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Rosetta
2020.50
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Classes | |
class | CPDataCorrespondence |
class | RotamerDescriptor |
class | RotamerDescriptorAtom |
class | RotamerTrie |
class | RotamerTrieBase |
class | TrieCollection |
class | TrieCountPairBase |
class | TrieNode |
class | TrieVsTrieCachedDataContainerBase |
A generic base class for passing data to the trie-vs-trie calculation, without having to cache it in mutable data in an EnergyMethod or whatnot. More... | |
Typedefs | |
typedef utility::pointer::shared_ptr < RotamerTrieBase > | RotamerTrieBaseOP |
typedef utility::pointer::shared_ptr < RotamerTrieBase const > | RotamerTrieBaseCOP |
typedef utility::pointer::shared_ptr < TrieCollection > | TrieCollectionOP |
typedef utility::pointer::shared_ptr < TrieCollection const > | TrieCollectionCOP |
typedef utility::pointer::shared_ptr < TrieCountPairBase > | TrieCountPairBaseOP |
typedef utility::pointer::shared_ptr < TrieCountPairBase const > | TrieCountPairBaseCOP |
using | TrieVsTrieCachedDataContainerBaseOP = utility::pointer::shared_ptr< TrieVsTrieCachedDataContainerBase > |
using | TrieVsTrieCachedDataContainerBaseCOP = utility::pointer::shared_ptr< TrieVsTrieCachedDataContainerBase const > |
Functions | |
CPDataCorrespondence | create_cpdata_correspondence_for_rotamerset (conformation::RotamerSetBase const &rotset) |
CPDataCorrespondence | create_cpdata_correspondence_for_rotamer (conformation::Residue const &example_rotamer) |
template<class AT , class CPDAT > | |
RotamerTrieBaseOP | create_trie (conformation::RotamerSetBase const &rotset, AT const &, CPDAT const &, CPDataCorrespondence const &cpdata_map, Distance atomic_interaction_cutoff) |
Create a trie where cpdata is initialized to reflect path distances to connection-point atoms. More... | |
template<class CPDAT > | |
void | initialize_cpdata_for_atom (CPDAT &cpdata, Size atom_index, conformation::Residue const &res, CPDataCorrespondence const &cpdata_map) |
template<class AT , class CPDAT > | |
RotamerTrieBaseOP | create_trie (conformation::Residue const &res, AT const &, CPDAT const &, CPDataCorrespondence const &cpdata_map, Distance atomic_interaction_cutoff) |
core::Size | lookup_cp_map (std::map< core::Size, core::Size > const &cp_reps, core::Size atm_idx) |
helper function: look up count-pair mapping More... | |
template<class AT , class CPDAT > | |
RotamerTrieBaseOP | create_trie (conformation::RotamerSetBase const &rotset, AT const &, CPDAT const &, CPDataCorrespondence const &cpdata_map, std::map< chemical::ResidueTypeCOP, std::map< core::Size, core::Size > > const &cp_reps, Distance atomic_interaction_cutoff) |
template<class AT , class CPDAT > | |
RotamerTrieBaseOP | create_trie (conformation::Residue const &res, AT const &, CPDAT const &, CPDataCorrespondence const &cpdata_map, std::map< chemical::ResidueTypeCOP, std::map< core::Size, core::Size > > const &cp_reps, Distance atomic_interaction_cutoff) |
void | convert_inorder_vector_to_original_order (utility::vector1< Size > const &total_rotamers_2_unique_rotamers, utility::vector1< core::PackerEnergy > &pair_energy_vector, utility::vector1< Energy > const &temp_vector) |
template<class AT , class CPDAT1 , class CPDAT2 , class CPFXN , class SFXN > | |
void | trie_vs_path (RotamerTrie< AT, CPDAT1 > const &trie1, RotamerTrie< AT, CPDAT2 > const &trie2, CPFXN &count_pair, SFXN &score_function, utility::vector1< core::PackerEnergy > &pair_energy_vector, utility::vector1< core::PackerEnergy > &temp_vector, core::scoring::trie::TrieVsTrieCachedDataContainerBase const *const cached_data) |
trie vs path algorithm, templated on the Atom type that each TrieAtom is templated on, along with the Count Pair data (two tries must share the same Atom type to be used for the trie-vs-trie algorithm, but may contain different peices of count-pair data), on the kind of count pair function used, and finally, on the score function itself. More... | |
void | convert_inorder_table_to_original_order (utility::vector1< Size > const &total_rotamers_2_unique_rotamers_1, utility::vector1< Size > const &total_rotamers_2_unique_rotamers_2, ObjexxFCL::FArray2D< core::PackerEnergy > &pair_energy_table, ObjexxFCL::FArray2A< core::PackerEnergy > const &rot_rot_table) |
template<class AT , class CPDAT1 , class CPDAT2 , class CPFXN , class SFXN > | |
void | trie_vs_trie (RotamerTrie< AT, CPDAT1 > &trie1, RotamerTrie< AT, CPDAT2 > &trie2, CPFXN &count_pair, SFXN &score_function, ObjexxFCL::FArray2D< core::PackerEnergy > &pair_energy_table, ObjexxFCL::FArray2D< core::PackerEnergy > &temp_table) |
template<class AT , class CPDAT1 , class CPDAT2 , class CPFXN , class SFXN > | |
void | trie_vs_trie (RotamerTrie< AT, CPDAT1 > const &trie1, RotamerTrie< AT, CPDAT2 > const &trie2, CPFXN &count_pair, SFXN &score_function, ObjexxFCL::FArray2D< core::PackerEnergy > &pair_energy_table, ObjexxFCL::FArray2D< core::PackerEnergy > &temp_table, TrieVsTrieCachedDataContainerBase const *const cached_data) |
trie vs trie algorithm, templated on the Atom type that each TrieAtom is templated on, along with the Count Pair data (two tries must share the same Atom type to be used for the trie-vs-trie algorithm, but may contain different peices of count-pair data), on the kind of count pair function used, and finally, on the score function itself. More... | |
typedef utility::pointer::shared_ptr< RotamerTrieBase const > core::scoring::trie::RotamerTrieBaseCOP |
typedef utility::pointer::shared_ptr< RotamerTrieBase > core::scoring::trie::RotamerTrieBaseOP |
typedef utility::pointer::shared_ptr< TrieCollection const > core::scoring::trie::TrieCollectionCOP |
typedef utility::pointer::shared_ptr< TrieCollection > core::scoring::trie::TrieCollectionOP |
typedef utility::pointer::shared_ptr< TrieCountPairBase const > core::scoring::trie::TrieCountPairBaseCOP |
typedef utility::pointer::shared_ptr< TrieCountPairBase > core::scoring::trie::TrieCountPairBaseOP |
using core::scoring::trie::TrieVsTrieCachedDataContainerBaseCOP = typedef utility::pointer::shared_ptr< TrieVsTrieCachedDataContainerBase const > |
using core::scoring::trie::TrieVsTrieCachedDataContainerBaseOP = typedef utility::pointer::shared_ptr< TrieVsTrieCachedDataContainerBase > |
void core::scoring::trie::convert_inorder_table_to_original_order | ( | utility::vector1< Size > const & | total_rotamers_2_unique_rotamers_1, |
utility::vector1< Size > const & | total_rotamers_2_unique_rotamers_2, | ||
ObjexxFCL::FArray2D< core::PackerEnergy > & | pair_energy_table, | ||
ObjexxFCL::FArray2A< core::PackerEnergy > const & | rot_rot_table | ||
) |
Referenced by trie_vs_trie().
void core::scoring::trie::convert_inorder_vector_to_original_order | ( | utility::vector1< Size > const & | total_rotamers_2_unique_rotamers, |
utility::vector1< core::PackerEnergy > & | pair_energy_vector, | ||
utility::vector1< Energy > const & | temp_vector | ||
) |
Referenced by trie_vs_path().
CPDataCorrespondence core::scoring::trie::create_cpdata_correspondence_for_rotamer | ( | conformation::Residue const & | example_rotamer | ) |
References core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::connection_incomplete(), core::chemical::ResConnID::connid(), core::scoring::trie::CPDataCorrespondence::n_entries(), core::conformation::Residue::n_possible_residue_connections(), core::chemical::PseudoBond, core::conformation::Residue::pseudobonds(), and core::conformation::Residue::seqpos().
Referenced by create_cpdata_correspondence_for_rotamerset(), core::scoring::methods::MMLJEnergyInter::create_rotamer_trie(), core::scoring::elec::FA_ElecEnergy::create_rotamer_trie(), core::scoring::lkball::LK_BallEnergy::create_rotamer_trie(), and core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie().
CPDataCorrespondence core::scoring::trie::create_cpdata_correspondence_for_rotamerset | ( | conformation::RotamerSetBase const & | rotset | ) |
ASSUMPTION: Connection topology is consistent across all rotamers. Any bond found on rotamer 1 is present on rotamer i. Any pseudobond on rotamer 1 is found on rotamer i.
References create_cpdata_correspondence_for_rotamer(), core::conformation::RotamerSetBase::num_rotamers(), and core::conformation::RotamerSetBase::rotamer().
Referenced by core::scoring::vdwaals::VDW_Energy::create_rotamer_trie(), core::scoring::methods::MMLJEnergyInter::create_rotamer_trie(), core::scoring::elec::FA_ElecEnergy::create_rotamer_trie(), core::scoring::lkball::LK_BallEnergy::create_rotamer_trie(), and core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie().
RotamerTrieBaseOP core::scoring::trie::create_trie | ( | conformation::RotamerSetBase const & | rotset, |
AT const & | , | ||
CPDAT const & | , | ||
CPDataCorrespondence const & | cpdata_map, | ||
Distance | atomic_interaction_cutoff | ||
) |
Create a trie where cpdata is initialized to reflect path distances to connection-point atoms.
Class AT must define a constructor that takes a residue const & and an atom index. Class AT must also define an operator < and an operator ==
References initialize_cpdata_for_atom(), core::scoring::trie::CPDataCorrespondence::n_entries(), core::conformation::RotamerSetBase::num_rotamers(), core::scoring::trie::CPDataCorrespondence::resid_for_entry(), and core::conformation::RotamerSetBase::rotamer().
Referenced by core::scoring::vdwaals::VDW_Energy::create_rotamer_trie(), core::scoring::methods::MMLJEnergyInter::create_rotamer_trie(), and core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie().
RotamerTrieBaseOP core::scoring::trie::create_trie | ( | conformation::Residue const & | res, |
AT const & | , | ||
CPDAT const & | , | ||
CPDataCorrespondence const & | cpdata_map, | ||
Distance | atomic_interaction_cutoff | ||
) |
Creates a rotamer trie given a single residue – a one-residue trie. Class AT must define a constructor that takes a residue const & and an atom index.
References core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), initialize_cpdata_for_atom(), core::scoring::trie::CPDataCorrespondence::n_entries(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), and core::scoring::trie::CPDataCorrespondence::resid_for_entry().
RotamerTrieBaseOP core::scoring::trie::create_trie | ( | conformation::RotamerSetBase const & | rotset, |
AT const & | , | ||
CPDAT const & | , | ||
CPDataCorrespondence const & | cpdata_map, | ||
std::map< chemical::ResidueTypeCOP, std::map< core::Size, core::Size > > const & | cp_reps, | ||
Distance | atomic_interaction_cutoff | ||
) |
version of the above that also takes a count-pair corespondence
References initialize_cpdata_for_atom(), lookup_cp_map(), core::scoring::trie::CPDataCorrespondence::n_entries(), core::conformation::RotamerSetBase::num_rotamers(), core::scoring::trie::CPDataCorrespondence::resid_for_entry(), and core::conformation::RotamerSetBase::rotamer().
RotamerTrieBaseOP core::scoring::trie::create_trie | ( | conformation::Residue const & | res, |
AT const & | , | ||
CPDAT const & | , | ||
CPDataCorrespondence const & | cpdata_map, | ||
std::map< chemical::ResidueTypeCOP, std::map< core::Size, core::Size > > const & | cp_reps, | ||
Distance | atomic_interaction_cutoff | ||
) |
version of the above that also takes a count-pair corespondence
References core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), initialize_cpdata_for_atom(), lookup_cp_map(), core::scoring::trie::CPDataCorrespondence::n_entries(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), core::scoring::trie::CPDataCorrespondence::resid_for_entry(), and core::conformation::Residue::type_ptr().
void core::scoring::trie::initialize_cpdata_for_atom | ( | CPDAT & | cpdata, |
Size | atom_index, | ||
conformation::Residue const & | res, | ||
CPDataCorrespondence const & | cpdata_map | ||
) |
References core::scoring::trie::CPDataCorrespondence::connid_for_entry_connpoint(), core::scoring::etable::count_pair::INFINITE_SEPARATION(), core::conformation::Residue::is_bonded(), core::scoring::trie::CPDataCorrespondence::n_connpoints_for_entry(), core::scoring::trie::CPDataCorrespondence::n_entries(), core::conformation::Residue::path_distance(), core::scoring::trie::CPDataCorrespondence::resid_for_entry(), and core::conformation::Residue::residue_connect_atom_index().
Referenced by core::scoring::elec::create_rotamer_descriptor(), core::scoring::lkball::create_rotamer_descriptor(), and create_trie().
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inline |
helper function: look up count-pair mapping
Referenced by core::scoring::elec::create_rotamer_descriptor(), and create_trie().
void core::scoring::trie::trie_vs_path | ( | RotamerTrie< AT, CPDAT1 > const & | trie1, |
RotamerTrie< AT, CPDAT2 > const & | trie2, | ||
CPFXN & | count_pair, | ||
SFXN & | score_function, | ||
utility::vector1< core::PackerEnergy > & | pair_energy_vector, | ||
utility::vector1< core::PackerEnergy > & | temp_vector, | ||
core::scoring::trie::TrieVsTrieCachedDataContainerBase const *const | cached_data | ||
) |
trie vs path algorithm, templated on the Atom type that each TrieAtom is templated on, along with the Count Pair data (two tries must share the same Atom type to be used for the trie-vs-trie algorithm, but may contain different peices of count-pair data), on the kind of count pair function used, and finally, on the score function itself.
References core::scoring::trie::TrieNode< AT, CPDATA >::atom(), core::scoring::trie::RotamerTrie< AT, CPDATA >::atoms(), convert_inorder_vector_to_original_order(), core::scoring::trie::TrieNode< AT, CPDATA >::cp_data(), core::scoring::trie::TrieNode< AT, CPDATA >::first_atom_in_branch(), core::scoring::trie::TrieNode< AT, CPDATA >::has_sibling(), core::scoring::trie::TrieNode< AT, CPDATA >::is_hydrogen(), core::scoring::trie::TrieNode< AT, CPDATA >::is_rotamer_terminal(), core::scoring::trie::RotamerTrie< AT, CPDATA >::max_atom_depth(), core::scoring::trie::RotamerTrie< AT, CPDATA >::max_branch_depth(), core::scoring::trie::RotamerTrie< AT, CPDATA >::max_heavyatom_depth(), core::scoring::trie::RotamerTrie< AT, CPDATA >::num_heavy_atoms(), core::scoring::trie::TrieNode< AT, CPDATA >::subtree_interaction_sphere_square_radius(), and core::scoring::trie::RotamerTrie< AT, CPDATA >::total_rotamers_2_unique_rotamers().
Referenced by core::scoring::etable::etrie::TrieCountPair1BC4::resolve_trie_vs_path(), core::scoring::etable::etrie::TrieCountPair1BC3::resolve_trie_vs_path(), core::scoring::etable::etrie::TrieCountPairGeneric::resolve_trie_vs_path(), core::scoring::etable::etrie::TrieCountPairAll::resolve_trie_vs_path(), core::scoring::hbonds::hbtrie::HBCountPairFunction::resolve_trie_vs_path(), and core::scoring::vdwaals::VDWTrieCountPair1B::resolve_trie_vs_path().
void core::scoring::trie::trie_vs_trie | ( | RotamerTrie< AT, CPDAT1 > & | trie1, |
RotamerTrie< AT, CPDAT2 > & | trie2, | ||
CPFXN & | count_pair, | ||
SFXN & | score_function, | ||
ObjexxFCL::FArray2D< core::PackerEnergy > & | pair_energy_table, | ||
ObjexxFCL::FArray2D< core::PackerEnergy > & | temp_table | ||
) |
Referenced by core::scoring::etable::etrie::TrieCountPair1BC4::resolve_trie_vs_trie(), core::scoring::etable::etrie::TrieCountPair1BC3::resolve_trie_vs_trie(), core::scoring::etable::etrie::TrieCountPairGeneric::resolve_trie_vs_trie(), core::scoring::etable::etrie::TrieCountPairAll::resolve_trie_vs_trie(), core::scoring::hbonds::hbtrie::HBCountPairFunction::resolve_trie_vs_trie(), and core::scoring::vdwaals::VDWTrieCountPair1B::resolve_trie_vs_trie().
void core::scoring::trie::trie_vs_trie | ( | RotamerTrie< AT, CPDAT1 > const & | trie1, |
RotamerTrie< AT, CPDAT2 > const & | trie2, | ||
CPFXN & | count_pair, | ||
SFXN & | score_function, | ||
ObjexxFCL::FArray2D< core::PackerEnergy > & | pair_energy_table, | ||
ObjexxFCL::FArray2D< core::PackerEnergy > & | temp_table, | ||
TrieVsTrieCachedDataContainerBase const *const | cached_data | ||
) |
trie vs trie algorithm, templated on the Atom type that each TrieAtom is templated on, along with the Count Pair data (two tries must share the same Atom type to be used for the trie-vs-trie algorithm, but may contain different peices of count-pair data), on the kind of count pair function used, and finally, on the score function itself.
References core::scoring::trie::TrieNode< AT, CPDATA >::atom(), core::scoring::trie::RotamerTrie< AT, CPDATA >::atoms(), convert_inorder_table_to_original_order(), core::scoring::trie::TrieNode< AT, CPDATA >::cp_data(), core::scoring::trie::TrieNode< AT, CPDATA >::first_atom_in_branch(), core::scoring::trie::TrieNode< AT, CPDATA >::has_sibling(), core::scoring::trie::TrieNode< AT, CPDATA >::is_hydrogen(), core::scoring::trie::TrieNode< AT, CPDATA >::is_rotamer_terminal(), protocols::mean_field::max(), core::scoring::trie::RotamerTrie< AT, CPDATA >::max_atom_depth(), core::scoring::trie::RotamerTrie< AT, CPDATA >::max_branch_depth(), core::scoring::trie::RotamerTrie< AT, CPDATA >::max_heavyatom_depth(), core::scoring::trie::RotamerTrie< AT, CPDATA >::num_heavy_atoms(), core::scoring::trie::TrieNode< AT, CPDATA >::num_rotamers_in_subtree(), core::scoring::trie::RotamerTrie< AT, CPDATA >::num_unique_rotamers(), core::scoring::trie::TrieNode< AT, CPDATA >::sibling(), core::scoring::trie::TrieNode< AT, CPDATA >::subtree_interaction_sphere_square_radius(), and core::scoring::trie::RotamerTrie< AT, CPDATA >::total_rotamers_2_unique_rotamers().