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core::conformation::RotamerSetBase Class Referenceabstract

#include <RotamerSetBase.hh>

Inheritance diagram for core::conformation::RotamerSetBase:
Inheritance graph
[legend]

Public Types

typedef
basic::datacache::BasicDataCache 
BasicDataCache
 
typedef
basic::datacache::BasicDataCacheOP 
BasicDataCacheOP
 

Public Member Functions

 RotamerSetBase ()
 
 ~RotamerSetBase () override
 
virtual core::Size get_n_residue_types () const =0
 
virtual Size get_residue_type_begin (Size which_restype) const =0
 
virtual Size get_n_rotamers_for_residue_type (Size which_restype) const =0
 
virtual Size get_residue_type_index_for_rotamer (Size which_rotamer) const =0
 Rotamers i to i+j of all the same residue type are grouped together. This function returns the index of the residue type in a contiguous block of rotamers. E.g. rotamers 100 to 120 might all be lysine rotamers, and might be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99. If new lysine rotamers are appended to the end of the rotamer set, they are considered to be in a separate residue type block. Lysine rotamers 200 to 210 might be block 15 while lysine rotamers 100 to 120 are still block 7. More...
 
virtual Size num_rotamers () const =0
 
virtual Size resid () const =0
 
virtual conformation::ResidueCOP rotamer (Size rot_id) const =0
 
virtual conformation::Residue
const & 
rotamer_ref (Size rot_id) const =0
 
virtual conformation::ResidueOP nonconst_rotamer (Size rot_id)=0
 mutatable access to a single rotamer in the set. More...
 
virtual void store_trie (Size method_enum_id, AbstractRotamerTrieOP trie)=0
 
virtual AbstractRotamerTrieCOP get_trie (Size method_enum_id) const =0
 
BasicDataCachedata ()
 BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh. More...
 
BasicDataCache const & data () const
 BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh. More...
 

Private Types

typedef utility::VirtualBase parent
 

Private Member Functions

 RotamerSetBase (RotamerSetBase const &)
 

Private Attributes

BasicDataCacheOP data_cache_
 BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh. More...
 

Member Typedef Documentation

typedef basic::datacache::BasicDataCache core::conformation::RotamerSetBase::BasicDataCache
typedef basic::datacache::BasicDataCacheOP core::conformation::RotamerSetBase::BasicDataCacheOP
typedef utility::VirtualBase core::conformation::RotamerSetBase::parent
private

Constructor & Destructor Documentation

core::conformation::RotamerSetBase::RotamerSetBase ( )
core::conformation::RotamerSetBase::~RotamerSetBase ( )
overridedefault
core::conformation::RotamerSetBase::RotamerSetBase ( RotamerSetBase const &  )
private

Member Function Documentation

RotamerSetBase::BasicDataCache & core::conformation::RotamerSetBase::data ( )

BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh.

References data_cache_.

Referenced by core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_pair_energies(), core::scoring::FACTSPotential::get_rotamers_born_radii(), core::scoring::GenBornPotential::get_rotamers_born_radii(), core::scoring::MultipoleElecPotential::get_rotamers_effective_radii(), core::scoring::MultipoleElecPotential::get_rotamers_multipole_info(), core::scoring::VdWTinkerPotential::get_rotamers_vdw_info(), core::scoring::lkball::LK_BallEnergy::prepare_rotamers_for_packing(), and core::scoring::lkball::retrieve_lkb_rotamer_set_info().

RotamerSetBase::BasicDataCache const & core::conformation::RotamerSetBase::data ( ) const

BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh.

References data_cache_.

virtual core::Size core::conformation::RotamerSetBase::get_n_residue_types ( ) const
pure virtual
virtual Size core::conformation::RotamerSetBase::get_n_rotamers_for_residue_type ( Size  which_restype) const
pure virtual
virtual Size core::conformation::RotamerSetBase::get_residue_type_begin ( Size  which_restype) const
pure virtual
virtual Size core::conformation::RotamerSetBase::get_residue_type_index_for_rotamer ( Size  which_rotamer) const
pure virtual

Rotamers i to i+j of all the same residue type are grouped together. This function returns the index of the residue type in a contiguous block of rotamers. E.g. rotamers 100 to 120 might all be lysine rotamers, and might be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99. If new lysine rotamers are appended to the end of the rotamer set, they are considered to be in a separate residue type block. Lysine rotamers 200 to 210 might be block 15 while lysine rotamers 100 to 120 are still block 7.

Implemented in core::pack::rotamer_set::RotamerSet, core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

virtual AbstractRotamerTrieCOP core::conformation::RotamerSetBase::get_trie ( Size  method_enum_id) const
pure virtual
virtual conformation::ResidueOP core::conformation::RotamerSetBase::nonconst_rotamer ( Size  rot_id)
pure virtual
virtual Size core::conformation::RotamerSetBase::num_rotamers ( ) const
pure virtual

Implemented in core::pack::rotamer_set::RotamerSet, core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

Referenced by core::scoring::trie::create_cpdata_correspondence_for_rotamerset(), core::scoring::hbonds::HBondEnergy::create_rotamer_trie(), core::scoring::elec::FA_ElecEnergy::create_rotamer_trie(), core::scoring::lkball::LK_BallEnergy::create_rotamer_trie(), core::scoring::trie::create_trie(), core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_ElecEnergyAroAro::evaluate_rotamer_background_energies(), core::scoring::elec::FA_ElecEnergyAroAll::evaluate_rotamer_background_energies(), core::scoring::methods::MMLJEnergyInter::evaluate_rotamer_background_energies(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::RNA_FA_ElecEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_background_energies(), core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies(), core::scoring::lkball::LK_BallEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energies(), core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energies(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energy_maps(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::evaluate_rotamer_pair_energies(), core::scoring::elec::FA_ElecEnergyAroAro::evaluate_rotamer_pair_energies(), core::scoring::elec::FA_ElecEnergyAroAll::evaluate_rotamer_pair_energies(), core::scoring::elec::RNA_FA_ElecEnergy::evaluate_rotamer_pair_energies(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_pair_energies(), core::scoring::FACTSPotential::get_rotamers_born_radii(), core::scoring::GenBornPotential::get_rotamers_born_radii(), core::scoring::MultipoleElecPotential::get_rotamers_effective_radii(), core::scoring::MultipoleElecPotential::get_rotamers_multipole_info(), core::scoring::VdWTinkerPotential::get_rotamers_vdw_info(), core::scoring::VdWTinkerRotamerSetInfo::initialize(), core::scoring::GenBornRotamerSetInfo::initialize(), core::scoring::FACTSRotamerSetInfo::initialize(), core::scoring::MultipoleElecRotamerSetInfo::initialize(), core::scoring::methods::CustomAtomPairEnergy::prepare_rotamers_for_packing(), core::scoring::methods::PairEnergy::prepare_rotamers_for_packing(), core::scoring::lkball::LK_BallEnergy::prepare_rotamers_for_packing(), core::scoring::elec::FA_ElecEnergy::prepare_rotamers_for_packing(), and core::scoring::orbitals::OrbitalsScore::prepare_rotamers_for_packing().

virtual Size core::conformation::RotamerSetBase::resid ( ) const
pure virtual

Implemented in core::pack::rotamer_set::RotamerSet.

Referenced by core::scoring::hbonds::HBondEnergy::create_rotamer_trie(), core::scoring::methods::MMLJEnergyInter::evaluate_rotamer_background_energies(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_background_energies(), core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies(), core::scoring::lkball::LK_BallEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_intrares_energies(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_intrares_energy_maps(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::evaluate_rotamer_pair_energies(), core::scoring::methods::MMLJEnergyInter::evaluate_rotamer_pair_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_pair_energies(), core::scoring::vdwaals::VDW_Energy::evaluate_rotamer_pair_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_pair_energies(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_pair_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_pair_energies(), core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_pair_energies(), core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_pair_energies(), core::scoring::lkball::LK_BallEnergy::evaluate_rotamer_pair_energies(), core::scoring::vdwaals::VDW_Energy::get_count_pair_function_trie(), core::scoring::methods::MMLJEnergyInter::get_count_pair_function_trie(), core::scoring::elec::FA_ElecEnergy::get_count_pair_function_trie(), core::scoring::lkball::LK_BallEnergy::get_count_pair_function_trie(), and core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie().

virtual conformation::ResidueCOP core::conformation::RotamerSetBase::rotamer ( Size  rot_id) const
pure virtual

Implemented in core::pack::rotamer_set::RotamerSet, core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

Referenced by core::scoring::trie::create_cpdata_correspondence_for_rotamerset(), core::scoring::hbonds::HBondEnergy::create_rotamer_trie(), core::scoring::elec::FA_ElecEnergy::create_rotamer_trie(), core::scoring::lkball::LK_BallEnergy::create_rotamer_trie(), core::scoring::trie::create_trie(), core::scoring::elec::FA_ElecEnergyAroAll::evaluate_rotamer_background_energies(), core::scoring::elec::FA_ElecEnergyAroAro::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::RNA_FA_ElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_intrares_energies(), core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::elec::FA_ElecEnergyAroAll::evaluate_rotamer_pair_energies(), core::scoring::elec::FA_ElecEnergyAroAro::evaluate_rotamer_pair_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_pair_energies(), core::scoring::elec::RNA_FA_ElecEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_pair_energies(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_pair_energies(), core::scoring::FACTSPotential::get_rotamers_born_radii(), core::scoring::GenBornPotential::get_rotamers_born_radii(), core::scoring::MultipoleElecPotential::get_rotamers_effective_radii(), core::scoring::MultipoleElecPotential::get_rotamers_multipole_info(), core::scoring::VdWTinkerPotential::get_rotamers_vdw_info(), core::scoring::VdWTinkerRotamerSetInfo::initialize(), core::scoring::GenBornRotamerSetInfo::initialize(), core::scoring::FACTSRotamerSetInfo::initialize(), core::scoring::MultipoleElecRotamerSetInfo::initialize(), and core::scoring::elec::FA_ElecEnergy::prepare_rotamers_for_packing().

virtual conformation::Residue const& core::conformation::RotamerSetBase::rotamer_ref ( Size  rot_id) const
pure virtual
virtual void core::conformation::RotamerSetBase::store_trie ( Size  method_enum_id,
AbstractRotamerTrieOP  trie 
)
pure virtual

Member Data Documentation

BasicDataCacheOP core::conformation::RotamerSetBase::data_cache_
private

BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh.

Warning
DataCache must always be initialized with the number of cacheable data types – see the last enum entry.

Referenced by data().


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