#include <SequenceSymmetricAnnealer.hh>

Inheritance diagram for core::pack::annealer::SequenceSymmetricAnnealer:

[legend]

Public Types
typedef interaction_graph::AnnealableGraphBaseOP	AnnealableGraphBaseOP

Public Types inherited from core::pack::annealer::RotamerAssigningAnnealer
typedef rotamer_set::FixbbRotamerSetsCOP	FixbbRotamerSetsCOP

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

Public Member Functions
	SequenceSymmetricAnnealer (core::pose::Pose const &pose, utility::vector0< int > &rot_to_pack, ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy, bool start_with_current, AnnealableGraphBaseOP ig, FixbbRotamerSetsCOP rotamer_sets, ObjexxFCL::FArray1_int &current_rot_index, bool calc_rot_freq, ObjexxFCL::FArray1D< core::PackerEnergy > &rot_freq, std::string const &rs_prefix)

	SequenceSymmetricAnnealer (core::pose::Pose const &pose, ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy, bool start_with_current, AnnealableGraphBaseOP ig, FixbbRotamerSetsCOP rotamer_sets, ObjexxFCL::FArray1_int &current_rot_index, bool calc_rot_freq, ObjexxFCL::FArray1D< core::PackerEnergy > &rot_freq, std::string const &rs_prefix)

	~SequenceSymmetricAnnealer () override
	virtual destructor More...

void	run () override
	sim_annealing for fixed backbone design mode More...

void	record_annealer_trajectory (bool setting)

void	trajectory_file_name (std::string const &setting)

NODISCARD_ATTR utility::vector1< utility::vector1< Size > >	create_corresponding_mress_for_mres () const

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)

	~RotamerAssigningAnnealer () override

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)

	~SimAnnealerBase () override
	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)

AnnealerObserverOP	get_annealer_observer ()

AnnealerObserverCOP	get_annealer_observer () const

void	set_annealer_observer (AnnealerObserverOP obs)

Private Member Functions
	SequenceSymmetricAnnealer (SequenceSymmetricAnnealer const &rhs)

void	search_pose_for_residue_subsets (core::pose::Pose const &pose)
	Determines whether the selection logic passed to the annealer is valid, must be equal to "type_only", "identity", or "try_identity". More...

void	print_linked_residues (utility::vector1< utility::vector1< core::Size > > const &corresponding_mress_for_mres) const
	Prints the linked residues in a useful, human readable format. Uses the Rosetta number for linked residues. More...

void	update_shared_residue_map (core::Size const id, std::unordered_map< std::string, core::Size > &map) const
	Updates map with all residue types for moltenresidue, id. Map contains a count for each type of residue previously seen. More...

std::unordered_set< std::string >	get_shared_residue_types (core::Size const curr_mres, utility::vector1< core::Size > const &linked_res) const
	Returns the common set of residues based on a vector of linked moltenred ids. More...

SeqSymmAnnealerSetup	setup_for_linked_residues ()
	Sets up the necessary objects required for running the annealer. Returns vector of vector of mres for linked residues and common residue types for each linked res set. More...

Private Attributes
std::string	starting_sequence_

pose::PDBInfoCOP	pdb_info_

AnnealableGraphBaseOP	ig_

bool	record_annealer_trajectory_

std::string	trajectory_file_name_

bool	power_mode_ = false

utility::vector1< utility::vector1< utility::vector1< bool > > >	residue_subsets_

std::string	rs_prefix_ = "SequenceSymmetricAnnealer__"

Additional Inherited Members
Protected Member Functions inherited from core::pack::annealer::RotamerAssigningAnnealer
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 () 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 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

◆ AnnealableGraphBaseOP

typedef interaction_graph::AnnealableGraphBaseOP core::pack::annealer::SequenceSymmetricAnnealer::AnnealableGraphBaseOP

Constructor & Destructor Documentation

◆ SequenceSymmetricAnnealer() [1/3]

core::pack::annealer::SequenceSymmetricAnnealer::SequenceSymmetricAnnealer	(	core::pose::Pose const &	pose,
		utility::vector0< int > &	rot_to_pack,
		ObjexxFCL::FArray1D_int &	bestrotamer_at_seqpos,
		core::PackerEnergy &	bestenergy,
		bool	start_with_current,
		AnnealableGraphBaseOP	ig,
		FixbbRotamerSetsCOP	rotamer_sets,
		ObjexxFCL::FArray1_int &	current_rot_index,
		bool	calc_rot_freq,
		ObjexxFCL::FArray1D< core::PackerEnergy > &	rot_freq,
		std::string const &	rs_prefix
	)

◆ SequenceSymmetricAnnealer() [2/3]

core::pack::annealer::SequenceSymmetricAnnealer::SequenceSymmetricAnnealer	(	core::pose::Pose const &	pose,
		ObjexxFCL::FArray1D_int &	bestrotamer_at_seqpos,
		core::PackerEnergy &	bestenergy,
		bool	start_with_current,
		AnnealableGraphBaseOP	ig,
		FixbbRotamerSetsCOP	rotamer_sets,
		ObjexxFCL::FArray1_int &	current_rot_index,
		bool	calc_rot_freq,
		ObjexxFCL::FArray1D< core::PackerEnergy > &	rot_freq,
		std::string const &	rs_prefix
	)

◆ ~SequenceSymmetricAnnealer()

core::pack::annealer::SequenceSymmetricAnnealer::~SequenceSymmetricAnnealer ( )

overridedefault

virtual destructor

◆ SequenceSymmetricAnnealer() [3/3]

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

private

Member Function Documentation

◆ create_corresponding_mress_for_mres()

utility::vector1< utility::vector1< Size > > core::pack::annealer::SequenceSymmetricAnnealer::create_corresponding_mress_for_mres ( ) const

References core::chemical::operator==(), core::scoring::pair, and core::pack::annealer::process_linked_res_set().

◆ get_shared_residue_types()

std::unordered_set< std::string > core::pack::annealer::SequenceSymmetricAnnealer::get_shared_residue_types	(	core::Size const	curr_mres,
		utility::vector1< core::Size > const &	linked_res
	)		const

private

Returns the common set of residues based on a vector of linked moltenred ids.

◆ print_linked_residues()

void core::pack::annealer::SequenceSymmetricAnnealer::print_linked_residues ( utility::vector1< utility::vector1< core::Size > > const & corresponding_mress_for_mres ) const

private

Prints the linked residues in a useful, human readable format. Uses the Rosetta number for linked residues.

References TR().

◆ record_annealer_trajectory()

void core::pack::annealer::SequenceSymmetricAnnealer::record_annealer_trajectory ( bool setting )

◆ run()

void core::pack::annealer::SequenceSymmetricAnnealer::run ( )

overridevirtual

sim_annealing for fixed backbone design mode

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

References core::sequence::end, core::conformation::Residue::name3(), core::pack::pass_metropolis(), and core::scoring::rg.

◆ search_pose_for_residue_subsets()

void core::pack::annealer::SequenceSymmetricAnnealer::search_pose_for_residue_subsets ( core::pose::Pose const & pose )

private

Determines whether the selection logic passed to the annealer is valid, must be equal to "type_only", "identity", or "try_identity".

Uses the rs_prefix_ to search the pose for stored residue subsets. It is expected that all relevant residue subsets will be prefixed by the rs_prefix_ and be in the form: <rs_prefix_>_<linked_residue_subset_id>_<residue_subset_number_in_group>

References core::pose::Pose::data(), core::select::residue_selector::CachedResidueSubset::get_subset(), core::select::residue_selector::CachedResidueSubset::has_subset(), core::select::residue_selector::CachedResidueSubset::has_subset_prefix(), core::pose::datacache::CacheableDataType::STORED_RESIDUE_SUBSET, core::id::to_string(), and TR().

◆ setup_for_linked_residues()

SeqSymmAnnealerSetup core::pack::annealer::SequenceSymmetricAnnealer::setup_for_linked_residues ( )

private

Sets up the necessary objects required for running the annealer. Returns vector of vector of mres for linked residues and common residue types for each linked res set.

References core::id::to_string().

◆ trajectory_file_name()

void core::pack::annealer::SequenceSymmetricAnnealer::trajectory_file_name ( std::string const & setting )

◆ update_shared_residue_map()

void core::pack::annealer::SequenceSymmetricAnnealer::update_shared_residue_map	(	core::Size const	id,
		std::unordered_map< std::string, core::Size > &	map
	)		const

private

Updates map with all residue types for moltenresidue, id. Map contains a count for each type of residue previously seen.

References core::id::to_string(), and TR().

Member Data Documentation

◆ ig_

AnnealableGraphBaseOP core::pack::annealer::SequenceSymmetricAnnealer::ig_

private

◆ pdb_info_

pose::PDBInfoCOP core::pack::annealer::SequenceSymmetricAnnealer::pdb_info_

private

◆ power_mode_

bool core::pack::annealer::SequenceSymmetricAnnealer::power_mode_ = false

private

◆ record_annealer_trajectory_

bool core::pack::annealer::SequenceSymmetricAnnealer::record_annealer_trajectory_

private

◆ residue_subsets_

utility::vector1< utility::vector1< utility::vector1< bool > > > core::pack::annealer::SequenceSymmetricAnnealer::residue_subsets_

private

◆ rs_prefix_

std::string core::pack::annealer::SequenceSymmetricAnnealer::rs_prefix_ = "SequenceSymmetricAnnealer__"

private

◆ starting_sequence_

std::string core::pack::annealer::SequenceSymmetricAnnealer::starting_sequence_

private

◆ trajectory_file_name_

std::string core::pack::annealer::SequenceSymmetricAnnealer::trajectory_file_name_

private

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

src/core/pack/annealer/SequenceSymmetricAnnealer.hh
src/core/pack/annealer/SequenceSymmetricAnnealer.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ AnnealableGraphBaseOP

Constructor & Destructor Documentation

◆ SequenceSymmetricAnnealer() [1/3]

◆ SequenceSymmetricAnnealer() [2/3]

◆ ~SequenceSymmetricAnnealer()

◆ SequenceSymmetricAnnealer() [3/3]

Member Function Documentation

◆ create_corresponding_mress_for_mres()

◆ get_shared_residue_types()

◆ print_linked_residues()

◆ record_annealer_trajectory()

◆ run()

◆ search_pose_for_residue_subsets()

◆ setup_for_linked_residues()

◆ trajectory_file_name()

◆ update_shared_residue_map()

Member Data Documentation

◆ ig_

◆ pdb_info_

◆ power_mode_

◆ record_annealer_trajectory_

◆ residue_subsets_

◆ rs_prefix_

◆ starting_sequence_

◆ trajectory_file_name_