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

#include <SymmetricRotamerSets.hh>

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

Constructor & Destructor Documentation

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

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

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