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core::pack::annealer::FixbbLinkingRotamerSimAnnealer Class Reference

#include <FixbbLinkingRotamerSimAnnealer.hh>

Inheritance diagram for core::pack::annealer::FixbbLinkingRotamerSimAnnealer:
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Collaboration diagram for core::pack::annealer::FixbbLinkingRotamerSimAnnealer:
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Public Types

typedef
interaction_graph::InteractionGraphBaseOP 		InteractionGraphBaseOP
 
typedef rotamer_set::RotamerSetsCOP RotamerSetsCOP
 
typedef rotamer_set::RotamerSetCOP RotamerSetCOP
 
typedef rotamer_set::RotamerLinksOP RotamerLinksOP
 
typedef
rotamer_set::RotamerLinksCOP 		RotamerLinksCOP
 
- 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

 FixbbLinkingRotamerSimAnnealer (utility::vector0< int > &rot_to_pack, ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy, bool start_with_current, InteractionGraphBaseOP ig, FixbbRotamerSetsCOP rotamer_sets, ObjexxFCL::FArray1_int &current_rot_index, bool calc_rot_freq, ObjexxFCL::FArray1D< core::PackerEnergy > &rot_freq, RotamerLinksCOP rotamer_links)
 
 FixbbLinkingRotamerSimAnnealer (ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy, bool start_with_current, InteractionGraphBaseOP ig, FixbbRotamerSetsCOP rotamer_sets, ObjexxFCL::FArray1_int &current_rot_index, bool calc_rot_freq, ObjexxFCL::FArray1D< core::PackerEnergy > &rot_freq, RotamerLinksCOP rotamer_links)
 
virtual ~FixbbLinkingRotamerSimAnnealer ()
 virtual destructor More...
 
void run ()
 sim_annealing for fixed backbone design mode More...
 
- 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 setup_rotamer_links (RotamerLinksCOP rotamer_links)
 
 FixbbLinkingRotamerSimAnnealer (const FixbbLinkingRotamerSimAnnealer &rhs)
 

Private Attributes

InteractionGraphBaseOP ig_
 
RotamerLinksOP rotamer_links_
 

Additional Inherited Members

- Protected Member Functions inherited from core::pack::annealer::RotamerAssigningAnnealer
FixbbRotamerSetsCOP rotamer_sets () const
 
utility::vector0< int > const & rot_to_pack () const
 
- 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
 

Detailed Description

Definition at line 35 of file FixbbLinkingRotamerSimAnnealer.hh.

Member Typedef Documentation

typedef interaction_graph::InteractionGraphBaseOP core::pack::annealer::FixbbLinkingRotamerSimAnnealer::InteractionGraphBaseOP

Definition at line 38 of file FixbbLinkingRotamerSimAnnealer.hh.

typedef rotamer_set::RotamerLinksCOP core::pack::annealer::FixbbLinkingRotamerSimAnnealer::RotamerLinksCOP

Definition at line 42 of file FixbbLinkingRotamerSimAnnealer.hh.

typedef rotamer_set::RotamerLinksOP core::pack::annealer::FixbbLinkingRotamerSimAnnealer::RotamerLinksOP

Definition at line 41 of file FixbbLinkingRotamerSimAnnealer.hh.

typedef rotamer_set::RotamerSetCOP core::pack::annealer::FixbbLinkingRotamerSimAnnealer::RotamerSetCOP

Definition at line 40 of file FixbbLinkingRotamerSimAnnealer.hh.

typedef rotamer_set::RotamerSetsCOP core::pack::annealer::FixbbLinkingRotamerSimAnnealer::RotamerSetsCOP

Definition at line 39 of file FixbbLinkingRotamerSimAnnealer.hh.

Constructor & Destructor Documentation

core::pack::annealer::FixbbLinkingRotamerSimAnnealer::FixbbLinkingRotamerSimAnnealer ( utility::vector0< int > &  rot_to_pack,
ObjexxFCL::FArray1D_int &  bestrotamer_at_seqpos,
core::PackerEnergy &  bestenergy,
bool  start_with_current,
InteractionGraphBaseOP  ig,
FixbbRotamerSetsCOP  rotamer_sets,
ObjexxFCL::FArray1_int &  current_rot_index,
bool  calc_rot_freq,
ObjexxFCL::FArray1D< core::PackerEnergy > &  rot_freq,
RotamerLinksCOP  rotamer_links 
)
core::pack::annealer::FixbbLinkingRotamerSimAnnealer::FixbbLinkingRotamerSimAnnealer ( ObjexxFCL::FArray1D_int &  bestrotamer_at_seqpos,
core::PackerEnergy &  bestenergy,
bool  start_with_current,
InteractionGraphBaseOP  ig,
FixbbRotamerSetsCOP  rotamer_sets,
ObjexxFCL::FArray1_int &  current_rot_index,
bool  calc_rot_freq,
ObjexxFCL::FArray1D< core::PackerEnergy > &  rot_freq,
RotamerLinksCOP  rotamer_links 
)
core::pack::annealer::FixbbLinkingRotamerSimAnnealer::~FixbbLinkingRotamerSimAnnealer ( )
virtual

virtual destructor

Definition at line 168 of file FixbbLinkingRotamerSimAnnealer.cc.

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

Member Function Documentation

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

sim_annealing for fixed backbone design mode

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

Definition at line 172 of file FixbbLinkingRotamerSimAnnealer.cc.

References core::pack::annealer::SimAnnealerBase::bestenergy(), core::pack::annealer::SimAnnealerBase::bestrotamer_at_seqpos(), core::pack::annealer::SimAnnealerBase::calc_freq_temp, core::pack::annealer::SimAnnealerBase::calc_rot_freq(), FBBCRSA_RG(), core::pack::annealer::SimAnnealerBase::get_inneriterations(), core::pack::annealer::SimAnnealerBase::get_outeriterations(), core::pack::annealer::SimAnnealerBase::get_temperature(), ig_, core::pack::annealer::SimAnnealerBase::maxouteriterations, core::pack::annealer::SimAnnealerBase::num_rots_to_pack(), core::pack::annealer::SimAnnealerBase::pass_metropolis(), core::pack::annealer::SimAnnealerBase::quench(), core::pack::annealer::RotamerAssigningAnnealer::rot_to_pack(), rotamer_links_, core::pack::annealer::RotamerAssigningAnnealer::rotamer_sets(), core::pack::annealer::SimAnnealerBase::setup_iterations(), core::pack::annealer::SimAnnealerBase::setup_temperature(), and core::pack::annealer::TR().

void core::pack::annealer::FixbbLinkingRotamerSimAnnealer::setup_rotamer_links ( RotamerLinksCOP  rotamer_links)
private

Definition at line 128 of file FixbbLinkingRotamerSimAnnealer.cc.

References rotamer_links_, and core::pack::annealer::RotamerAssigningAnnealer::rotamer_sets().

Member Data Documentation

InteractionGraphBaseOP core::pack::annealer::FixbbLinkingRotamerSimAnnealer::ig_
private

Definition at line 80 of file FixbbLinkingRotamerSimAnnealer.hh.

Referenced by run().

RotamerLinksOP core::pack::annealer::FixbbLinkingRotamerSimAnnealer::rotamer_links_
private

Definition at line 82 of file FixbbLinkingRotamerSimAnnealer.hh.

Referenced by run(), and setup_rotamer_links().

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