#include <FlexbbSimAnnealer.hh>

Inheritance diagram for protocols::flexpack::annealer::FlexbbSimAnnealer:

Collaboration diagram for protocols::flexpack::annealer::FlexbbSimAnnealer:

Public Types
typedef core::pack::annealer::SimAnnealerBase	parent

typedef core::Size	Size

typedef core::PackerEnergy	PackerEnergy

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

Public Member Functions
	FlexbbSimAnnealer (ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, PackerEnergy &bestenergy, bool start_with_current, interaction_graph::FlexbbInteractionGraphOP ig, rotamer_set::FlexbbRotamerSetsCOP rotsets, ObjexxFCL::FArray1D_int &current_rot_index, bool calc_rot_freq, ObjexxFCL::FArray1D< PackerEnergy > &rot_freq)

virtual	~FlexbbSimAnnealer ()

void	run ()

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)

Protected Member Functions
Size	pick_a_rotamer (Size outercycle, Size innercycle, Size cycle_number, utility::vector1< Size > &accessible_state_list) const

bool	pass_metropolis_multiple_nodes_changing (PackerEnergy previous_fragmentE, PackerEnergy deltaE, Size num_changing_nodes) 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 ()

Private Member Functions
	FlexbbSimAnnealer (const FlexbbSimAnnealer &rhs)

Private Attributes
interaction_graph::FlexbbInteractionGraphOP	ig_

rotamer_set::FlexbbRotamerSetsCOP	rotsets_

Additional Inherited Members
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 core::PackerEnergy protocols::flexpack::annealer::FlexbbSimAnnealer::PackerEnergy

typedef core::pack::annealer::SimAnnealerBase protocols::flexpack::annealer::FlexbbSimAnnealer::parent

typedef core::Size protocols::flexpack::annealer::FlexbbSimAnnealer::Size

Constructor & Destructor Documentation

protocols::flexpack::annealer::FlexbbSimAnnealer::FlexbbSimAnnealer	(	ObjexxFCL::FArray1D_int &	bestrotamer_at_seqpos,
		PackerEnergy &	bestenergy,
		bool	start_with_current,
		interaction_graph::FlexbbInteractionGraphOP	ig,
		rotamer_set::FlexbbRotamerSetsCOP	rotsets,
		ObjexxFCL::FArray1D_int &	current_rot_index,
		bool	calc_rot_freq,
		ObjexxFCL::FArray1D< PackerEnergy > &	rot_freq
	)

protocols::flexpack::annealer::FlexbbSimAnnealer::~FlexbbSimAnnealer ( )

virtual

protocols::flexpack::annealer::FlexbbSimAnnealer::FlexbbSimAnnealer ( const FlexbbSimAnnealer & rhs)

private

Member Function Documentation

bool protocols::flexpack::annealer::FlexbbSimAnnealer::pass_metropolis_multiple_nodes_changing	(	PackerEnergy	previous_fragmentE,
		PackerEnergy	deltaE,
		Size	num_changing_nodes
	)		const

protected

References core::pack::annealer::SimAnnealerBase::get_temperature(), and core::pack::annealer::SimAnnealerBase::pass_metropolis().

Referenced by run().

core::Size protocols::flexpack::annealer::FlexbbSimAnnealer::pick_a_rotamer	(	Size	outercycle,
		Size	innercycle,
		Size	cycle_number,
		utility::vector1< Size > &	accessible_state_list
	)		const

protected

References core::pack::annealer::SimAnnealerBase::quench().

Referenced by run().

void protocols::flexpack::annealer::FlexbbSimAnnealer::run ( )

virtual

The FlexbbSimAnnealer operates with three submodes: mvsc_only : same as the fixbb mode, only consider moving the side chains mvbb_only : no movement with the side chain, but only move the backbone both_sc_and bb:default mode would be a combination of move side chain and backbone fragments

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

Member Data Documentation

interaction_graph::FlexbbInteractionGraphOP protocols::flexpack::annealer::FlexbbSimAnnealer::ig_

private

Referenced by run().

rotamer_set::FlexbbRotamerSetsCOP protocols::flexpack::annealer::FlexbbSimAnnealer::rotsets_

private

Referenced by run().

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

src/protocols/flexpack/annealer/FlexbbSimAnnealer.hh
src/protocols/flexpack/annealer/FlexbbSimAnnealer.cc

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation