#include <GreenPacker.hh>

Inheritance diagram for protocols::minimization_packing::GreenPacker:

[legend]

Public Types
typedef utility::graph::Graph	Graph
	Types. More...

typedef utility::graph::GraphOP	GraphOP

typedef core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph	PrecomputedPairEnergiesInteractionGraph

typedef core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraphOP	PrecomputedPairEnergiesInteractionGraphOP

typedef core::pack::rotamer_set::RotamerSets	RotamerSets

typedef core::pack::rotamer_set::RotamerSetsOP	RotamerSetsOP

typedef core::pack::task::TaskFactory	TaskFactory

typedef core::pack::task::TaskFactoryOP	TaskFactoryOP

typedef core::pack::task::PackerTaskOP	PackerTaskOP

typedef core::pose::Pose	Pose

typedef core::scoring::EnergyMap	EnergyMap

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef core::scoring::ScoreTypes	ScoreTypes

typedef core::scoring::methods::LongRangeTwoBodyEnergy	LongRangeTwoBodyEnergy

typedef core::Size	Size

typedef core::Real	Real

typedef core::Vector	Vector

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Public Member Functions
	GreenPacker ()
	Green Packer. More...

	~GreenPacker () override

void	apply (Pose &) override
	Main Method. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

void	set_scorefunction (ScoreFunction const &)

void	set_group_discriminator (protocols::minimization_packing::GroupDiscriminatorOP)

void	set_task_factory (TaskFactoryOP)

void	set_reference_round_task_factory (TaskFactoryOP)

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	set_weights_for_sfxn (ScoreFunction &sfxn, ScoreTypes const &scoretypes, EnergyMap const &weights) const
	Private methods. More...

void	setup_reference_data (Pose &pose)

void	repack (Pose &pose)

void	split_pose_into_groups (Pose &pose)

void	create_reference_packer_task (Pose &pose)

void	create_reference_packer_neighbor_graph (Pose &pose)

void	create_reference_rotamers (Pose &pose)

void	compute_reference_intragroup_rpes (Pose &pose, core::Size const threads_to_request)

void	create_fresh_task (Pose &pose)

void	create_fresh_packer_neighbor_graph (Pose &pose)

void	create_fresh_rotamers (Pose &pose)

void	find_reference_and_current_rotamer_correspondence (Pose &pose)

void	initialize_internal_correspondence_data (Pose &pose)

void	compute_energies (Pose &pose, core::Size const threads_to_request)

void	run_sa (Pose &pose)

void	cleanup (core::pose::Pose &pose)

void	add_precomputed_energies (Pose &pose, PrecomputedPairEnergiesInteractionGraphOP pig)

void	compute_absent_energies (Pose &pose, PrecomputedPairEnergiesInteractionGraphOP pig)

void	compute_absent_srci_energies_for_residue_pair (Pose &pose, PrecomputedPairEnergiesInteractionGraphOP pig, core::Size lower_res, core::Size upper_res)

void	compute_absent_lrci_energies_for_residue_pair (Pose &pose, LongRangeTwoBodyEnergy const &lre, PrecomputedPairEnergiesInteractionGraphOP pig, core::Size lower_res, core::Size upper_res)

void	drop_inter_group_edges (Pose &pose, GraphOP packer_neighbor_graph) const

void	drop_intra_group_edges (Pose &pose, GraphOP packer_neighbor_graph) const

void	store_reference_pose_geometry (Pose &pose)

void	compare_input_pose_geometry_to_reference (Pose &pose)

Private Attributes
ScoreFunctionOP	full_sfxn_

ScoreFunctionOP	ci_sfxn_

ScoreFunctionOP	cd_sfxn_

bool	create_reference_data_

protocols::minimization_packing::GroupDiscriminatorOP	group_discriminator_

utility::vector1< core::Size >	group_ids_

std::vector< utility::vector1< core::Size > >	group_members_

TaskFactoryOP	reference_task_factory_

TaskFactoryOP	task_factory_

PackerTaskOP	reference_task_
	Data captured from the reference apply() More...

