#include <RotamerAssigningAnnealer.hh>

Public Types
typedef rotamer_set::FixbbRotamerSetsCOP	FixbbRotamerSetsCOP

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

Public Member Functions
	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...

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
FixbbRotamerSetsCOP	rotamer_sets () const

utility::vector0< int > const &	rot_to_pack () 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
void	setup_rots_for_node (FixbbRotamerSetsCOP rotamer_sets)

Private Attributes
FixbbRotamerSetsCOP	rotamer_sets_

utility::vector0< int >	rot_to_pack_

utility::vector1 < utility::vector1< int > >	rots_for_nodes_

int	current_to_pick_

int	n_assigned_at_start_

bool	assign_state_to_all_nodes_immediately_

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 rotamer_set::FixbbRotamerSetsCOP core::pack::annealer::RotamerAssigningAnnealer::FixbbRotamerSetsCOP

Constructor & Destructor Documentation

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
	)

core::pack::annealer::RotamerAssigningAnnealer::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
	)

core::pack::annealer::RotamerAssigningAnnealer::~RotamerAssigningAnnealer ( )

virtual

Member Function Documentation

int core::pack::annealer::RotamerAssigningAnnealer::pick_a_rotamer ( int cycle )

pick a rotamer from a list

if no rotamer is available, return a nonsense number, like -1

References assign_state_to_all_nodes_immediately_, core::pack::annealer::SimAnnealerBase::current_rot_index(), current_to_pick_, core::pack::annealer::SimAnnealerBase::get_start_with_current(), mod(), n_assigned_at_start_, core::pack::annealer::SimAnnealerBase::num_rots_to_pack(), pick_a_rotamer_for_node(), core::pack::annealer::SimAnnealerBase::quench(), numeric::random::random_permutation(), core::pack::annealer::RG, rot_to_pack_, rots_for_nodes_, core::io::serialization::size(), and numeric::random::RandomGenerator::uniform().

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

int core::pack::annealer::RotamerAssigningAnnealer::pick_a_rotamer_for_node ( int node ) const

References core::pack::annealer::RG, rots_for_nodes_, and numeric::random::RandomGenerator::uniform().

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

utility::vector0< int > const & core::pack::annealer::RotamerAssigningAnnealer::rot_to_pack ( ) const

protected

References rot_to_pack_.

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

RotamerAssigningAnnealer::FixbbRotamerSetsCOP core::pack::annealer::RotamerAssigningAnnealer::rotamer_sets ( ) const

protected

References rotamer_sets_.

void core::pack::annealer::RotamerAssigningAnnealer::set_assign_state_to_all_nodes_immediately ( bool setting )

References assign_state_to_all_nodes_immediately_.

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

void core::pack::annealer::RotamerAssigningAnnealer::setup_rots_for_node ( FixbbRotamerSetsCOP rotamer_sets )

private

if you want to make a single rotamer substitution for a single node then you'll want to grab a random rotamer for that node – this function creates a mapping from moltenres id to the set of accessible rotamers for that moltenres. It also makes sure that the user has provided a valid set of rotamers: each molten residue must have at least one pickable rotamer, or the final rotamer assignment will have some molten residues in an unassigned state. Bad user input is most common when the annealer is constructed using the rot_to_pack vector.

References rot_to_pack_, rots_for_nodes_, and utility_exit.