annealer::FASTERAnnealer::set_num_sa_trajectories

(

int

setting

)

References num_sa_trajectories_.

void core::pack::annealer::FASTERAnnealer::set_sa_length_scale

(

Real

setting

)

References sa_inner_iterations_length_scale_.

void core::pack::annealer::FASTERAnnealer::shuffle_sBR_rotamers ( )

private

References progress_through_sBR_, numeric::random::random_permutation(), core::pack::annealer::RG, and sBR_rotamers_.

Referenced by sBR().

bool core::pack::annealer::FASTERAnnealer::stuck_in_network_state_loop ( )

private

References netstate_duplicated_.

Referenced by ciBR(), and iBR().

void core::pack::annealer::FASTERAnnealer::trySeveral_ciBRs ( )

private

References ciBR(), and ig_.

Member Data Documentation

bool core::pack::annealer::FASTERAnnealer::ciBR_only_

private

Referenced by run(), and set_ciBR_only().

int core::pack::annealer::FASTERAnnealer::curr_in_recent_history_

private

Referenced by note_current_network_state(), and reset_recent_network_state_history().

int const core::pack::annealer::FASTERAnnealer::hash_size_ = 2017

staticprivate

Referenced by hash_recent_history().

interaction_graph::FASTERInteractionGraphOP core::pack::annealer::FASTERAnnealer::ig_

private

Referenced by ciBR(), dBR(), finalize_output(), iBR(), pick_rotamer_for_node(), run(), run_quench_cycles(), sBR(), and trySeveral_ciBRs().

bool core::pack::annealer::FASTERAnnealer::netstate_duplicated_

private

Referenced by note_current_network_state(), reset_recent_network_state_history(), and stuck_in_network_state_loop().

int const core::pack::annealer::FASTERAnnealer::num_nodes_

private

Referenced by ciBR(), dBR(), finalize_output(), hash_recent_history(), iBR(), note_current_network_state(), and run().

int core::pack::annealer::FASTERAnnealer::num_sa_trajectories_

private

Referenced by run(), and set_num_sa_trajectories().

int core::pack::annealer::FASTERAnnealer::progress_through_sBR_

private

Referenced by pick_a_rotamer_for_sBR(), and shuffle_sBR_rotamers().

ObjexxFCL::FArray1D_int core::pack::annealer::FASTERAnnealer::recent_history_hash_count_

private

Referenced by note_current_network_state(), and reset_recent_network_state_history().

ObjexxFCL::FArray1D_int core::pack::annealer::FASTERAnnealer::recent_history_hash_values_

private

Referenced by note_current_network_state(), and reset_recent_network_state_history().

int core::pack::annealer::FASTERAnnealer::recent_history_head_

private

Referenced by note_current_network_state(), and reset_recent_network_state_history().

int const core::pack::annealer::FASTERAnnealer::recent_history_size_ = 100

staticprivate

Referenced by note_current_network_state().

ObjexxFCL::FArray2D_int core::pack::annealer::FASTERAnnealer::recent_network_state_history_

private

Referenced by hash_recent_history(), note_current_network_state(), and reset_recent_network_state_history().

FixbbRotamerSetsCOP core::pack::annealer::FASTERAnnealer::rotamer_sets_

private

Referenced by finalize_output(), run(), run_quench_cycles(), and sBR().

Real core::pack::annealer::FASTERAnnealer::sa_inner_iterations_length_scale_

private

Referenced by run(), and set_sa_length_scale().

int core::pack::annealer::FASTERAnnealer::sBR_limit_

private

Referenced by sBR().

utility::vector0< int > core::pack::annealer::FASTERAnnealer::sBR_rotamers_

private

Referenced by FASTERAnnealer(), pick_a_rotamer_for_sBR(), run_quench_cycles(), sBR(), and shuffle_sBR_rotamers().

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

• src/core/pack/annealer/FASTERAnnealer.hh
• src/core/pack/annealer/FASTERAnnealer.cc