core::scoring::trie Namespace Reference

Classes
class	CPDataCorrespondence
class	RotamerDescriptor
class	RotamerDescriptorAtom
class	RotamerTrie
class	RotamerTrieBase
class	TrieCollection
class	TrieCountPairBase
class	TrieNode

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 Documentation

typedef utility::pointer::owning_ptr< RotamerTrieBase const > core::scoring::trie::RotamerTrieBaseCOP

typedef utility::pointer::owning_ptr< RotamerTrieBase > core::scoring::trie::RotamerTrieBaseOP

typedef utility::pointer::owning_ptr< TrieCollection const > core::scoring::trie::TrieCollectionCOP

typedef utility::pointer::owning_ptr< TrieCollection > core::scoring::trie::TrieCollectionOP

typedef utility::pointer::owning_ptr< TrieCountPairBase const > core::scoring::trie::TrieCountPairBaseCOP

typedef utility::pointer::owning_ptr< TrieCountPairBase > core::scoring::trie::TrieCountPairBaseOP

Function Documentation

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_residue_connections(), 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(), 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(), and core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie().

template<class AT , class CPDAT >

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(), core::conformation::RotamerSetBase::rotamer(), and core::scoring::trie::RotamerTrieBase::set_resid_2_connection_entry().

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(), and core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie().

template<class AT , class CPDAT >

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::natoms(), core::conformation::Residue::nheavyatoms(), and core::scoring::trie::CPDataCorrespondence::resid_for_entry().

template<class CPDAT >

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 create_trie().

template<class AT , class CPDAT1 , class CPDAT2 , class CPFXN , class SFXN >

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.

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(), s, core::scoring::trie::TrieNode< AT, CPDATA >::subtree_interaction_sphere_square_radius(), core::scoring::trie::RotamerTrie< AT, CPDATA >::total_rotamers_2_unique_rotamers(), and weight.

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().

template<class AT , class CPDAT1 , class CPDAT2 , class CPFXN , class SFXN >

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().

template<class AT , class CPDAT1 , class CPDAT2 , class CPFXN , class SFXN >

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.

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(), s, core::scoring::trie::TrieNode< AT, CPDATA >::sibling(), core::scoring::trie::TrieNode< AT, CPDATA >::subtree_interaction_sphere_square_radius(), core::scoring::trie::RotamerTrie< AT, CPDATA >::total_rotamers_2_unique_rotamers(), and weight.