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

#include <SimAnnealerBase.hh>

Public Types
typedef rotamer_set::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)
virtual	~SimAnnealerBase ()
	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)

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 ()
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_

Member Typedef Documentation

typedef rotamer_set::RotamerSetsBaseCOP core::pack::annealer::SimAnnealerBase::RotamerSetsBaseCOP

Constructor & Destructor Documentation

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
	)

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

virtual

virtual destructor

SimAnnealerBase::~SimAnnealerBase()

Detailed:

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Remarks

References:

Authors

Last Modified:

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

private

Member Function Documentation

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

protected

References bestenergy_.

Referenced by core::pack::annealer::FASTERAnnealer::run(), core::pack::annealer::MultiCoolAnnealer::run(), core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), and core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run().

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

protected

References bestrotamer_at_seqpos_.

Referenced by core::pack::annealer::FASTERAnnealer::finalize_output(), core::pack::annealer::FASTERAnnealer::run(), core::pack::annealer::DebuggingAnnealer::run(), core::pack::annealer::MultiCoolAnnealer::run(), core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), and core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run().

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

protected

References bestrotamer_at_seqpos_.

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

protected

References calc_rot_freq_.

Referenced by core::pack::annealer::FASTERAnnealer::run(), core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run(), and core::pack::annealer::MultiCoolAnnealer::run_constant_temp_rotamer_substitutions().

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

protected

References calc_rot_freq_.

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

protected

References jump_.

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

protected

References current_rot_index_.

Referenced by core::pack::annealer::RotamerAssigningAnnealer::pick_a_rotamer().

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

protected

References current_rot_index_.

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

(

)

const

References calc_rot_freq_.

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

inlineprotected

References hightemp_.

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

(

)

const

SimAnnealerBase::get_inneriterations()

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References get_temperature(), inneriterations_, inneriterations_scaling_, and low_temp_annealing_.

Referenced by core::pack::annealer::MultiCoolAnnealer::run(), core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), and core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run().

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

inlineprotected

References lowtemp_.

Referenced by core::pack::annealer::MultiCoolAnnealer::cool().

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

(

)

const

get the iterations number for simulation

SimAnnealerBase::get_outeriterations()

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References outeriterations_, and outeriterations_scaling_.

Referenced by core::pack::annealer::MultiCoolAnnealer::run(), core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run(), and setup_temperature().

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

(

)

const

References start_with_current_.

Referenced by core::pack::annealer::RotamerAssigningAnnealer::pick_a_rotamer().

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

(

)

const

References temperature_.

Referenced by core::pack::annealer::MultiCoolAnnealer::cool(), get_inneriterations(), core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run(), and core::pack::annealer::MultiCoolAnnealer::run_constant_temp_rotamer_substitutions().

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

inlineprotected

References num_rots_to_pack_.

Referenced by core::pack::annealer::RotamerAssigningAnnealer::pick_a_rotamer(), core::pack::annealer::DebuggingAnnealer::run(), core::pack::annealer::MultiCoolAnnealer::run(), core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run(), and core::pack::annealer::MultiCoolAnnealer::run_constant_temp_rotamer_substitutions().

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

protected

References num_rots_to_pack_.

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.

SimAnnealerBase::pass_metropolis

Detailed:

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Referenced by core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run(), and core::pack::annealer::MultiCoolAnnealer::run_constant_temp_rotamer_substitutions().

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

References beta, quench_, sab_RG, temperature_, and numeric::random::RandomGenerator::uniform().

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

(

)

const

References quench_.

Referenced by core::pack::annealer::RotamerAssigningAnnealer::pick_a_rotamer(), core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run(), and core::pack::annealer::MultiCoolAnnealer::run_constant_temp_rotamer_substitutions().

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

protected

References rot_freq_.

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

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

protected

References rot_freq_.

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

pure virtual

Implemented in core::pack::annealer::FixbbCoupledRotamerSimAnnealer, core::pack::annealer::FixbbLinkingRotamerSimAnnealer, core::pack::annealer::FixbbSimAnnealer, core::pack::annealer::MultiCoolAnnealer, core::pack::annealer::DebuggingAnnealer, and core::pack::annealer::FASTERAnnealer.

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

inline

References inneriterations_scaling_.

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

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

inline

References outeriterations_scaling_.

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

(

bool const &

setting

)

References disallow_quench_.

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

(

core::PackerEnergy

high

)

References hightemp_.

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

(

core::PackerEnergy

low

)

References lowtemp_.

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

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

(

)

References quench_.

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

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

(

core::PackerEnergy

new_temperature

)

References temperature_.

Referenced by core::pack::annealer::MultiCoolAnnealer::cool(), and core::pack::annealer::MultiCoolAnnealer::run().

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

(

)

References quench_.

Referenced by core::pack::annealer::FASTERAnnealer::run_quench_cycles(), and setup_temperature().

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

(

)

SimAnnealerBase::setup_iterations(bool start_with_current)

Detailed:

Global Read:

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Remarks

References:

Authors

Last Modified:

References num_rots_to_pack_.

Referenced by core::pack::annealer::DebuggingAnnealer::run(), core::pack::annealer::MultiCoolAnnealer::run(), core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), and core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run().

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

(

const int &

num_of_state_changes

)

References current_rot_index_, inneriterations_, low_temp_annealing_, outeriterations_, and start_with_current_.

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

(

const int &

nn

)

References disallow_quench_, get_outeriterations(), hightemp_, jump_, lowtemp_, set_to_quench(), and temperature_.

Referenced by core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), and core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run().

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

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

protected

References start_with_current_.

Member Data Documentation

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

private

Referenced by bestenergy().

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

private

Referenced by bestrotamer_at_seqpos().

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

staticprotected

Referenced by core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run(), and core::pack::annealer::MultiCoolAnnealer::run_constant_temp_rotamer_substitutions().

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

private

Referenced by calc_rot_freq(), and get_calc_rot_freq().

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

private

Referenced by current_rot_index(), and setup_iterations().

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

private

Referenced by set_disallow_quench(), and setup_temperature().

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

staticprotected

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

private

Referenced by get_hightemp(), set_hightemp(), and setup_temperature().

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

private

Referenced by get_inneriterations(), and setup_iterations().

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

private

Referenced by get_inneriterations(), and scale_inneriterations().

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

private

Referenced by clear(), and setup_temperature().

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

private

Referenced by get_inneriterations(), and setup_iterations().

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

staticprotected

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

private

Referenced by get_lowtemp(), set_lowtemp(), and setup_temperature().

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

staticprotected

Referenced by core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), and core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run().

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

private

Referenced by num_rots_to_pack(), and setup_iterations().

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

private

Referenced by get_outeriterations(), and setup_iterations().

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

private

Referenced by get_outeriterations(), and scale_outeriterations().

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

private

Referenced by pass_metropolis(), quench(), set_not_to_quench(), and set_to_quench().

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

private

Referenced by rot_freq().

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

private

Referenced by get_start_with_current(), setup_iterations(), and start_with_current().

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

private

Referenced by get_temperature(), pass_metropolis(), set_temperature(), and setup_temperature().

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

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