core::pack::rotamer_set::symmetry::SymmetricRotamerSets Class Reference

#include <SymmetricRotamerSets.hh>

Inheritance diagram for core::pack::rotamer_set::symmetry::SymmetricRotamerSets:

Public Types
typedef task::PackerTaskCOP	PackerTaskCOP
typedef conformation::symmetry::SymmetricConformation	SymmetricConformation
typedef conformation::symmetry::SymmetryInfoCOP	SymmetryInfoCOP
Public Types inherited from core::pack::rotamer_set::RotamerSets
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
	SymmetricRotamerSets ()
	~SymmetricRotamerSets () override
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) override
	Precompute all rotamer pair and rotamer one-body energies, populating the given interaction graph. More...
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 override
	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...
void	initialize_pose_for_rotsets_creation (pose::Pose &pose) const override
	Give the pose a chance to stash any data needed by the rotset need nonconst access to pose. More...
Public Member Functions inherited from core::pack::rotamer_set::RotamerSets
	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	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...
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 RotamerSetOP	orient_rotamer_set_to_symmetric_partner (pose::Pose const &pose, RotamerSetCOP rotset_for_seqpos, uint const &symmpos, bool const set_up_mirror_types_if_has_mirror_symmetry=false)
	Generate a new rotamer set oriented onto a reference rotamer set by cloning the reference set and reorienting using symmetry information. Return an owning pointer to the new, reoriented rotamer set. More...
Static Public Member Functions inherited from core::pack::rotamer_set::RotamerSets
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	prepare_symm_otf_interaction_graph (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, utility::graph::GraphCOP packer_neighbor_graph, interaction_graph::SymmOnTheFlyInteractionGraphOP ig)
void	compute_proline_correction_energies_for_otf_graph (pose::Pose const &pose, conformation::symmetry::SymmetryInfoCOP symm_info, scoring::ScoreFunction const &scfxn, utility::graph::GraphCOP packer_neighbor_graph, interaction_graph::SymmOnTheFlyInteractionGraphOP otfig)
bool	final_visit_to_edge (pose::Pose const &pose, utility::graph::GraphCOP packer_neighbor_graph, uint ii_resid, uint jj_resid)

Member Typedef Documentation

PackerTaskCOP

typedef task::PackerTaskCOP core::pack::rotamer_set::symmetry::SymmetricRotamerSets::PackerTaskCOP

SymmetricConformation

typedef conformation::symmetry::SymmetricConformation core::pack::rotamer_set::symmetry::SymmetricRotamerSets::SymmetricConformation

SymmetryInfoCOP

typedef conformation::symmetry::SymmetryInfoCOP core::pack::rotamer_set::symmetry::SymmetricRotamerSets::SymmetryInfoCOP

Constructor & Destructor Documentation

SymmetricRotamerSets()

core::pack::rotamer_set::symmetry::SymmetricRotamerSets::SymmetricRotamerSets ( )

default

~SymmetricRotamerSets()

core::pack::rotamer_set::symmetry::SymmetricRotamerSets::~SymmetricRotamerSets ( )

overridedefault

Member Function Documentation

append_two_body_energy_computations_to_work_vector()

void core::pack::rotamer_set::symmetry::SymmetricRotamerSets::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

overridevirtual

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. This version is for the symmetric case.

Author

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

Reimplemented from core::pack::rotamer_set::RotamerSets.

References core::pose::Pose::conformation(), 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::id::swap(), and SYMM_INFO_SCORE_MULTIPLY_CUTOFF.

compute_energies()

void core::pack::rotamer_set::symmetry::SymmetricRotamerSets::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  )

overridevirtual

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 from core::pack::rotamer_set::RotamerSets.

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

compute_proline_correction_energies_for_otf_graph()

void core::pack::rotamer_set::symmetry::SymmetricRotamerSets::compute_proline_correction_energies_for_otf_graph ( pose::Pose const &  pose, conformation::symmetry::SymmetryInfoCOP  symm_info, scoring::ScoreFunction const &  scfxn, utility::graph::GraphCOP  packer_neighbor_graph, interaction_graph::SymmOnTheFlyInteractionGraphOP  otfig  )

private

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

final_visit_to_edge()

bool core::pack::rotamer_set::symmetry::SymmetricRotamerSets::final_visit_to_edge ( pose::Pose const &  pose, utility::graph::GraphCOP  packer_neighbor_graph, uint  ii_resid, uint  jj_resid  )

private

References core::pose::Pose::conformation().

initialize_pose_for_rotsets_creation()

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

overridevirtual

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

Reimplemented from core::pack::rotamer_set::RotamerSets.

References core::pose::Pose::conformation().

orient_rotamer_set_to_symmetric_partner()

RotamerSetOP core::pack::rotamer_set::symmetry::SymmetricRotamerSets::orient_rotamer_set_to_symmetric_partner ( pose::Pose const &  pose, RotamerSetCOP  rotset_for_seqpos, uint const &  sympos, bool const  set_up_mirror_types_if_has_mirror_symmetry = false  )

static

Generate a new rotamer set oriented onto a reference rotamer set by cloning the reference set and reorienting using symmetry information. Return an owning pointer to the new, reoriented rotamer set.

Orients all rotamers in a rotamer_set to a different (symmetrical) position

Note

If set_up_mirror_symmetry_if_has_mirror_symmetry_ is true, then residues in mirrored subunits have their ResidueTypes switched to the types of the opposite chirality. If false (the default), then they keep the same types, and only have their geometry mirrored. The default is false, which is computationally less expensive at the expense of having the incorrect types in mirrored subunits.

References core::pose::Pose::conformation(), core::pose::Pose::conformation_ptr(), core::pose::Pose::residue_type_set_for_pose(), and rot().

Referenced by core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_longrange_twobody_energies_multithreaded(), and core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_twobody_energies_multithreaded().

prepare_symm_otf_interaction_graph()

void core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph ( pose::Pose const &  pose, scoring::ScoreFunction const &  sfxn, utility::graph::GraphCOP  packer_neighbor_graph, interaction_graph::SymmOnTheFlyInteractionGraphOP  ig  )

private

Add edges between all adjacent nodes in the interaction graph, and note which of the subunit pairs are interacting.

References core::pose::Pose::conformation(), 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::chemical::num_canonical_aas, and core::id::swap().

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

• src/core/pack/rotamer_set/symmetry/SymmetricRotamerSets.hh
• src/core/pack/rotamer_set/symmetry/SymmetricRotamerSets.cc