#include <SymmetricRotamerSets.hh>

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

Collaboration 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 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)

Detailed Description

Definition at line 39 of file SymmetricRotamerSets.hh.

Member Typedef Documentation

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

Definition at line 42 of file SymmetricRotamerSets.hh.

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

Definition at line 43 of file SymmetricRotamerSets.hh.

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

Definition at line 44 of file SymmetricRotamerSets.hh.

Constructor & Destructor Documentation

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

Definition at line 57 of file SymmetricRotamerSets.cc.

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

Definition at line 58 of file SymmetricRotamerSets.cc.

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
	)

Definition at line 65 of file SymmetricRotamerSets.cc.

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
	)

Definition at line 98 of file SymmetricRotamerSets.cc.

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
	)

Definition at line 455 of file SymmetricRotamerSets.cc.

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
	)

Definition at line 627 of file SymmetricRotamerSets.cc.

References core::io::serialization::clone(), 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
	)

Definition at line 603 of file SymmetricRotamerSets.cc.

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

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.

Definition at line 119 of file SymmetricRotamerSets.cc.

References core::scoring::ScoreFunction::any_lr_residue_pair_energy(), 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(), 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.

Definition at line 319 of file SymmetricRotamerSets.cc.

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().

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

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation