#include <RotamerSets.hh>

Inheritance diagram for core::pack::rotamer_set::RotamerSets:

[legend]

Public Types
typedef task::PackerTaskCOP	PackerTaskCOP

Public Types inherited from core::pack::rotamer_set::FixbbRotamerSets
typedef pack_basic::RotamerSetsBase	parent

typedef utility::vector1< RotamerSetOP >	RotamerSetVector

Public Member Functions
	RotamerSets ()

	~RotamerSets () override

void	set_task (task::PackerTaskCOP task)

void	build_rotamers (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, utility::graph::GraphCOP packer_neighbor_graph)

void	set_explicit_rotamers (core::Size moltenresid, RotamerSetOP rotamers)

void	dump_pdb (pose::Pose const &pose, std::string const &filename) const

uint	nrotamers () const override

uint	nrotamers_for_moltenres (uint) const override

uint	nmoltenres () const override

uint	total_residue () const override

uint	moltenres_2_resid (uint) const override

uint	resid_2_moltenres (uint) const override

uint	moltenres_for_rotamer (uint) const override

uint	res_for_rotamer (uint) const override

core::conformation::ResidueCOP	rotamer (uint) const override

core::conformation::ResidueCOP	rotamer_for_moltenres (uint moltenres_id, uint rotamerid) const override

uint	nrotamer_offset_for_moltenres (uint) const override

void	drop_rotamers (utility::vector1< bool > const &rotamers_to_delete)
	rotamers_to_delete must be of size nrotmaers – each position in the array that's "true" is removed from the set of rotamers More...

bool	has_rotamer_set_for_residue (uint const resid) const
	Does this RotamerSets object store a rotamer set for a residue at position resid in the pose? More...

RotamerSetCOP	rotamer_set_for_residue (uint resid) const override

RotamerSetOP	rotamer_set_for_residue (uint resid) override

RotamerSetCOP	rotamer_set_for_moltenresidue (uint moltenresid) const override

RotamerSetOP	rotamer_set_for_moltenresidue (uint moltenresid) override

RotamerSetVector::const_iterator	begin () override

RotamerSetVector::const_iterator	end () override

uint	rotid_on_moltenresidue (uint rotid) const override
	convert rotid in full rotamer enumeration into rotamer id on its source residue More...

uint	moltenres_rotid_2_rotid (uint moltenres, uint moltenresrotid) const override
	convert moltenres rotid to id in full rotamer enumeration More...

PackerTaskCOP	task () const
	access to packer_task_ More...

void	prepare_sets_for_packing (pose::Pose const &pose, scoring::ScoreFunction const &)

void	initialize_pose_for_rotsets_creation (pose::Pose &) const override
	Give the pose a chance to stash any data needed by the rotset need nonconst access to pose. More...

void	update_offset_data ()

bool	offset_data_up_to_date ()
	Used as a debug assert to ensure that RotamerSetsOperations call update_offset_data() More...

virtual utility::vector1< basic::thread_manager::RosettaThreadFunction >	construct_one_body_energy_work_vector (core::pose::Pose const &pose, core::scoring::ScoreFunction const &scfxn, utility::graph::GraphCOP packer_neighbor_graph, interaction_graph::InteractionGraphBaseOP ig, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_assignment_info) const
	Construct a vector of calculations for the one-body energies in the interaction graph, for subsequent multi-threaded evaluation. More...

virtual void	append_two_body_energy_computations_to_work_vector (core::pose::Pose const &pose, core::scoring::ScoreFunction const &scfxn, utility::graph::GraphCOP packer_neighbor_graph, interaction_graph::PrecomputedPairEnergiesInteractionGraphOP pig, utility::vector1< basic::thread_manager::RosettaThreadFunction > &work_vector, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_assignment_info) const
	Append to a vector of calculations that already contains one-body energy calculations additonal work units for two-body energy calculations, for subsequent multi-threaded evaluation. More...

virtual void	compute_energies (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, utility::graph::GraphCOP packer_neighbor_graph, interaction_graph::InteractionGraphBaseOP ig, core::Size const threads_to_request)
	Precompute all rotamer pair and rotamer one-body energies, populating the given interaction graph. More...

utility::vector1< uint > const &	resid_2_moltenres_vector () const override

utility::vector1< uint > const &	moltenres_2_resid_vector () const override

void	show (std::ostream &out) const override

Public Member Functions inherited from core::pack::rotamer_set::FixbbRotamerSets
	FixbbRotamerSets ()

	~FixbbRotamerSets () override

Public Member Functions inherited from core::pack_basic::RotamerSetsBase
	RotamerSetsBase ()

	~RotamerSetsBase () override

Static Public Member Functions
static core::PackerEnergy	get_bb_bbE (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, conformation::Residue const &res1, conformation::Residue const &res2)

static core::PackerEnergy	get_sc_bbE (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, conformation::Residue const &res1, conformation::Residue const &res2)

Private Member Functions
void	copy_residue_conenctions_and_variants (pose::Pose const &pose, conformation::ResidueOP cloneRes, Size seqpos, Size asym_length)

void	prepare_otf_graph (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, utility::graph::GraphCOP packer_neighbor_graph, interaction_graph::OnTheFlyInteractionGraphOP otfig)
	Marks all protein vertices in the on-the-fly interaction graph as ones that should distinguish between the backbones and sidechains. Then, adds edges to the on-the-fly interaction graph between neighboring RotamerSets, and figures out, for those edges, which pairs of rotamer groups (e.g. ala1/arg2, ser1/phe2) are close enough to interact for their energies to need calculation. More...

void	compute_proline_correction_energies_for_otf_graph (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, utility::graph::GraphCOP packer_neighbor_graph, interaction_graph::OnTheFlyInteractionGraphOP otfig)
	computes one body energies for the on-the-fly graph, calculating proline-correction terms for protien-residues that allow prolines and storing them on the otf edges More...

Private Attributes
uint	nmoltenres_ = 0

uint	total_residue_ = 0

uint	nrotamers_ = 0

RotamerSetVector	set_of_rotamer_sets_

utility::vector1< uint >	resid_2_moltenres_

utility::vector1< uint >	moltenres_2_resid_

utility::vector1< uint >	nrotamer_offsets_

utility::vector1< uint >	moltenres_for_rotamer_

utility::vector1< uint >	nrotamers_for_moltenres_

PackerTaskCOP	task_

Member Typedef Documentation

◆ PackerTaskCOP

typedef task::PackerTaskCOP core::pack::rotamer_set::RotamerSets::PackerTaskCOP

Constructor & Destructor Documentation

◆ RotamerSets()

core::pack::rotamer_set::RotamerSets::RotamerSets ( )

default

◆ ~RotamerSets()

core::pack::rotamer_set::RotamerSets::~RotamerSets ( )

overridedefault

Member Function Documentation

◆ append_two_body_energy_computations_to_work_vector()

void core::pack::rotamer_set::RotamerSets::append_two_body_energy_computations_to_work_vector	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunction const &	scfxn,
		utility::graph::GraphCOP	packer_neighbor_graph,
		interaction_graph::PrecomputedPairEnergiesInteractionGraphOP	pig,
		utility::vector1< basic::thread_manager::RosettaThreadFunction > &	work_vector,
		basic::thread_manager::RosettaThreadAssignmentInfo const &	thread_assignment_info
	)		const

virtual

Append to a vector of calculations that already contains one-body energy calculations additonal work units for two-body energy calculations, for subsequent multi-threaded evaluation.

Each individual calculation is for the interaction of all possible rotamer pairs at two positions. Again, not as granular as conceivably possible, but easier to set up.

Note: The work_vector vector is extended by this operation.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tue..nosp@m.org).

Reimplemented in core::pack::rotamer_set::symmetry::SymmetricRotamerSets.

References core::pose::Pose::energies(), core::scoring::Energies::long_range_container(), core::scoring::ScoreFunction::long_range_energies_begin(), core::scoring::ScoreFunction::long_range_energies_end(), and TR().

◆ begin()

RotamerSetVector::const_iterator core::pack::rotamer_set::RotamerSets::begin ( )

inlineoverridevirtual

Implements core::pack::rotamer_set::FixbbRotamerSets.

References set_of_rotamer_sets_.

◆ build_rotamers()

void core::pack::rotamer_set::RotamerSets::build_rotamers	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scfxn,
		utility::graph::GraphCOP	packer_neighbor_graph
	)

References core::pose::add_variant_type_to_residue(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Residue::has_variant_type(), core::pose::symmetry::is_symmetric(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::remove_variant_type_from_residue(), core::pose::Pose::residue(), core::pose::Pose::size(), core::pose::symmetry::symmetry_info(), TR(), and core::chemical::UPPER_TERMINUS_VARIANT.

◆ compute_energies()

void core::pack::rotamer_set::RotamerSets::compute_energies	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scfxn,
		utility::graph::GraphCOP	packer_neighbor_graph,
		interaction_graph::InteractionGraphBaseOP	ig,
		core::Size const	threads_to_request
	)

virtual

Precompute all rotamer pair and rotamer one-body energies, populating the given interaction graph.

Note: In the multithreaded case, this function requests that work be done in threads. It takes as input the number of threads to request.

Reimplemented in core::pack::rotamer_set::symmetry::SymmetricRotamerSets.

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

Referenced by core::pack::interaction_graph::InteractionGraphFactory::create_and_initialize_two_body_interaction_graph().

