core::pack::annealer::SimAnnealerBase Class Reference

#include <SimAnnealerBase.hh>

Inheritance diagram for core::pack::annealer::SimAnnealerBase:

Public Types
typedef pack_basic::RotamerSetsBaseCOP	RotamerSetsBaseCOP

Public Member Functions
	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...
virtual void	run ()=0
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)

Protected Member Functions
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
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

Private Member Functions
	SimAnnealerBase (const SimAnnealerBase &rhs)

Private Attributes
Size	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_
int	outeriterations_
int	inneriterations_
bool	quench_
core::PackerEnergy	hightemp_
core::PackerEnergy	lowtemp_
core::PackerEnergy	temperature_
int	jump_
core::PackerEnergy	outeriterations_scaling_
core::PackerEnergy	inneriterations_scaling_
bool const	low_temp_annealing_
bool	disallow_quench_
AnnealerObserverOP	observer_ = nullptr

Member Typedef Documentation

RotamerSetsBaseCOP

typedef pack_basic::RotamerSetsBaseCOP core::pack::annealer::SimAnnealerBase::RotamerSetsBaseCOP

Constructor & Destructor Documentation

SimAnnealerBase() [1/2]

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()

core::pack::annealer::SimAnnealerBase::~SimAnnealerBase ( )

overridedefault

virtual destructor

Global Read:

Global Write:

Remarks

References:

Author

SimAnnealerBase() [2/2]

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

private

Member Function Documentation

bestenergy()

core::PackerEnergy & core::pack::annealer::SimAnnealerBase::bestenergy ( )

protected

Referenced by core::pack::annealer::FASTERAnnealer::run(), and protocols::flexpack::annealer::FlexbbSimAnnealer::run().

bestrotamer_at_seqpos() [1/2]

FArray1D_int & core::pack::annealer::SimAnnealerBase::bestrotamer_at_seqpos ( )

protected

Referenced by core::pack::annealer::FASTERAnnealer::finalize_output(), core::pack::annealer::DebuggingAnnealer::run(), core::pack::annealer::FASTERAnnealer::run(), and protocols::flexpack::annealer::FlexbbSimAnnealer::run().

bestrotamer_at_seqpos() [2/2]

FArray1D_int const & core::pack::annealer::SimAnnealerBase::bestrotamer_at_seqpos ( ) const

protected

calc_rot_freq()

bool core::pack::annealer::SimAnnealerBase::calc_rot_freq ( ) const

protected

Referenced by core::pack::annealer::FASTERAnnealer::run(), and protocols::flexpack::annealer::FlexbbSimAnnealer::run().

clear()

void core::pack::annealer::SimAnnealerBase::clear ( )

protected

current_rot_index() [1/2]

FArray1_int & core::pack::annealer::SimAnnealerBase::current_rot_index ( )

protected

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::run().

current_rot_index() [2/2]

FArray1_int const & core::pack::annealer::SimAnnealerBase::current_rot_index ( ) const

protected

get_annealer_observer() [1/2]

AnnealerObserverOP core::pack::annealer::SimAnnealerBase::get_annealer_observer ( )

inline

References observer_.

get_annealer_observer() [2/2]

AnnealerObserverCOP core::pack::annealer::SimAnnealerBase::get_annealer_observer ( ) const

inline

References observer_.

get_calc_rot_freq()

bool core::pack::annealer::SimAnnealerBase::get_calc_rot_freq

(

)

const

get_hightemp()

core::PackerEnergy core::pack::annealer::SimAnnealerBase::get_hightemp ( ) const

inlineprotected

References hightemp_.

get_inneriterations()

int core::pack::annealer::SimAnnealerBase::get_inneriterations

(

)

const

Global Read:

Global Write:

Remarks

References:

Author

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::run().

get_lowtemp()

core::PackerEnergy core::pack::annealer::SimAnnealerBase::get_lowtemp ( ) const

inlineprotected

References lowtemp_.

get_outeriterations()

int core::pack::annealer::SimAnnealerBase::get_outeriterations

(

)

const

get the iterations number for simulation

Global Read:

