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

#include <SymmetricRotamerSets.hh>

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 RotamerSetsBase	parent
typedef utility::vector1 < RotamerSetOP >	RotamerSetVector

Public Member Functions
	SymmetricRotamerSets ()
	~SymmetricRotamerSets ()
void	compute_energies (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, graph::GraphCOP packer_neighbor_graph, interaction_graph::InteractionGraphBaseOP ig)
void	compute_one_body_energies (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, graph::GraphCOP packer_neighbor_graph, interaction_graph::InteractionGraphBaseOP ig)
void	precompute_two_body_energies (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, graph::GraphCOP packer_neighbor_graph, interaction_graph::PrecomputedPairEnergiesInteractionGraphOP pig, bool const finalize_edges=true)
	precomputes all rotamer pair energies between neighboring RotamerSets( residues ) and stores those energies in an intereaction graph capable of storing them public so it can be used by the GreenPacker. More...
void	prepare_symm_otf_interaction_graph (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, 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, graph::GraphCOP packer_neighbor_graph, interaction_graph::SymmOnTheFlyInteractionGraphOP otfig)
RotamerSetOP	orient_rotamer_set_to_symmetric_partner (pose::Pose const &pose, uint const &setpos, uint const &symmpos)
bool	final_visit_to_edge (pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, uint ii_resid, uint jj_resid)
Public Member Functions inherited from core::pack::rotamer_set::RotamerSets
	RotamerSets ()
	~RotamerSets ()
void	set_task (task::PackerTaskCOP task)
void	build_rotamers (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, graph::GraphCOP packer_neighbor_graph)
void	compute_energies (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, graph::GraphCOP packer_neighbor_graph, interaction_graph::InteractionGraphBaseOP ig)
void	dump_pdb (pose::Pose const &pose, std::string const &filename) const
virtual uint	nrotamers () const
virtual uint	nrotamers_for_moltenres (uint) const
virtual uint	nmoltenres () const
virtual uint	total_residue () const
virtual uint	moltenres_2_resid (uint) const
virtual uint	resid_2_moltenres (uint) const
virtual uint	moltenres_for_rotamer (uint) const
virtual uint	res_for_rotamer (uint) const
virtual core::conformation::ResidueCOP	rotamer (uint) const
virtual core::conformation::ResidueCOP	rotamer_for_moltenres (uint moltenres_id, uint rotamerid) const
virtual uint	nrotamer_offset_for_moltenres (uint) const
virtual RotamerSetCOP	rotamer_set_for_residue (uint resid) const
virtual RotamerSetOP	rotamer_set_for_residue (uint resid)
virtual RotamerSetCOP	rotamer_set_for_moltenresidue (uint moltenresid) const
virtual RotamerSetOP	rotamer_set_for_moltenresidue (uint moltenresid)
virtual RotamerSetVector::const_iterator	begin ()
virtual RotamerSetVector::const_iterator	end ()
virtual uint	rotid_on_moltenresidue (uint rotid) const
	convert rotid in full rotamer enumeration into rotamer id on its source residue More...
virtual uint	moltenres_rotid_2_rotid (uint moltenres, uint moltenresrotid) const
	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	compute_one_body_energies (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, graph::GraphCOP packer_neighbor_graph, interaction_graph::InteractionGraphBaseOP ig)
void	precompute_two_body_energies (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, graph::GraphCOP packer_neighbor_graph, interaction_graph::PrecomputedPairEnergiesInteractionGraphOP pig, bool const finalize_edges=true)
	precomputes all rotamer pair energies between neighboring RotamerSets( residues ) and stores those energies in an intereaction graph capable of storing them public so it can be used by the GreenPacker. More...
virtual utility::vector1< uint > const &	resid_2_moltenres_vector () const
virtual utility::vector1< uint > const &	moltenres_2_resid_vector () const
Public Member Functions inherited from core::pack::rotamer_set::FixbbRotamerSets
	FixbbRotamerSets ()
virtual	~FixbbRotamerSets ()
Public Member Functions inherited from core::pack::rotamer_set::RotamerSetsBase
	RotamerSetsBase ()
virtual	~RotamerSetsBase ()

Additional Inherited Members
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)

Member Typedef Documentation

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

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

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

Constructor & Destructor Documentation

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

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core::pack::rotamer_set::symmetry::SymmetricRotamerSets::~SymmetricRotamerSets

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Member Function Documentation

void core::pack::rotamer_set::symmetry::SymmetricRotamerSets::compute_energies	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scfxn,
		graph::GraphCOP	packer_neighbor_graph,
		interaction_graph::InteractionGraphBaseOP	ig
	)

References utility::pointer::owning_ptr< T >::get(), scoring, and utility_exit_with_message.

void core::pack::rotamer_set::symmetry::SymmetricRotamerSets::compute_one_body_energies	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scfxn,
		graph::GraphCOP	packer_neighbor_graph,
		interaction_graph::InteractionGraphBaseOP	ig
	)

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,
		graph::GraphCOP	packer_neighbor_graph,
		interaction_graph::SymmOnTheFlyInteractionGraphOP	otfig
	)

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

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

References core::pose::Pose::conformation(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

RotamerSetOP core::pack::rotamer_set::symmetry::SymmetricRotamerSets::orient_rotamer_set_to_symmetric_partner	(	pose::Pose const &	pose,
		uint const &	setpos,
		uint const &	symmpos
	)

References core::pack::rotamer_set::symmetry::SymmetricRotamerSetFactory::create_rotamer_set(), core::conformation::Residue::orient_onto_residue(), and core::pose::Pose::residue().

void core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scfxn,
		graph::GraphCOP	packer_neighbor_graph,
		interaction_graph::PrecomputedPairEnergiesInteractionGraphOP	pig,
		bool const	finalize_edges = true
	)

precomputes all rotamer pair energies between neighboring RotamerSets( residues ) and stores those energies in an intereaction graph capable of storing them public so it can be used by the GreenPacker.

References core::pose::Pose::conformation(), core::pose::Pose::energies(), core::scoring::ScoreFunction::evaluate_rotamer_pair_energies(), core::scoring::Energies::long_range_container(), core::scoring::ScoreFunction::long_range_energies_begin(), core::scoring::ScoreFunction::long_range_energies_end(), core::scoring::ScoreFunction::prepare_rotamers_for_packing(), scoring, core::id::swap(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::scoring::ScoreFunction::weights().

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

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, core::id::swap(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

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

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