#include <GreenPacker.hh>

Inheritance diagram for protocols::simple_moves::GreenPacker:

Collaboration diagram for protocols::simple_moves::GreenPacker:

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

typedef core::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::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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

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

virtual	~GreenPacker ()

virtual void	apply (Pose &)

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

void	set_scorefunction (ScoreFunction const &)

void	set_group_discriminator (protocols::simple_moves::GroupDiscriminatorOP)

void	set_task_factory (TaskFactoryOP)

void	set_reference_round_task_factory (TaskFactoryOP)

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

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

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...

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 bool	reinitialize_for_each_job () const
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

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

jobdist::BasicJobCOP	get_current_job () const

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 &)

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)

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)

void	run_sa (Pose &pose)

void	cleanup ()

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, Size lower_res, Size upper_res)

void	compute_absent_lrci_energies_for_residue_pair (Pose &pose, LongRangeTwoBodyEnergy const &lre, PrecomputedPairEnergiesInteractionGraphOP pig, Size lower_res, 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::simple_moves::GroupDiscriminatorOP	group_discriminator_

utility::vector1< Size >	group_ids_

std::vector< utility::vector1 < 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< Size >	reference_resid_2_moltenres_

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

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

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

utility::vector1 < utility::vector1< 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...

Detailed Description

Definition at line 190 of file GreenPacker.hh.

Member Typedef Documentation

typedef core::scoring::EnergyMap protocols::simple_moves::GreenPacker::EnergyMap

Definition at line 204 of file GreenPacker.hh.

typedef core::graph::Graph protocols::simple_moves::GreenPacker::Graph

Types.

Definition at line 194 of file GreenPacker.hh.

typedef core::graph::GraphOP protocols::simple_moves::GreenPacker::GraphOP

Definition at line 195 of file GreenPacker.hh.

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

Definition at line 208 of file GreenPacker.hh.

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

Definition at line 202 of file GreenPacker.hh.

typedef core::pose::Pose protocols::simple_moves::GreenPacker::Pose

Definition at line 203 of file GreenPacker.hh.

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

Definition at line 196 of file GreenPacker.hh.

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

Definition at line 197 of file GreenPacker.hh.

typedef core::Real protocols::simple_moves::GreenPacker::Real

Definition at line 210 of file GreenPacker.hh.

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

Definition at line 198 of file GreenPacker.hh.

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

Definition at line 199 of file GreenPacker.hh.

typedef core::scoring::ScoreFunction protocols::simple_moves::GreenPacker::ScoreFunction

Definition at line 205 of file GreenPacker.hh.

typedef core::scoring::ScoreFunctionOP protocols::simple_moves::GreenPacker::ScoreFunctionOP

Definition at line 206 of file GreenPacker.hh.

typedef core::scoring::ScoreTypes protocols::simple_moves::GreenPacker::ScoreTypes

Definition at line 207 of file GreenPacker.hh.

typedef core::Size protocols::simple_moves::GreenPacker::Size

Definition at line 209 of file GreenPacker.hh.

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

Definition at line 200 of file GreenPacker.hh.

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

Definition at line 201 of file GreenPacker.hh.

typedef core::Vector protocols::simple_moves::GreenPacker::Vector

Definition at line 211 of file GreenPacker.hh.

Constructor & Destructor Documentation

protocols::simple_moves::GreenPacker::GreenPacker ( )

Green Packer.

Definition at line 349 of file GreenPacker.cc.

protocols::simple_moves::GreenPacker::~GreenPacker ( )

virtual

Definition at line 351 of file GreenPacker.cc.

Member Function Documentation

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

private

Definition at line 840 of file GreenPacker.cc.

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

Referenced by compute_energies().

void protocols::simple_moves::GreenPacker::apply ( Pose & pose)

virtual

Implements protocols::moves::Mover.

Definition at line 355 of file GreenPacker.cc.

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

void protocols::simple_moves::GreenPacker::cleanup ( )

private

Free memory that is no longer needed

Definition at line 1117 of file GreenPacker.cc.

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_, and orig_rot_2_curr_rot_.

Referenced by repack().

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

private

Definition at line 1145 of file GreenPacker.cc.

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

void protocols::simple_moves::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.

Definition at line 910 of file GreenPacker.cc.

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::total_residue().

Referenced by compute_energies().

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

private

Definition at line 1045 of file GreenPacker.cc.

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().

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

private

Definition at line 983 of file GreenPacker.cc.

References ci_sfxn_, curr_rot_2_orig_rot_, curr_rotamers_without_correspondence_, and current_rotamer_sets_.

Referenced by compute_absent_energies().

void protocols::simple_moves::GreenPacker::compute_energies ( Pose & pose)

private

Definition at line 785 of file GreenPacker.cc.

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().

void protocols::simple_moves::GreenPacker::compute_reference_intragroup_rpes ( Pose & pose)

private

Definition at line 531 of file GreenPacker.cc.

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

Referenced by setup_reference_data().

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

private

Definition at line 583 of file GreenPacker.cc.

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().

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

private

Definition at line 645 of file GreenPacker.cc.

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

Referenced by repack().

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

private

Definition at line 570 of file GreenPacker.cc.

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

Referenced by repack().

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

private

Definition at line 485 of file GreenPacker.cc.

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

Referenced by setup_reference_data().

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

private

Definition at line 470 of file GreenPacker.cc.

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().

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

private

Definition at line 494 of file GreenPacker.cc.

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::total_residue().

Referenced by setup_reference_data().

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

private

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

Definition at line 596 of file GreenPacker.cc.

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

Referenced by create_fresh_packer_neighbor_graph(), and create_reference_packer_neighbor_graph().

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

private

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

Definition at line 620 of file GreenPacker.cc.

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

Referenced by create_fresh_packer_neighbor_graph().

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

private

Definition at line 671 of file GreenPacker.cc.

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::total_residue(), and protocols::simple_moves::TR().

Referenced by repack().

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 367 of file GreenPacker.cc.

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

private

Definition at line 762 of file GreenPacker.cc.

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_, core::io::serialization::size(), and core::pose::Pose::total_residue().

Referenced by find_reference_and_current_rotamer_correspondence().

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

private

Definition at line 440 of file GreenPacker.cc.

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

Referenced by apply().

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

private

Definition at line 1108 of file GreenPacker.cc.

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

Referenced by repack().

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

Definition at line 404 of file GreenPacker.cc.

References group_discriminator_.

void protocols::simple_moves::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.

Definition at line 421 of file GreenPacker.cc.

References reference_task_factory_.

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

Definition at line 372 of file GreenPacker.cc.

References cd_sfxn_, ci_sfxn_, create_reference_data_, full_sfxn_, and set_weights_for_sfxn().

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

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

Definition at line 413 of file GreenPacker.cc.

References task_factory_.

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

private

Private methods.

Definition at line 392 of file GreenPacker.cc.

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

Referenced by set_scorefunction().

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

private

Definition at line 429 of file GreenPacker.cc.

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

Referenced by apply().

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

private

Definition at line 454 of file GreenPacker.cc.

References group_discriminator_, group_ids_, group_members_, and core::pose::Pose::total_residue().

Referenced by repack(), and setup_reference_data().

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

private

Definition at line 1135 of file GreenPacker.cc.

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

Member Data Documentation

ScoreFunctionOP protocols::simple_moves::GreenPacker::cd_sfxn_

private

Definition at line 295 of file GreenPacker.hh.

Referenced by compute_energies(), and set_scorefunction().

PrecomputedPairEnergiesInteractionGraphOP protocols::simple_moves::GreenPacker::ci_rpes_

private

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

Definition at line 321 of file GreenPacker.hh.

Referenced by add_precomputed_energies(), and compute_reference_intragroup_rpes().

ScoreFunctionOP protocols::simple_moves::GreenPacker::ci_sfxn_

private

Definition at line 294 of file GreenPacker.hh.

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().

bool protocols::simple_moves::GreenPacker::create_reference_data_

private

Definition at line 298 of file GreenPacker.hh.

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

utility::vector1< utility::vector1< Size > > protocols::simple_moves::GreenPacker::curr_rot_2_orig_rot_

private

Definition at line 350 of file GreenPacker.hh.

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().

utility::vector1< utility::vector1< Size > > protocols::simple_moves::GreenPacker::curr_rotamers_with_correspondence_

private

Definition at line 351 of file GreenPacker.hh.

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

utility::vector1< utility::vector1< Size > > protocols::simple_moves::GreenPacker::curr_rotamers_without_correspondence_

private

Definition at line 352 of file GreenPacker.hh.

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().

PrecomputedPairEnergiesInteractionGraphOP protocols::simple_moves::GreenPacker::current_ig_

private

Definition at line 339 of file GreenPacker.hh.

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

GraphOP protocols::simple_moves::GreenPacker::current_inter_group_packer_neighbor_graph_

private

Definition at line 345 of file GreenPacker.hh.

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

GraphOP protocols::simple_moves::GreenPacker::current_intra_group_packer_neighbor_graph_

private

Definition at line 346 of file GreenPacker.hh.

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

GraphOP protocols::simple_moves::GreenPacker::current_packer_neighbor_graph_

private

Definition at line 344 of file GreenPacker.hh.

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

RotamerSetsOP protocols::simple_moves::GreenPacker::current_rotamer_sets_

private

Definition at line 338 of file GreenPacker.hh.

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().

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

private

the internal geometry of the rotamers created in the first round

Definition at line 342 of file GreenPacker.hh.

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

PackerTaskOP protocols::simple_moves::GreenPacker::current_task_

private

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

Definition at line 337 of file GreenPacker.hh.

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

ScoreFunctionOP protocols::simple_moves::GreenPacker::full_sfxn_

private

Definition at line 293 of file GreenPacker.hh.

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

protocols::simple_moves::GroupDiscriminatorOP protocols::simple_moves::GreenPacker::group_discriminator_

private

Definition at line 300 of file GreenPacker.hh.

Referenced by set_group_discriminator(), and split_pose_into_groups().

utility::vector1< Size > protocols::simple_moves::GreenPacker::group_ids_

private

Definition at line 301 of file GreenPacker.hh.

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

std::vector< utility::vector1< Size > > protocols::simple_moves::GreenPacker::group_members_

private

Definition at line 302 of file GreenPacker.hh.

Referenced by split_pose_into_groups().

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

private

the internal geometry of the backbone used in the first round

Definition at line 327 of file GreenPacker.hh.

Referenced by compare_input_pose_geometry_to_reference(), and store_reference_pose_geometry().

utility::vector1< utility::vector1< Size > > protocols::simple_moves::GreenPacker::orig_rot_2_curr_rot_

private

correspondence between current rotamer set and original rotamer set.

Definition at line 349 of file GreenPacker.hh.

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

utility::vector1< Vector > protocols::simple_moves::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.

Definition at line 332 of file GreenPacker.hh.

Referenced by store_reference_pose_geometry().

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

private

the internal geometry of the rotamers created in the first round

Definition at line 324 of file GreenPacker.hh.

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