Global Write:

Remarks

References:

Author

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::run().

get_start_with_current()

bool core::pack::annealer::SimAnnealerBase::get_start_with_current

(

)

const

get_temperature()

core::PackerEnergy core::pack::annealer::SimAnnealerBase::get_temperature

(

)

const

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::pass_metropolis_multiple_nodes_changing(), and protocols::flexpack::annealer::FlexbbSimAnnealer::run().

num_rots_to_pack() [1/2]

Size core::pack::annealer::SimAnnealerBase::num_rots_to_pack ( ) const

inlineprotected

References num_rots_to_pack_.

Referenced by core::pack::annealer::DebuggingAnnealer::run().

num_rots_to_pack() [2/2]

void core::pack::annealer::SimAnnealerBase::num_rots_to_pack ( Size  setting )

protected

pass_metropolis() [1/2]

bool core::pack::annealer::SimAnnealerBase::pass_metropolis

(

core::PackerEnergy

delta_energy

)

const

accept or reject movement based on Metropolis criterion if this is the first movement, accept by default.

Global Read:

Global Write:

Remarks

References:

Author

References core::pack::pass_metropolis().

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::pass_metropolis_multiple_nodes_changing(), and protocols::flexpack::annealer::FlexbbSimAnnealer::run().

pass_metropolis() [2/2]

bool core::pack::annealer::SimAnnealerBase::pass_metropolis	(	core::PackerEnergy	previous_energy,
		core::PackerEnergy	delta_energy
	)		const

References protocols::simple_moves::bb_sampler::probability, and core::scoring::rg.

quench()

bool core::pack::annealer::SimAnnealerBase::quench

(

)

const

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::pick_a_rotamer(), and protocols::flexpack::annealer::FlexbbSimAnnealer::run().

rot_freq() [1/2]

FArray1D< core::PackerEnergy > & core::pack::annealer::SimAnnealerBase::rot_freq ( )

protected

Referenced by core::pack::annealer::FASTERAnnealer::run().

rot_freq() [2/2]

FArray1D< core::PackerEnergy > const & core::pack::annealer::SimAnnealerBase::rot_freq ( ) const

protected

run()

virtual void core::pack::annealer::SimAnnealerBase::run ( )

pure virtual

Implemented in protocols::flexpack::annealer::FlexbbSimAnnealer, core::pack::annealer::SmartFixbbSimAnnealer, core::pack::annealer::SequenceSymmetricAnnealer, core::pack::annealer::MultiCoolAnnealer, core::pack::annealer::FixbbSimAnnealer, core::pack::annealer::FixbbPwatSimAnnealer, core::pack::annealer::FixbbLinkingRotamerSimAnnealer, core::pack::annealer::FixbbCoupledRotamerSimAnnealer, core::pack::annealer::FASTERAnnealer, and core::pack::annealer::DebuggingAnnealer.

scale_inneriterations()

void core::pack::annealer::SimAnnealerBase::scale_inneriterations ( core::PackerEnergy const  si )

inline

References inneriterations_scaling_.

Referenced by core::pack::annealer::FASTERAnnealer::run().

scale_outeriterations()

void core::pack::annealer::SimAnnealerBase::scale_outeriterations ( core::PackerEnergy const  so )

inline

References outeriterations_scaling_.

set_annealer_observer()

void core::pack::annealer::SimAnnealerBase::set_annealer_observer ( AnnealerObserverOP  obs )

inline

References observer_.

set_disallow_quench()

void core::pack::annealer::SimAnnealerBase::set_disallow_quench

(

bool const &

setting

)

set_hightemp()

void core::pack::annealer::SimAnnealerBase::set_hightemp

(

core::PackerEnergy

high

)

set_lowtemp()

void core::pack::annealer::SimAnnealerBase::set_lowtemp

(

core::PackerEnergy

low

)

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::run().

set_not_to_quench()

void core::pack::annealer::SimAnnealerBase::set_not_to_quench

(

)

Referenced by core::pack::annealer::FASTERAnnealer::run_quench_cycles().

set_temperature()

void core::pack::annealer::SimAnnealerBase::set_temperature

(

core::PackerEnergy

new_temperature

)

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::run().

set_to_quench()

void core::pack::annealer::SimAnnealerBase::set_to_quench

(

)

Referenced by core::pack::annealer::FASTERAnnealer::run_quench_cycles().

setup_iterations() [1/2]

void core::pack::annealer::SimAnnealerBase::setup_iterations

(

)

Global Read:

Global Write:

Remarks

References:

Author

Referenced by core::pack::annealer::DebuggingAnnealer::run(), and protocols::flexpack::annealer::FlexbbSimAnnealer::run().

setup_iterations() [2/2]

void core::pack::annealer::SimAnnealerBase::setup_iterations

(

const int &

num_of_state_changes

)

References protocols::mean_field::max().

setup_temperature() [1/2]

void core::pack::annealer::SimAnnealerBase::setup_temperature

(

const int &

nn

)

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::run().

setup_temperature() [2/2]

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

start_with_current()

bool core::pack::annealer::SimAnnealerBase::start_with_current ( ) const

protected

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::run().

Member Data Documentation

bestenergy_

core::PackerEnergy& core::pack::annealer::SimAnnealerBase::bestenergy_

private

bestrotamer_at_seqpos_

ObjexxFCL::FArray1D_int& core::pack::annealer::SimAnnealerBase::bestrotamer_at_seqpos_

private

calc_freq_temp

const core::PackerEnergy core::pack::annealer::SimAnnealerBase::calc_freq_temp = 1.0

staticprotected

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::run().

calc_rot_freq_

bool core::pack::annealer::SimAnnealerBase::calc_rot_freq_

private

current_rot_index_

ObjexxFCL::FArray1_int& core::pack::annealer::SimAnnealerBase::current_rot_index_

private

disallow_quench_

bool core::pack::annealer::SimAnnealerBase::disallow_quench_

private

hightemp

const core::PackerEnergy core::pack::annealer::SimAnnealerBase::hightemp = 100.0

staticprotected

hightemp_

core::PackerEnergy core::pack::annealer::SimAnnealerBase::hightemp_

private

Referenced by get_hightemp().

inneriterations_

int core::pack::annealer::SimAnnealerBase::inneriterations_

private

inneriterations_scaling_

core::PackerEnergy core::pack::annealer::SimAnnealerBase::inneriterations_scaling_

private

Referenced by scale_inneriterations().

jump_

int core::pack::annealer::SimAnnealerBase::jump_

private

low_temp_annealing_

bool const core::pack::annealer::SimAnnealerBase::low_temp_annealing_

private

lowtemp

const core::PackerEnergy core::pack::annealer::SimAnnealerBase::lowtemp = 0.3

staticprotected

lowtemp_

core::PackerEnergy core::pack::annealer::SimAnnealerBase::lowtemp_

private

Referenced by get_lowtemp().

maxouteriterations

const int core::pack::annealer::SimAnnealerBase::maxouteriterations = 500

staticprotected

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::run().

num_rots_to_pack_

Size core::pack::annealer::SimAnnealerBase::num_rots_to_pack_

private

Referenced by num_rots_to_pack().

observer_

AnnealerObserverOP core::pack::annealer::SimAnnealerBase::observer_ = nullptr

private

Referenced by get_annealer_observer(), and set_annealer_observer().

outeriterations_

int core::pack::annealer::SimAnnealerBase::outeriterations_

private

outeriterations_scaling_

core::PackerEnergy core::pack::annealer::SimAnnealerBase::outeriterations_scaling_

private

Referenced by scale_outeriterations().

quench_

bool core::pack::annealer::SimAnnealerBase::quench_

private

rot_freq_

ObjexxFCL::FArray1D< core::PackerEnergy >& core::pack::annealer::SimAnnealerBase::rot_freq_

private

start_with_current_

bool core::pack::annealer::SimAnnealerBase::start_with_current_

private

temperature_

core::PackerEnergy core::pack::annealer::SimAnnealerBase::temperature_

private

---

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

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