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core::pack::annealer::SimAnnealerBase Class Referenceabstract

#include <SimAnnealerBase.hh>

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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_
 

Detailed Description

Definition at line 46 of file SimAnnealerBase.hh.

Member Typedef Documentation

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

Definition at line 49 of file SimAnnealerBase.hh.

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()

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Definition at line 115 of file SimAnnealerBase.cc.

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

Member Function Documentation

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

Definition at line 294 of file SimAnnealerBase.cc.

References bestenergy_.

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

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

Definition at line 292 of file SimAnnealerBase.cc.

References bestrotamer_at_seqpos_.

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

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

Definition at line 293 of file SimAnnealerBase.cc.

References bestrotamer_at_seqpos_.

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

Definition at line 298 of file SimAnnealerBase.cc.

References calc_rot_freq_.

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

Definition at line 299 of file SimAnnealerBase.cc.

References calc_rot_freq_.

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

Definition at line 278 of file SimAnnealerBase.cc.

References jump_.

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

Definition at line 296 of file SimAnnealerBase.cc.

References current_rot_index_.

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

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

Definition at line 297 of file SimAnnealerBase.cc.

References current_rot_index_.

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

Definition at line 289 of file SimAnnealerBase.cc.

References calc_rot_freq_.

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

Definition at line 119 of file SimAnnealerBase.hh.

References hightemp_.

int core::pack::annealer::SimAnnealerBase::get_inneriterations ( ) const

SimAnnealerBase::get_inneriterations()

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Definition at line 163 of file SimAnnealerBase.cc.

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

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

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

Definition at line 120 of file SimAnnealerBase.hh.

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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Definition at line 138 of file SimAnnealerBase.cc.

References outeriterations_, and outeriterations_scaling_.

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

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

Definition at line 288 of file SimAnnealerBase.cc.

References start_with_current_.

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

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

Definition at line 284 of file SimAnnealerBase.cc.

References temperature_.

Referenced by core::pack::annealer::MultiCoolAnnealer::cool(), get_inneriterations(), protocols::flexpack::annealer::FlexbbSimAnnealer::pass_metropolis_multiple_nodes_changing(), protocols::flexpack::annealer::FlexbbSimAnnealer::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().

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

Definition at line 105 of file SimAnnealerBase.hh.

References num_rots_to_pack_.

Referenced by core::pack::annealer::RotamerAssigningAnnealer::pick_a_rotamer(), core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::MultiCoolAnnealer::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

Definition at line 291 of file SimAnnealerBase.cc.

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

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Definition at line 329 of file SimAnnealerBase.cc.

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::pass_metropolis_multiple_nodes_changing(), protocols::flexpack::annealer::FlexbbSimAnnealer::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::pass_metropolis ( core::PackerEnergy  previous_energy,
core::PackerEnergy  delta_energy 
) const

Definition at line 335 of file SimAnnealerBase.cc.

References quench_, sab_RG(), and temperature_.

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

Definition at line 287 of file SimAnnealerBase.cc.

References quench_.

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::pick_a_rotamer(), core::pack::annealer::RotamerAssigningAnnealer::pick_a_rotamer(), protocols::flexpack::annealer::FlexbbSimAnnealer::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().

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

Definition at line 300 of file SimAnnealerBase.cc.

References rot_freq_.

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

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

Definition at line 301 of file SimAnnealerBase.cc.

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::MultiCoolAnnealer, core::pack::annealer::FixbbSimAnnealer, core::pack::annealer::FASTERAnnealer, core::pack::annealer::DebuggingAnnealer, and protocols::flexpack::annealer::FlexbbSimAnnealer.

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

Definition at line 93 of file SimAnnealerBase.hh.

References inneriterations_scaling_.

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

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

Definition at line 88 of file SimAnnealerBase.hh.

References outeriterations_scaling_.

void core::pack::annealer::SimAnnealerBase::set_disallow_quench ( bool const &  setting)

Definition at line 306 of file SimAnnealerBase.cc.

References disallow_quench_.

void core::pack::annealer::SimAnnealerBase::set_hightemp ( core::PackerEnergy  high)

Definition at line 303 of file SimAnnealerBase.cc.

References hightemp_.

void core::pack::annealer::SimAnnealerBase::set_lowtemp ( core::PackerEnergy  low)

Definition at line 304 of file SimAnnealerBase.cc.

References lowtemp_.

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

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

Definition at line 286 of file SimAnnealerBase.cc.

References quench_.

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

void core::pack::annealer::SimAnnealerBase::set_temperature ( core::PackerEnergy  new_temperature)

Definition at line 282 of file SimAnnealerBase.cc.

References temperature_.

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

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

Definition at line 285 of file SimAnnealerBase.cc.

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)

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Definition at line 195 of file SimAnnealerBase.cc.

References num_rots_to_pack_.

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::run(), core::pack::annealer::DebuggingAnnealer::run(), core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::MultiCoolAnnealer::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)

Definition at line 201 of file SimAnnealerBase.cc.

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

void core::pack::annealer::SimAnnealerBase::setup_temperature ( const int &  nn)

Definition at line 224 of file SimAnnealerBase.cc.

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

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

Definition at line 295 of file SimAnnealerBase.cc.

References start_with_current_.

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

Member Data Documentation

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

Definition at line 128 of file SimAnnealerBase.hh.

Referenced by bestenergy().

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

Definition at line 127 of file SimAnnealerBase.hh.

Referenced by bestrotamer_at_seqpos(), and core::pack::annealer::DebuggingAnnealer::run().

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

Definition at line 103 of file SimAnnealerBase.hh.

Referenced by protocols::flexpack::annealer::FlexbbSimAnnealer::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_
private

Definition at line 131 of file SimAnnealerBase.hh.

Referenced by calc_rot_freq(), and get_calc_rot_freq().

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

Definition at line 130 of file SimAnnealerBase.hh.

Referenced by current_rot_index(), and setup_iterations().

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

Definition at line 147 of file SimAnnealerBase.hh.

Referenced by set_disallow_quench(), and setup_temperature().

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

Definition at line 100 of file SimAnnealerBase.hh.

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

Definition at line 138 of file SimAnnealerBase.hh.

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

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

Definition at line 136 of file SimAnnealerBase.hh.

Referenced by get_inneriterations(), and setup_iterations().

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

Definition at line 144 of file SimAnnealerBase.hh.

Referenced by get_inneriterations(), and scale_inneriterations().

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

Definition at line 141 of file SimAnnealerBase.hh.

Referenced by clear(), and setup_temperature().

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

Definition at line 146 of file SimAnnealerBase.hh.

Referenced by get_inneriterations(), and setup_iterations().

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

Definition at line 101 of file SimAnnealerBase.hh.

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

Definition at line 139 of file SimAnnealerBase.hh.

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

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

Definition at line 102 of file SimAnnealerBase.hh.

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

Definition at line 126 of file SimAnnealerBase.hh.

Referenced by num_rots_to_pack(), and setup_iterations().

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

Definition at line 135 of file SimAnnealerBase.hh.

Referenced by get_outeriterations(), and setup_iterations().

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

Definition at line 143 of file SimAnnealerBase.hh.

Referenced by get_outeriterations(), and scale_outeriterations().

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

Definition at line 137 of file SimAnnealerBase.hh.

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

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

Definition at line 132 of file SimAnnealerBase.hh.

Referenced by rot_freq().

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

Definition at line 129 of file SimAnnealerBase.hh.

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

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

Definition at line 140 of file SimAnnealerBase.hh.

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

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