◆ compute_proline_correction_energies_for_otf_graph()

void core::pack::rotamer_set::RotamerSets::compute_proline_correction_energies_for_otf_graph	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scfxn,
		utility::graph::GraphCOP	packer_neighbor_graph,
		interaction_graph::OnTheFlyInteractionGraphOP	otfig
	)

private

computes one body energies for the on-the-fly graph, calculating proline-correction terms for protien-residues that allow prolines and storing them on the otf edges

0. Find example proline and glycine residues where possible.

Iterate across all edges in the graph
1. Calculate proline-correction terms between neighbors

References core::chemical::aa_gly, and core::chemical::aa_pro.

◆ construct_one_body_energy_work_vector()

utility::vector1< basic::thread_manager::RosettaThreadFunction > core::pack::rotamer_set::RotamerSets::construct_one_body_energy_work_vector	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunction const &	scfxn,
		utility::graph::GraphCOP	packer_neighbor_graph,
		interaction_graph::InteractionGraphBaseOP	ig,
		basic::thread_manager::RosettaThreadAssignmentInfo const &	thread_assignment_info
	)		const

virtual

Construct a vector of calculations for the one-body energies in the interaction graph, for subsequent multi-threaded evaluation.

Each individual calculation is for all one-body energies at a packable position. This isn't as granular as possible, but more finely-grained parallelism would be harder to implement (and anyways the one-body energies are much less expensive than the two-body energies).

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tue..nosp@m.org).

References TR().

◆ copy_residue_conenctions_and_variants()

void core::pack::rotamer_set::RotamerSets::copy_residue_conenctions_and_variants	(	pose::Pose const &	pose,
		conformation::ResidueOP	cloneRes,
		Size	seqpos,
		Size	asym_length
	)

private

References core::pose::add_variant_type_to_residue(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_UPPER, core::conformation::Residue::has_variant_type(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::remove_variant_type_from_residue(), core::pose::Pose::residue(), and core::chemical::UPPER_TERMINUS_VARIANT.

◆ drop_rotamers()

void core::pack::rotamer_set::RotamerSets::drop_rotamers ( utility::vector1< bool > const & rotamers_to_delete )

rotamers_to_delete must be of size nrotmaers – each position in the array that's "true" is removed from the set of rotamers

Referenced by core::pack::rotamer_set::PyRotamerEliminator::alter_rotamer_sets().

◆ dump_pdb()

void core::pack::rotamer_set::RotamerSets::dump_pdb	(	pose::Pose const &	pose,
		std::string const &	filename
	)		const

References core::io::pdb::dump_pdb_residue(), protocols::abinitio::filename(), core::chemical::element::I, core::conformation::membrane::out, core::pose::Pose::residue(), and core::pose::Pose::size().

◆ end()

RotamerSetVector::const_iterator core::pack::rotamer_set::RotamerSets::end ( )

inlineoverridevirtual

Implements core::pack::rotamer_set::FixbbRotamerSets.

References set_of_rotamer_sets_.

◆ get_bb_bbE()

core::PackerEnergy core::pack::rotamer_set::RotamerSets::get_bb_bbE	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scfxn,
		conformation::Residue const &	res1,
		conformation::Residue const &	res2
	)

static

References core::scoring::EMapVector::dot(), core::scoring::ScoreFunction::eval_cd_2b_bb_bb(), core::scoring::ScoreFunction::eval_ci_2b_bb_bb(), and core::scoring::ScoreFunction::weights().

Referenced by protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets(), and protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution().

◆ get_sc_bbE()

core::PackerEnergy core::pack::rotamer_set::RotamerSets::get_sc_bbE	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scfxn,
		conformation::Residue const &	res1,
		conformation::Residue const &	res2
	)

static

References core::scoring::EMapVector::dot(), core::scoring::ScoreFunction::eval_cd_2b_bb_sc(), core::scoring::ScoreFunction::eval_ci_2b_bb_sc(), and core::scoring::ScoreFunction::weights().

Referenced by protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets(), and protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution().

◆ has_rotamer_set_for_residue()

bool core::pack::rotamer_set::RotamerSets::has_rotamer_set_for_residue ( uint const resid ) const

Does this RotamerSets object store a rotamer set for a residue at position resid in the pose?

Rotamer sets for non-packable residues aren't generated, but could conceivably be queried by protocols or energy functions.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

◆ initialize_pose_for_rotsets_creation()

void core::pack::rotamer_set::RotamerSets::initialize_pose_for_rotsets_creation ( pose::Pose & ) const

inlineoverridevirtual

Give the pose a chance to stash any data needed by the rotset need nonconst access to pose.

Implements core::pack_basic::RotamerSetsBase.

Reimplemented in core::pack::rotamer_set::symmetry::SymmetricRotamerSets.

◆ moltenres_2_resid()

uint core::pack::rotamer_set::RotamerSets::moltenres_2_resid ( uint mresid ) const

overridevirtual

Implements core::pack_basic::RotamerSetsBase.

Referenced by core::pack::scmin::AtomTreeCollection::AtomTreeCollection(), core::pack::hbonds::determine_atom_level_node_info(), core::pack::hbonds::find_satisfying_interactions_with_background(), core::pack::interaction_graph::get_annealable_graph_summary(), core::pack::get_total_energy_for_state(), and core::pack::interaction_graph::InteractionGraphFactory::setup_IG_res_res_weights().

◆ moltenres_2_resid_vector()

utility::vector1< uint > const& core::pack::rotamer_set::RotamerSets::moltenres_2_resid_vector ( ) const

inlineoverridevirtual

Implements core::pack::rotamer_set::FixbbRotamerSets.

References moltenres_2_resid_.

◆ moltenres_for_rotamer()

uint core::pack::rotamer_set::RotamerSets::moltenres_for_rotamer ( uint rotid ) const

overridevirtual

Implements core::pack_basic::RotamerSetsBase.

Referenced by core::pack::hbonds::determine_atom_level_node_info(), and core::pack::hbonds::init_node_info().

◆ moltenres_rotid_2_rotid()

uint core::pack::rotamer_set::RotamerSets::moltenres_rotid_2_rotid	(	uint	moltenres,
		uint	moltenresrotid
	)		const

overridevirtual

convert moltenres rotid to id in full rotamer enumeration

Implements core::pack_basic::RotamerSetsBase.

◆ nmoltenres()

uint core::pack::rotamer_set::RotamerSets::nmoltenres ( ) const

overridevirtual

Implements core::pack_basic::RotamerSetsBase.

Referenced by core::pack::scmin::AtomTreeCollection::AtomTreeCollection(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), core::pack::interaction_graph::get_annealable_graph_summary(), core::pack::get_total_energy_for_state(), core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::initialize(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::initialize(), core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::initialize(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::initialize(), and core::pack::interaction_graph::InteractionGraphFactory::setup_IG_res_res_weights().

◆ nrotamer_offset_for_moltenres()

uint core::pack::rotamer_set::RotamerSets::nrotamer_offset_for_moltenres ( uint mresid ) const

overridevirtual

Implements core::pack_basic::RotamerSetsBase.

◆ nrotamers()

uint core::pack::rotamer_set::RotamerSets::nrotamers ( ) const

overridevirtual

Implements core::pack_basic::RotamerSetsBase.

Referenced by protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation::alter_rotamer_sets(), core::pack::rotamer_set::PyRotamerEliminator::alter_rotamer_sets(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::convert_block_sasa_to_sasa_score(), core::pack::hbonds::create_and_init_hbond_graph(), core::pack::interaction_graph::estimate_n_2body_calcs_for_linmem_ig(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_block_params(), core::pack::hbonds::init_node_info(), protocols::multistate_design::limit_rotamer_set(), and protocols::multistate_design::restrict_to_canonical_aas().

◆ nrotamers_for_moltenres()

uint core::pack::rotamer_set::RotamerSets::nrotamers_for_moltenres ( uint mresid ) const

overridevirtual

Implements core::pack_basic::RotamerSetsBase.

Referenced by core::pack::interaction_graph::estimate_n_2body_calcs_for_precomputation().

◆ offset_data_up_to_date()

bool core::pack::rotamer_set::RotamerSets::offset_data_up_to_date ( )

Used as a debug assert to ensure that RotamerSetsOperations call update_offset_data()

Without this check, rotamer sets operations could potentially introduce very-hard-to-debug glitches if they don't call update_offset_data().

◆ prepare_otf_graph()

void core::pack::rotamer_set::RotamerSets::prepare_otf_graph	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scfxn,
		utility::graph::GraphCOP	packer_neighbor_graph,
		interaction_graph::OnTheFlyInteractionGraphOP	otfig
	)

private

Marks all protein vertices in the on-the-fly interaction graph as ones that should distinguish between the backbones and sidechains. Then, adds edges to the on-the-fly interaction graph between neighboring RotamerSets, and figures out, for those edges, which pairs of rotamer groups (e.g. ala1/arg2, ser1/phe2) are close enough to interact for their energies to need calculation.

References core::scoring::ScoreFunction::any_lr_residue_pair_energy(), core::pose::Pose::energies(), core::scoring::Energies::long_range_container(), core::scoring::ScoreFunction::long_range_energies_begin(), core::scoring::ScoreFunction::long_range_energies_end(), core::scoring::ScoreFunction::max_atomic_interaction_cutoff(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), core::chemical::num_canonical_aas, and core::conformation::Residue::xyz().