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 Documentation

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 >

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_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().

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(), 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().

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

template<class AT , class CPDAT >

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().

template<class AT , class CPDAT >

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().

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 core::scoring::elec::create_rotamer_descriptor(), core::scoring::lkball::create_rotamer_descriptor(), and create_trie().

core::Size core::scoring::trie::lookup_cp_map	(	std::map< core::Size, core::Size > const &	cp_reps,
		core::Size	atm_idx
	)

inline

helper function: look up count-pair mapping

Referenced by core::scoring::elec::create_rotamer_descriptor(), and 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,
		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().

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,
		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.

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation