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Rosetta 3.5
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Rosetta 3.5
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Classes | |
| class | CPDataCorrespondence |
| class | RotamerDescriptor |
| class | RotamerDescriptorAtom |
| class | RotamerTrie |
| class | TrieNode |
| class | RotamerTrieBase |
| class | TrieCollection |
| class | TrieCountPairBase |
Typedefs | |
| typedef utility::pointer::owning_ptr < RotamerTrieBase > | RotamerTrieBaseOP |
| typedef utility::pointer::owning_ptr < RotamerTrieBase const > | RotamerTrieBaseCOP |
| typedef utility::pointer::owning_ptr < TrieCollection > | TrieCollectionOP |
| typedef utility::pointer::owning_ptr < TrieCollection const > | TrieCollectionCOP |
| typedef utility::pointer::owning_ptr < TrieCountPairBase > | TrieCountPairBaseOP |
| typedef utility::pointer::owning_ptr < TrieCountPairBase const > | TrieCountPairBaseCOP |
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) |
| 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) |
| 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) |
| 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::owning_ptr< RotamerTrieBase const > core::scoring::trie::RotamerTrieBaseCOP |
Definition at line 26 of file RotamerTrieBase.fwd.hh.
Definition at line 24 of file RotamerTrieBase.fwd.hh.
Definition at line 26 of file TrieCollection.fwd.hh.
Definition at line 23 of file TrieCollection.fwd.hh.
| typedef utility::pointer::owning_ptr< TrieCountPairBase const > core::scoring::trie::TrieCountPairBaseCOP |
Definition at line 26 of file TrieCountPairBase.fwd.hh.
Definition at line 23 of file TrieCountPairBase.fwd.hh.
| 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 | ||
| ) |
Definition at line 25 of file trie_vs_trie.cc.
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 | ||
| ) |
Definition at line 32 of file trie_vs_path.cc.
Referenced by trie_vs_path().
| CPDataCorrespondence core::scoring::trie::create_cpdata_correspondence_for_rotamer | ( | conformation::Residue const & | example_rotamer) |
Definition at line 116 of file CPDataCorrespondence.cc.
References core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::connection_incomplete(), core::chemical::ResConnID::connid(), core::conformation::PseudoBond::lr_conn_id(), core::scoring::trie::CPDataCorrespondence::n_entries(), core::conformation::Residue::n_residue_connections(), core::conformation::Residue::pseudobonds(), core::conformation::Residue::seqpos(), and core::conformation::PseudoBond::ur_conn_id().
Referenced by create_cpdata_correspondence_for_rotamerset(), core::scoring::methods::MMLJEnergyInter::create_rotamer_trie(), core::scoring::hackelec::HackElecEnergy::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.
Definition at line 106 of file CPDataCorrespondence.cc.
References create_cpdata_correspondence_for_rotamer(), core::conformation::RotamerSetBase::num_rotamers(), and core::conformation::RotamerSetBase::rotamer().
Referenced by core::scoring::methods::MMLJEnergyInter::create_rotamer_trie(), core::scoring::hackelec::HackElecEnergy::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.
Definition at line 43 of file trie.functions.hh.
References initialize_cpdata_for_atom(), core::scoring::trie::CPDataCorrespondence::n_entries(), core::conformation::RotamerSetBase::num_rotamers(), core::scoring::trie::CPDataCorrespondence::resid_for_entry(), core::conformation::RotamerSetBase::rotamer(), and core::scoring::trie::RotamerTrieBase::set_resid_2_connection_entry().
Referenced by core::scoring::methods::MMLJEnergyInter::create_rotamer_trie(), core::scoring::hackelec::HackElecEnergy::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.
Definition at line 102 of file trie.functions.hh.
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::natoms(), core::conformation::Residue::nheavyatoms(), and core::scoring::trie::CPDataCorrespondence::resid_for_entry().
| void core::scoring::trie::initialize_cpdata_for_atom | ( | CPDAT & | cpdata, |
| Size | atom_index, | ||
| conformation::Residue const & | res, | ||
| CPDataCorrespondence const & | cpdata_map | ||
| ) |
Definition at line 152 of file trie.functions.hh.
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 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 | ||
| ) |
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.
Definition at line 58 of file trie_vs_path.hh.
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::hydrogen_interaction_cutoff, 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::TrieCountPairAll::resolve_trie_vs_path(), 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(), and core::scoring::hbonds::hbtrie::HBCountPairFunction::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::TrieCountPairAll::resolve_trie_vs_trie(), 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(), and core::scoring::hbonds::hbtrie::HBCountPairFunction::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 | ||
| ) |
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.
Definition at line 55 of file trie_vs_trie.hh.
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::hydrogen_interaction_cutoff, 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 >::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().
1.8.4