GraphOP	reference_packer_neighbor_graph_

RotamerSetsOP	reference_rotamer_sets_
	rotamer sets created by the reference task More...

utility::vector1< core::Size >	reference_resid_2_moltenres_

utility::vector1< core::Size >	reference_moltenres_2_resid_

PrecomputedPairEnergiesInteractionGraphOP	ci_rpes_
	the stored intra-group RPEs from the context independent components of the score function More...

utility::vector1< utility::vector1< protocols::minimization_packing::MinimalRotamerOP > >	original_rotamers_
	the internal geometry of the rotamers created in the first round More...

utility::vector1< utility::vector1< Real > >	orig_bb_tors_
	the internal geometry of the backbone used in the first round More...

utility::vector1< Vector >	original_bb_rep_coords_
	for debugging; a set of coordinates of each residue for backbone atom #1 (N in proteins, Phos for NA's) so that if the backbone DOFs do change, and the structure of the input pose cannot be superimposed back onto the original coordinates, then a debug runtime_assert statementmet will get caught. More...

PackerTaskOP	current_task_
	Data for the "current" packing – valid between the beginning and end of a call to "apply". More...

RotamerSetsOP	current_rotamer_sets_

PrecomputedPairEnergiesInteractionGraphOP	current_ig_

utility::vector1< utility::vector1< protocols::minimization_packing::MinimalRotamerOP > >	current_rotamers_
	the internal geometry of the rotamers created in the first round More...

GraphOP	current_packer_neighbor_graph_

GraphOP	current_inter_group_packer_neighbor_graph_

GraphOP	current_intra_group_packer_neighbor_graph_

utility::vector1< utility::vector1< core::Size > >	orig_rot_2_curr_rot_
	correspondence between current rotamer set and original rotamer set. More...

utility::vector1< utility::vector1< core::Size > >	curr_rot_2_orig_rot_

utility::vector1< utility::vector1< core::Size > >	curr_rotamers_with_correspondence_

utility::vector1< utility::vector1< core::Size > >	curr_rotamers_without_correspondence_

Additional Inherited Members
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Member Typedef Documentation

◆ EnergyMap

typedef core::scoring::EnergyMap protocols::minimization_packing::GreenPacker::EnergyMap

◆ Graph

typedef utility::graph::Graph protocols::minimization_packing::GreenPacker::Graph

Types.

◆ GraphOP

typedef utility::graph::GraphOP protocols::minimization_packing::GreenPacker::GraphOP

◆ LongRangeTwoBodyEnergy

typedef core::scoring::methods::LongRangeTwoBodyEnergy protocols::minimization_packing::GreenPacker::LongRangeTwoBodyEnergy

◆ PackerTaskOP

typedef core::pack::task::PackerTaskOP protocols::minimization_packing::GreenPacker::PackerTaskOP

◆ Pose

typedef core::pose::Pose protocols::minimization_packing::GreenPacker::Pose

◆ PrecomputedPairEnergiesInteractionGraph

typedef core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph protocols::minimization_packing::GreenPacker::PrecomputedPairEnergiesInteractionGraph

◆ PrecomputedPairEnergiesInteractionGraphOP

typedef core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraphOP protocols::minimization_packing::GreenPacker::PrecomputedPairEnergiesInteractionGraphOP

◆ Real

typedef core::Real protocols::minimization_packing::GreenPacker::Real

◆ RotamerSets

typedef core::pack::rotamer_set::RotamerSets protocols::minimization_packing::GreenPacker::RotamerSets

◆ RotamerSetsOP

typedef core::pack::rotamer_set::RotamerSetsOP protocols::minimization_packing::GreenPacker::RotamerSetsOP

◆ ScoreFunction

typedef core::scoring::ScoreFunction protocols::minimization_packing::GreenPacker::ScoreFunction

◆ ScoreFunctionOP

typedef core::scoring::ScoreFunctionOP protocols::minimization_packing::GreenPacker::ScoreFunctionOP

◆ ScoreTypes

typedef core::scoring::ScoreTypes protocols::minimization_packing::GreenPacker::ScoreTypes

◆ Size

typedef core::Size protocols::minimization_packing::GreenPacker::Size

◆ TaskFactory

typedef core::pack::task::TaskFactory protocols::minimization_packing::GreenPacker::TaskFactory

◆ TaskFactoryOP

typedef core::pack::task::TaskFactoryOP protocols::minimization_packing::GreenPacker::TaskFactoryOP

◆ Vector

typedef core::Vector protocols::minimization_packing::GreenPacker::Vector

Constructor & Destructor Documentation

◆ GreenPacker()

protocols::minimization_packing::GreenPacker::GreenPacker ( )

Green Packer.

◆ ~GreenPacker()

protocols::minimization_packing::GreenPacker::~GreenPacker ( )

overridedefault

Member Function Documentation

◆ add_precomputed_energies()

void protocols::minimization_packing::GreenPacker::add_precomputed_energies	(	Pose &	pose,
		PrecomputedPairEnergiesInteractionGraphOP	pig
	)

private

References ci_rpes_, curr_rot_2_orig_rot_, curr_rotamers_with_correspondence_, current_rotamer_sets_, core::pack::interaction_graph::EdgeBase::get_other_ind(), reference_moltenres_2_resid_, reference_resid_2_moltenres_, and core::pose::Pose::size().

Referenced by compute_energies().

◆ apply()

void protocols::minimization_packing::GreenPacker::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References create_reference_data_, repack(), setup_reference_data(), and protocols::minimization_packing::TR().

◆ cleanup()

void protocols::minimization_packing::GreenPacker::cleanup ( core::pose::Pose & pose )

private

Free memory that is no longer needed

References curr_rot_2_orig_rot_, curr_rotamers_with_correspondence_, curr_rotamers_without_correspondence_, current_ig_, current_inter_group_packer_neighbor_graph_, current_intra_group_packer_neighbor_graph_, current_packer_neighbor_graph_, current_rotamer_sets_, current_rotamers_, current_task_, orig_rot_2_curr_rot_, and core::pack::pack_rotamers_cleanup().

Referenced by repack().

◆ compare_input_pose_geometry_to_reference()

void protocols::minimization_packing::GreenPacker::compare_input_pose_geometry_to_reference ( Pose & pose )

private

References core::conformation::Residue::mainchain_torsions(), orig_bb_tors_, core::pose::Pose::residue(), and core::pose::Pose::size().

◆ compute_absent_energies()

void protocols::minimization_packing::GreenPacker::compute_absent_energies	(	Pose &	pose,
		PrecomputedPairEnergiesInteractionGraphOP	pig
	)

private

this time, iterate across edges in the packer neighbor graph and compute pair interaction energies between rotamers that do not correspond to any of the original rotamers with all other rotamers in the neighboring set. This has to be careful not to double-count interactions between rotamer pairs that both lack a correspondence.

References ci_sfxn_, compute_absent_lrci_energies_for_residue_pair(), compute_absent_srci_energies_for_residue_pair(), curr_rotamers_without_correspondence_, current_intra_group_packer_neighbor_graph_, current_rotamer_sets_, core::pose::Pose::energies(), core::scoring::Energies::long_range_container(), and core::pose::Pose::size().

Referenced by compute_energies().

◆ compute_absent_lrci_energies_for_residue_pair()

void protocols::minimization_packing::GreenPacker::compute_absent_lrci_energies_for_residue_pair	(	Pose &	pose,
		LongRangeTwoBodyEnergy const &	lre,
		PrecomputedPairEnergiesInteractionGraphOP	pig,
		core::Size	lower_res,
		core::Size	upper_res
	)

private

References ci_sfxn_, curr_rot_2_orig_rot_, curr_rotamers_without_correspondence_, current_rotamer_sets_, and core::scoring::methods::TwoBodyEnergy::residue_pair_energy().

Referenced by compute_absent_energies().

◆ compute_absent_srci_energies_for_residue_pair()

void protocols::minimization_packing::GreenPacker::compute_absent_srci_energies_for_residue_pair	(	Pose &	pose,
		PrecomputedPairEnergiesInteractionGraphOP	pig,
		core::Size	lower_res,
		core::Size	upper_res
	)

private

References ci_sfxn_, curr_rot_2_orig_rot_, curr_rotamers_without_correspondence_, and current_rotamer_sets_.

Referenced by compute_absent_energies().

◆ compute_energies()

void protocols::minimization_packing::GreenPacker::compute_energies	(	Pose &	pose,
		core::Size const	threads_to_request
	)

private

References add_precomputed_energies(), cd_sfxn_, compute_absent_energies(), current_ig_, current_inter_group_packer_neighbor_graph_, current_intra_group_packer_neighbor_graph_, current_packer_neighbor_graph_, current_rotamer_sets_, current_task_, and full_sfxn_.

Referenced by repack().

◆ compute_reference_intragroup_rpes()

void protocols::minimization_packing::GreenPacker::compute_reference_intragroup_rpes	(	Pose &	pose,
		core::Size const	threads_to_request
	)

private

References ci_rpes_, ci_sfxn_, reference_packer_neighbor_graph_, reference_rotamer_sets_, and reference_task_.

Referenced by setup_reference_data().

◆ create_fresh_packer_neighbor_graph()

void protocols::minimization_packing::GreenPacker::create_fresh_packer_neighbor_graph ( Pose & pose )

private

References core::pack::create_packer_graph(), current_inter_group_packer_neighbor_graph_, current_intra_group_packer_neighbor_graph_, current_packer_neighbor_graph_, current_task_, drop_inter_group_edges(), drop_intra_group_edges(), and full_sfxn_.

Referenced by repack().

◆ create_fresh_rotamers()

void protocols::minimization_packing::GreenPacker::create_fresh_rotamers ( Pose & pose )

private

References current_packer_neighbor_graph_, current_rotamer_sets_, current_rotamers_, current_task_, full_sfxn_, and core::pose::Pose::size().

Referenced by repack().

◆ create_fresh_task()

void protocols::minimization_packing::GreenPacker::create_fresh_task ( Pose & pose )

private

References current_task_, full_sfxn_, core::pack::pack_scorefxn_pose_handshake(), task_factory_, and core::pose::Pose::update_residue_neighbors().

Referenced by repack().

◆ create_reference_packer_neighbor_graph()

void protocols::minimization_packing::GreenPacker::create_reference_packer_neighbor_graph ( Pose & pose )

private

References ci_sfxn_, core::pack::create_packer_graph(), drop_inter_group_edges(), reference_packer_neighbor_graph_, and reference_task_.

Referenced by setup_reference_data().

◆ create_reference_packer_task()

void protocols::minimization_packing::GreenPacker::create_reference_packer_task ( Pose & pose )

private

References ci_sfxn_, full_sfxn_, core::pack::pack_scorefxn_pose_handshake(), reference_task_, reference_task_factory_, and core::pose::Pose::update_residue_neighbors().

Referenced by setup_reference_data().

◆ create_reference_rotamers()

void protocols::minimization_packing::GreenPacker::create_reference_rotamers ( Pose & pose )

private

References ci_sfxn_, original_rotamers_, reference_moltenres_2_resid_, reference_packer_neighbor_graph_, reference_resid_2_moltenres_, reference_rotamer_sets_, reference_task_, and core::pose::Pose::size().

Referenced by setup_reference_data().

◆ drop_inter_group_edges()

void protocols::minimization_packing::GreenPacker::drop_inter_group_edges	(	Pose &	pose,
		GraphOP	packer_neighbor_graph
	)		const

private

All edges to group 0 are considered inter-group edges.

References group_ids_, and core::pose::Pose::size().

Referenced by create_fresh_packer_neighbor_graph(), and create_reference_packer_neighbor_graph().

◆ drop_intra_group_edges()

void protocols::minimization_packing::GreenPacker::drop_intra_group_edges	(	Pose &	pose,
		GraphOP	packer_neighbor_graph
	)		const

private

All edges to group 0 are considered inter-group edges.

References group_ids_, and core::pose::Pose::size().

Referenced by create_fresh_packer_neighbor_graph().

◆ find_reference_and_current_rotamer_correspondence()

void protocols::minimization_packing::GreenPacker::find_reference_and_current_rotamer_correspondence ( Pose & pose )

private

References curr_rot_2_orig_rot_, curr_rotamers_with_correspondence_, curr_rotamers_without_correspondence_, current_rotamer_sets_, current_rotamers_, initialize_internal_correspondence_data(), orig_rot_2_curr_rot_, original_rotamers_, core::pose::Pose::size(), and protocols::minimization_packing::TR().

Referenced by repack().

◆ get_name()

std::string protocols::minimization_packing::GreenPacker::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

◆ initialize_internal_correspondence_data()

void protocols::minimization_packing::GreenPacker::initialize_internal_correspondence_data ( Pose & pose )

private

References curr_rot_2_orig_rot_, curr_rotamers_with_correspondence_, curr_rotamers_without_correspondence_, current_rotamer_sets_, core::sequence::end, orig_rot_2_curr_rot_, original_rotamers_, and core::pose::Pose::size().

Referenced by find_reference_and_current_rotamer_correspondence().

◆ repack()

void protocols::minimization_packing::GreenPacker::repack ( Pose & pose )

private

References cleanup(), compute_energies(), create_fresh_packer_neighbor_graph(), create_fresh_rotamers(), create_fresh_task(), current_task_, find_reference_and_current_rotamer_correspondence(), run_sa(), and split_pose_into_groups().

Referenced by apply().

◆ run_sa()

void protocols::minimization_packing::GreenPacker::run_sa ( Pose & pose )

private

References current_ig_, current_rotamer_sets_, current_task_, and core::pack::pack_rotamers_run().

Referenced by repack().

◆ set_group_discriminator()

void protocols::minimization_packing::GreenPacker::set_group_discriminator ( protocols::minimization_packing::GroupDiscriminatorOP discriminator )

References group_discriminator_.

◆ set_reference_round_task_factory()

void protocols::minimization_packing::GreenPacker::set_reference_round_task_factory ( TaskFactoryOP factory )

Pointer copy, atm, since there's no good way to clone task factories and all of their contents.

References reference_task_factory_.

◆ set_scorefunction()

void protocols::minimization_packing::GreenPacker::set_scorefunction ( ScoreFunction const & sfxn )

References cd_sfxn_, ci_sfxn_, core::scoring::ScoreFunction::clone(), create_reference_data_, full_sfxn_, and set_weights_for_sfxn().

◆ set_task_factory()

void protocols::minimization_packing::GreenPacker::set_task_factory ( TaskFactoryOP factory )

Pointer copy, atm, since there's no good way to clone task factories and all of their contents.

References task_factory_.

◆ set_weights_for_sfxn()

void protocols::minimization_packing::GreenPacker::set_weights_for_sfxn	(	ScoreFunction &	sfxn,
		ScoreTypes const &	scoretypes,
		EnergyMap const &	weights
	)		const

private

Private methods.

References core::scoring::ScoreFunction::set_weight().

Referenced by set_scorefunction().

◆ setup_reference_data()

void protocols::minimization_packing::GreenPacker::setup_reference_data ( Pose & pose )

private

References compute_reference_intragroup_rpes(), create_reference_data_, create_reference_packer_neighbor_graph(), create_reference_packer_task(), create_reference_rotamers(), reference_task_, and split_pose_into_groups().

Referenced by apply().

◆ split_pose_into_groups()

void protocols::minimization_packing::GreenPacker::split_pose_into_groups ( Pose & pose )

private

References group_discriminator_, group_ids_, group_members_, protocols::mean_field::max(), and core::pose::Pose::size().

Referenced by repack(), and setup_reference_data().

◆ store_reference_pose_geometry()

void protocols::minimization_packing::GreenPacker::store_reference_pose_geometry ( Pose & pose )

private

References core::conformation::Residue::mainchain_torsions(), orig_bb_tors_, original_bb_rep_coords_, core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Member Data Documentation

◆ cd_sfxn_

ScoreFunctionOP protocols::minimization_packing::GreenPacker::cd_sfxn_

private

Referenced by compute_energies(), and set_scorefunction().

◆ ci_rpes_

PrecomputedPairEnergiesInteractionGraphOP protocols::minimization_packing::GreenPacker::ci_rpes_

private

the stored intra-group RPEs from the context independent components of the score function

Referenced by add_precomputed_energies(), and compute_reference_intragroup_rpes().

◆ ci_sfxn_

ScoreFunctionOP protocols::minimization_packing::GreenPacker::ci_sfxn_

private

Referenced by compute_absent_energies(), compute_absent_lrci_energies_for_residue_pair(), compute_absent_srci_energies_for_residue_pair(), compute_reference_intragroup_rpes(), create_reference_packer_neighbor_graph(), create_reference_packer_task(), create_reference_rotamers(), and set_scorefunction().

◆ create_reference_data_

bool protocols::minimization_packing::GreenPacker::create_reference_data_

private

Referenced by apply(), set_scorefunction(), and setup_reference_data().

◆ curr_rot_2_orig_rot_

utility::vector1< utility::vector1< core::Size > > protocols::minimization_packing::GreenPacker::curr_rot_2_orig_rot_

private

Referenced by add_precomputed_energies(), cleanup(), compute_absent_lrci_energies_for_residue_pair(), compute_absent_srci_energies_for_residue_pair(), find_reference_and_current_rotamer_correspondence(), and initialize_internal_correspondence_data().

◆ curr_rotamers_with_correspondence_

utility::vector1< utility::vector1< core::Size > > protocols::minimization_packing::GreenPacker::curr_rotamers_with_correspondence_

private

Referenced by add_precomputed_energies(), cleanup(), find_reference_and_current_rotamer_correspondence(), and initialize_internal_correspondence_data().

◆ curr_rotamers_without_correspondence_

utility::vector1< utility::vector1< core::Size > > protocols::minimization_packing::GreenPacker::curr_rotamers_without_correspondence_

private

Referenced by cleanup(), compute_absent_energies(), compute_absent_lrci_energies_for_residue_pair(), compute_absent_srci_energies_for_residue_pair(), find_reference_and_current_rotamer_correspondence(), and initialize_internal_correspondence_data().

◆ current_ig_

PrecomputedPairEnergiesInteractionGraphOP protocols::minimization_packing::GreenPacker::current_ig_

private

Referenced by cleanup(), compute_energies(), and run_sa().

◆ current_inter_group_packer_neighbor_graph_

GraphOP protocols::minimization_packing::GreenPacker::current_inter_group_packer_neighbor_graph_

private

Referenced by cleanup(), compute_energies(), and create_fresh_packer_neighbor_graph().

◆ current_intra_group_packer_neighbor_graph_

GraphOP protocols::minimization_packing::GreenPacker::current_intra_group_packer_neighbor_graph_

private

Referenced by cleanup(), compute_absent_energies(), compute_energies(), and create_fresh_packer_neighbor_graph().

◆ current_packer_neighbor_graph_

GraphOP protocols::minimization_packing::GreenPacker::current_packer_neighbor_graph_

private

Referenced by cleanup(), compute_energies(), create_fresh_packer_neighbor_graph(), and create_fresh_rotamers().

◆ current_rotamer_sets_

RotamerSetsOP protocols::minimization_packing::GreenPacker::current_rotamer_sets_

private

Referenced by add_precomputed_energies(), cleanup(), compute_absent_energies(), compute_absent_lrci_energies_for_residue_pair(), compute_absent_srci_energies_for_residue_pair(), compute_energies(), create_fresh_rotamers(), find_reference_and_current_rotamer_correspondence(), initialize_internal_correspondence_data(), and run_sa().

◆ current_rotamers_

utility::vector1< utility::vector1< protocols::minimization_packing::MinimalRotamerOP > > protocols::minimization_packing::GreenPacker::current_rotamers_

private

the internal geometry of the rotamers created in the first round

Referenced by cleanup(), create_fresh_rotamers(), and find_reference_and_current_rotamer_correspondence().

◆ current_task_

PackerTaskOP protocols::minimization_packing::GreenPacker::current_task_

private

Data for the "current" packing – valid between the beginning and end of a call to "apply".

Referenced by cleanup(), compute_energies(), create_fresh_packer_neighbor_graph(), create_fresh_rotamers(), create_fresh_task(), repack(), and run_sa().

◆ full_sfxn_

ScoreFunctionOP protocols::minimization_packing::GreenPacker::full_sfxn_

private

Referenced by compute_energies(), create_fresh_packer_neighbor_graph(), create_fresh_rotamers(), create_fresh_task(), create_reference_packer_task(), and set_scorefunction().

◆ group_discriminator_

protocols::minimization_packing::GroupDiscriminatorOP protocols::minimization_packing::GreenPacker::group_discriminator_

private

Referenced by set_group_discriminator(), and split_pose_into_groups().

◆ group_ids_

utility::vector1< core::Size > protocols::minimization_packing::GreenPacker::group_ids_

private

Referenced by drop_inter_group_edges(), drop_intra_group_edges(), and split_pose_into_groups().

◆ group_members_

std::vector< utility::vector1< core::Size > > protocols::minimization_packing::GreenPacker::group_members_

private

Referenced by split_pose_into_groups().

◆ orig_bb_tors_

utility::vector1< utility::vector1< Real > > protocols::minimization_packing::GreenPacker::orig_bb_tors_

private

the internal geometry of the backbone used in the first round

Referenced by compare_input_pose_geometry_to_reference(), and store_reference_pose_geometry().

◆ orig_rot_2_curr_rot_

utility::vector1< utility::vector1< core::Size > > protocols::minimization_packing::GreenPacker::orig_rot_2_curr_rot_

private

correspondence between current rotamer set and original rotamer set.

Referenced by cleanup(), find_reference_and_current_rotamer_correspondence(), and initialize_internal_correspondence_data().

◆ original_bb_rep_coords_

utility::vector1< Vector > protocols::minimization_packing::GreenPacker::original_bb_rep_coords_

private

for debugging; a set of coordinates of each residue for backbone atom #1 (N in proteins, Phos for NA's) so that if the backbone DOFs do change, and the structure of the input pose cannot be superimposed back onto the original coordinates, then a debug runtime_assert statementmet will get caught.

Referenced by store_reference_pose_geometry().

◆ original_rotamers_

utility::vector1< utility::vector1< protocols::minimization_packing::MinimalRotamerOP > > protocols::minimization_packing::GreenPacker::original_rotamers_

private

the internal geometry of the rotamers created in the first round

Referenced by create_reference_rotamers(), find_reference_and_current_rotamer_correspondence(), and initialize_internal_correspondence_data().

◆ reference_moltenres_2_resid_

utility::vector1< core::Size > protocols::minimization_packing::GreenPacker::reference_moltenres_2_resid_

private

Referenced by add_precomputed_energies(), and create_reference_rotamers().

◆ reference_packer_neighbor_graph_

GraphOP protocols::minimization_packing::GreenPacker::reference_packer_neighbor_graph_

private

Referenced by compute_reference_intragroup_rpes(), create_reference_packer_neighbor_graph(), and create_reference_rotamers().

◆ reference_resid_2_moltenres_

utility::vector1< core::Size > protocols::minimization_packing::GreenPacker::reference_resid_2_moltenres_

private

Referenced by add_precomputed_energies(), and create_reference_rotamers().

◆ reference_rotamer_sets_

RotamerSetsOP protocols::minimization_packing::GreenPacker::reference_rotamer_sets_

private

rotamer sets created by the reference task

Referenced by compute_reference_intragroup_rpes(), and create_reference_rotamers().

◆ reference_task_

PackerTaskOP protocols::minimization_packing::GreenPacker::reference_task_

private

Data captured from the reference apply()

task used in construction of the reference data

Referenced by compute_reference_intragroup_rpes(), create_reference_packer_neighbor_graph(), create_reference_packer_task(), create_reference_rotamers(), and setup_reference_data().

◆ reference_task_factory_

TaskFactoryOP protocols::minimization_packing::GreenPacker::reference_task_factory_

private

Referenced by create_reference_packer_task(), and set_reference_round_task_factory().

◆ task_factory_

TaskFactoryOP protocols::minimization_packing::GreenPacker::task_factory_

private

Referenced by create_fresh_task(), and set_task_factory().

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

src/protocols/minimization_packing/GreenPacker.hh
src/protocols/minimization_packing/GreenPacker.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ EnergyMap

◆ Graph

◆ GraphOP

◆ LongRangeTwoBodyEnergy

◆ PackerTaskOP

◆ Pose

◆ PrecomputedPairEnergiesInteractionGraph

◆ PrecomputedPairEnergiesInteractionGraphOP

◆ Real

◆ RotamerSets

◆ RotamerSetsOP

◆ ScoreFunction

◆ ScoreFunctionOP

◆ ScoreTypes

◆ Size

◆ TaskFactory

◆ TaskFactoryOP

◆ Vector

Constructor & Destructor Documentation

◆ GreenPacker()

◆ ~GreenPacker()

Member Function Documentation

◆ add_precomputed_energies()

◆ apply()

◆ cleanup()

◆ compare_input_pose_geometry_to_reference()

◆ compute_absent_energies()

◆ compute_absent_lrci_energies_for_residue_pair()

◆ compute_absent_srci_energies_for_residue_pair()

◆ compute_energies()

◆ compute_reference_intragroup_rpes()

◆ create_fresh_packer_neighbor_graph()

◆ create_fresh_rotamers()

◆ create_fresh_task()

◆ create_reference_packer_neighbor_graph()

◆ create_reference_packer_task()

◆ create_reference_rotamers()

◆ drop_inter_group_edges()

◆ drop_intra_group_edges()

◆ find_reference_and_current_rotamer_correspondence()

◆ get_name()

◆ initialize_internal_correspondence_data()

◆ repack()

◆ run_sa()

◆ set_group_discriminator()

◆ set_reference_round_task_factory()

◆ set_scorefunction()

◆ set_task_factory()

◆ set_weights_for_sfxn()

◆ setup_reference_data()

◆ split_pose_into_groups()

◆ store_reference_pose_geometry()

Member Data Documentation

◆ cd_sfxn_

◆ ci_rpes_

◆ ci_sfxn_

◆ create_reference_data_

◆ curr_rot_2_orig_rot_

◆ curr_rotamers_with_correspondence_

◆ curr_rotamers_without_correspondence_

◆ current_ig_

◆ current_inter_group_packer_neighbor_graph_

◆ current_intra_group_packer_neighbor_graph_

◆ current_packer_neighbor_graph_

◆ current_rotamer_sets_

◆ current_rotamers_

◆ current_task_

◆ full_sfxn_

◆ group_discriminator_

◆ group_ids_

◆ group_members_

◆ orig_bb_tors_

◆ orig_rot_2_curr_rot_

◆ original_bb_rep_coords_