Container for a subset of rotamers that have been created by another rotamer set. This subset object copies pointers to the rotamers contained in another set, as opposed to cloning the rotamers. It's main purpose is to manage the bookkeeping involved in packing with a subset of rotamers (when it might be faster to use a subset and to create an interaction graph specifically for that subset than to simply pass an abreviated list of rotamers to the SimAnnealer with the "rot_to_pack" vector). More...

#include <RotamerSubset.hh>

Inheritance diagram for core::pack::rotamer_set::RotamerSubset:

[legend]

Public Types
typedef conformation::ResidueOP	ResidueOP

typedef conformation::ResidueCOP	ResidueCOP

typedef scoring::trie::RotamerTrieBaseOP	RotamerTrieBaseOP

Public Types inherited from core::conformation::RotamerSetBase
typedef basic::datacache::BasicDataCache	BasicDataCache

typedef basic::datacache::BasicDataCacheOP	BasicDataCacheOP

Public Member Functions
	RotamerSubset (RotamerSet &rotset, utility::vector1< Size > const &rotamer_subset)

	~RotamerSubset () override

void	add_rotamer (conformation::Residue const &rotamer) override
	Append a rotamer to the list; it will not be sorted into the same group as other rotamers of the same group or amino acid unless the last group/amino acid is already the same. Instead it will sit at the end of the list of Rotamers. There are performance implications of using this function instead of add_rotamer_into_existing_group: there are several places in the code which scale quadratically with the number of amino acid groups (but where we assume that this number is small) so if you call this function N times oscilating between ASP and ASN rotamers, you will get O(N^2) performance. If you do not need your rotamers to appear in a particular order, use add_rotamer_into_existing_group instead. More...

void	add_rotamer_into_existing_group (conformation::Residue const &rotamer) override
	Add a rotamer to the RotamerSet where you will group it with other residues of the same type or barring that, the same group. This will keep the total number of residue type groups down. It will not guarantee (it cannot guarantee) that the newly added rotamer will appear after existing rotamers or at the end of the list of rotamers – if you need that kind of guarantee, use add_rotamer instead. More...

Size	get_n_residue_types () const override
	Return the number of different residue types; two residue types are considered different if they have a different address. More...

Size	get_n_residue_groups () const override
	Return the number of different residue groups. Two residue types are considered to be part of the same block of residues if 1. they have the same address or 2. they have the same "name3" and the same neighbor radius. More...

Size	get_residue_type_begin (Size which_restype) const override
	Return the first rotamer of a particular residue type. More...

Size	get_residue_group_begin (Size which_resgroup) const override
	Return the first rotamer that belongs to a particular rotamer group. More...

Size	get_n_rotamers_for_residue_type (Size which_restype) const override

Size	get_n_rotamers_for_residue_group (Size which_resgroup) const override

Size	get_residue_type_index_for_rotamer (Size which_rotamer) const override
	given a rotamer id, return an int which represents a type for this rotamer. More...

Size	get_residue_group_index_for_rotamer (Size which_rotamer) const override
	given a rotamer id, return an int which represents a type for this rotamer. INCOMPLETELY IMPLEMENTED. ANDREW: FIX THIS. More...

Size	num_rotamers () const override

Size	id_for_current_rotamer () const override
	Return the index in the RotamerSet for the current rotamer. More...

conformation::ResidueCOP	rotamer (Size rot_id) const override

basic::datacache::BasicDataCache &	rotamer_data_cache (Size rot_id) const override

conformation::Residue const &	rotamer_ref (Size rot_id) const override

Rotamers::const_iterator	begin () const override

Rotamers::const_iterator	end () const override

conformation::ResidueOP	nonconst_rotamer (Size rot_id) override

void	store_trie (Size method_enum_id, conformation::AbstractRotamerTrieOP trie) override

conformation::AbstractRotamerTrieCOP	get_trie (Size method_enum_id) const override

void	drop_rotamer (Size rot_id) override
	removes a single rotamer and causes a rotamer index update More...

void	drop_rotamers (utility::vector1< bool > const &rotamers_to_delete) override
	rotamers_to_delete must be of size nrotmaers – each position in the array that's "true" is removed from the set of rotamers More...

void	drop_rotamers_by_index (utility::vector1< Size > const &rotamer_indices_to_delete) override
	deletes the rotamers in the list with the given indices. The indices of these rotamers is presumed to be those before any delete operation. e.g. if there are four rotamers, and rotamer_indices_to_delete includes 1 & 3, then the rotamers that will remain are the rotamers originally indexed as 2 and 4, even though their new indices will be 1 & 2. More...

void	initialize_pose_for_rotset_creation (pose::Pose &) const override
	Give the pose a chance to stash any data needed by the rotset need nonconst access to pose. More...

void	show (std::ostream &out) const override

void	build_rotamers (pose::Pose const &the_pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, bool use_neighbor_context=true) override

void	build_dependent_rotamers (RotamerSets const &rotamer_sets, pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph) override

virtual void	build_pwat_rotamers (pose::Pose const &pose, core::Size resid, utility::vector1< Vector > const &new_pwat_rotset)

void	compute_one_body_energies (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< core::PackerEnergy > &energies, bool const no_update=false) const override

void	compute_one_and_two_body_energies (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< core::PackerEnergy > &one_body_energies, utility::vector1< utility::vector1< core::PackerEnergy > > &two_body_energies, utility::vector1< core::Size > &packable_neighbors) const override

void	compute_one_body_energy_maps (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< scoring::EnergyMap > &energies) const override
	for OptE More...

Public Member Functions inherited from core::pack::rotamer_set::RotamerSet
	RotamerSet ()

	~RotamerSet () override

void	set_resid (Size resid)

Size	resid () const override

Public Member Functions inherited from core::conformation::RotamerSetBase
	RotamerSetBase ()

	~RotamerSetBase () override

BasicDataCache &	data ()
	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 Member Functions
	RotamerSubset (RotamerSubset const &)
	(private) No copy-constructor More...

void	steal_rotamer (conformation::ResidueOP rotamer)
	declare that a new block of residue types has begun, and that new residues are about to be pushed back. NOT IMPLEMENTED. More...

void	prepare_for_new_residue_type (core::chemical::ResidueType const &restype)
	declare that a new block of residue types has begun, and that new residues are about to be pushed back. More...

bool	different_restype (core::chemical::ResidueType const &rt1, core::chemical::ResidueType const &rt2) const
	should two residue types be considered the same residue type? More...

bool	different_resgroup (core::chemical::ResidueType const &rt1, core::chemical::ResidueType const &rt2) const
	should two residue types be considered to belong to the same residue-type group? More...

void	new_residue_type ()
	This function should not be called directly – it ought to be called only from prepare_for_new_residue_type. More...

void	new_residue_group ()
	This function should not be called directly – it ought to be called only from prepare_for_new_residue_type. More...

void	push_back_rotamer (conformation::ResidueOP)
	appends a rotamer to the list of rotamers, and increments the count for the number of rotamers for the current value of n_residue_types. More...

void	update_rotamer_offsets () const override
	Lazy update of rotamer indices and offsets and integration of those rotamers in the rotamers_waiting_for_sort_ list. More...

Private Attributes
Rotamers	rotamers_

std::list< ResidueOP >	rotamers_waiting_for_sort_

Size	n_residue_types_

Size	n_residue_groups_

utility::vector1< Size >	residue_type_rotamers_begin_

utility::vector1< Size >	residue_group_rotamers_begin_

utility::vector1< Size >	n_rotamers_for_restype_

utility::vector1< Size >	n_rotamers_for_resgroup_

utility::vector1< Size >	residue_type_for_rotamers_

utility::vector1< Size >	residue_group_for_rotamers_

utility::vector1 < conformation::AbstractRotamerTrieOP >	cached_tries_

Size	id_for_current_rotamer_

ResidueOP	current_rotamer_copy_

bool	rotamer_offsets_require_update_

Detailed Description

Container for a subset of rotamers that have been created by another rotamer set. This subset object copies pointers to the rotamers contained in another set, as opposed to cloning the rotamers. It's main purpose is to manage the bookkeeping involved in packing with a subset of rotamers (when it might be faster to use a subset and to create an interaction graph specifically for that subset than to simply pass an abreviated list of rotamers to the SimAnnealer with the "rot_to_pack" vector).

Member Typedef Documentation

typedef conformation::ResidueCOP core::pack::rotamer_set::RotamerSubset::ResidueCOP

typedef conformation::ResidueOP core::pack::rotamer_set::RotamerSubset::ResidueOP

typedef scoring::trie::RotamerTrieBaseOP core::pack::rotamer_set::RotamerSubset::RotamerTrieBaseOP

Constructor & Destructor Documentation

core::pack::rotamer_set::RotamerSubset::RotamerSubset	(	RotamerSet &	rotset,
		utility::vector1< Size > const &	rotamer_subset
	)

References core::pack::rotamer_set::RotamerSet::id_for_current_rotamer(), id_for_current_rotamer_, core::pack::rotamer_set::RotamerSet::nonconst_rotamer(), rotamers_, and steal_rotamer().

core::pack::rotamer_set::RotamerSubset::~RotamerSubset ( )

overridedefault

core::pack::rotamer_set::RotamerSubset::RotamerSubset ( RotamerSubset const & )

private

(private) No copy-constructor

Member Function Documentation

void core::pack::rotamer_set::RotamerSubset::add_rotamer ( conformation::Residue const & rotamer )

overridevirtual

Append a rotamer to the list; it will not be sorted into the same group as other rotamers of the same group or amino acid unless the last group/amino acid is already the same. Instead it will sit at the end of the list of Rotamers. There are performance implications of using this function instead of add_rotamer_into_existing_group: there are several places in the code which scale quadratically with the number of amino acid groups (but where we assume that this number is small) so if you call this function N times oscilating between ASP and ASN rotamers, you will get O(N^2) performance. If you do not need your rotamers to appear in a particular order, use add_rotamer_into_existing_group instead.

Implements core::pack::rotamer_set::RotamerSet.

References core::conformation::Residue::clone(), prepare_for_new_residue_type(), push_back_rotamer(), and core::conformation::Residue::type().

void core::pack::rotamer_set::RotamerSubset::add_rotamer_into_existing_group ( conformation::Residue const & rotamer )

overridevirtual

Add a rotamer to the RotamerSet where you will group it with other residues of the same type or barring that, the same group. This will keep the total number of residue type groups down. It will not guarantee (it cannot guarantee) that the newly added rotamer will appear after existing rotamers or at the end of the list of rotamers – if you need that kind of guarantee, use add_rotamer instead.

Implements core::pack::rotamer_set::RotamerSet.

References core::conformation::Residue::clone(), rotamer_offsets_require_update_, and rotamers_waiting_for_sort_.

Rotamers::const_iterator core::pack::rotamer_set::RotamerSubset::begin ( ) const

inlineoverridevirtual

Implements core::pack::rotamer_set::RotamerSet.

References rotamers_.

void core::pack::rotamer_set::RotamerSubset::build_dependent_rotamers	(	RotamerSets const &	rotamer_sets,
		pose::Pose const &	pose,
		scoring::ScoreFunction const &	scorefxn,
		task::PackerTask const &	task,
		utility::graph::GraphCOP	packer_neighbor_graph
	)

overridevirtual

Implements core::pack::rotamer_set::RotamerSet.

void core::pack::rotamer_set::RotamerSubset::build_pwat_rotamers	(	pose::Pose const &	pose,
		core::Size	resid,
		utility::vector1< Vector > const &	new_pwat_rotset
	)

virtual

void core::pack::rotamer_set::RotamerSubset::build_rotamers	(	pose::Pose const &	the_pose,
		scoring::ScoreFunction const &	scorefxn,
		task::PackerTask const &	task,
		utility::graph::GraphCOP	packer_neighbor_graph,
		bool	use_neighbor_context = `true`
	)

overridevirtual

Implements core::pack::rotamer_set::RotamerSet.

void core::pack::rotamer_set::RotamerSubset::compute_one_and_two_body_energies	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scorefxn,
		task::PackerTask const &	task,
		utility::graph::GraphCOP	packer_neighbor_graph,
		utility::vector1< core::PackerEnergy > &	one_body_energies,
		utility::vector1< utility::vector1< core::PackerEnergy > > &	two_body_energies,
		utility::vector1< core::Size > &	packable_neighbors
	)		const

overridevirtual

Implements core::pack::rotamer_set::RotamerSet.

void core::pack::rotamer_set::RotamerSubset::compute_one_body_energies	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scorefxn,
		task::PackerTask const &	task,
		utility::graph::GraphCOP	packer_neighbor_graph,
		utility::vector1< core::PackerEnergy > &	energies,
		bool const	no_update = `false`
	)		const

overridevirtual

Implements core::pack::rotamer_set::RotamerSet.

void core::pack::rotamer_set::RotamerSubset::compute_one_body_energy_maps	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scorefxn,
		task::PackerTask const &	task,
		utility::graph::GraphCOP	packer_neighbor_graph,
		utility::vector1< scoring::EnergyMap > &	energies
	)		const

overridevirtual

for OptE

Implements core::pack::rotamer_set::RotamerSet.

bool core::pack::rotamer_set::RotamerSubset::different_resgroup	(	core::chemical::ResidueType const &	rt1,
		core::chemical::ResidueType const &	rt2
	)		const

private

should two residue types be considered to belong to the same residue-type group?

The logic to determine if two residue types should be classified as part of the same group. The thinking is as follows. Two residue types are in the same group if they have the same residue type. They're in the same group if their residue types differ, but they have the same name3 (HIS vs HIS_D have the same name3) and they have the same neighbor radius (SER and PhosphoSER should have different groups). The goal is to organize residue types together which will be packed together (as happens in multistate design with HIS and HISD) and that have the same reach (as is needed for the AANeighborSparseMatrix).

References core::chemical::ResidueTypeBase::name3(), and core::chemical::ResidueType::nbr_radius().

Referenced by prepare_for_new_residue_type(), and update_rotamer_offsets().

bool core::pack::rotamer_set::RotamerSubset::different_restype	(	core::chemical::ResidueType const &	rt1,
		core::chemical::ResidueType const &	rt2
	)		const

private

should two residue types be considered the same residue type?

Referenced by prepare_for_new_residue_type(), and update_rotamer_offsets().

void core::pack::rotamer_set::RotamerSubset::drop_rotamer ( Size rot_id )

overridevirtual

removes a single rotamer and causes a rotamer index update

O(n) operation; if you have a lot of rotamers you want to remove, use drop_rotamers() instead.

Implements core::pack::rotamer_set::RotamerSet.

References id_for_current_rotamer_, rotamer_offsets_require_update_, rotamers_, and update_rotamer_offsets().

void core::pack::rotamer_set::RotamerSubset::drop_rotamers ( utility::vector1< bool > const & rotamers_to_delete )

overridevirtual

rotamers_to_delete must be of size nrotmaers – each position in the array that's "true" is removed from the set of rotamers

Implements core::pack::rotamer_set::RotamerSet.

References current_rotamer_copy_, id_for_current_rotamer_, rotamer_offsets_require_update_, rotamers_, and update_rotamer_offsets().

Referenced by drop_rotamers_by_index().

void core::pack::rotamer_set::RotamerSubset::drop_rotamers_by_index ( utility::vector1< Size > const & rotamer_indices_to_delete )

overridevirtual

deletes the rotamers in the list with the given indices. The indices of these rotamers is presumed to be those before any delete operation. e.g. if there are four rotamers, and rotamer_indices_to_delete includes 1 & 3, then the rotamers that will remain are the rotamers originally indexed as 2 and 4, even though their new indices will be 1 & 2.

Implements core::pack::rotamer_set::RotamerSet.

References drop_rotamers(), and rotamers_.

Rotamers::const_iterator core::pack::rotamer_set::RotamerSubset::end ( ) const

inlineoverridevirtual

Implements core::pack::rotamer_set::RotamerSet.

References rotamers_.

Size core::pack::rotamer_set::RotamerSubset::get_n_residue_groups ( ) const

overridevirtual

Return the number of different residue groups. Two residue types are considered to be part of the same block of residues if 1. they have the same address or 2. they have the same "name3" and the same neighbor radius.

Implements core::pack::rotamer_set::RotamerSet.

References n_residue_groups_, and update_rotamer_offsets().

Referenced by show().

Size core::pack::rotamer_set::RotamerSubset::get_n_residue_types ( ) const

overridevirtual

Return the number of different residue types; two residue types are considered different if they have a different address.

Implements core::pack::rotamer_set::RotamerSet.

References n_residue_types_, and update_rotamer_offsets().

Referenced by show().

Size core::pack::rotamer_set::RotamerSubset::get_n_rotamers_for_residue_group ( Size which_resgroup ) const

overridevirtual

Implements core::pack::rotamer_set::RotamerSet.

References n_residue_groups_, n_rotamers_for_resgroup_, and update_rotamer_offsets().

Size core::pack::rotamer_set::RotamerSubset::get_n_rotamers_for_residue_type ( Size which_restype ) const

overridevirtual

Implements core::pack::rotamer_set::RotamerSet.

References n_residue_types_, n_rotamers_for_restype_, and update_rotamer_offsets().

Size core::pack::rotamer_set::RotamerSubset::get_residue_group_begin ( Size which_resgroup ) const

overridevirtual

Return the first rotamer that belongs to a particular rotamer group.

Implements core::pack::rotamer_set::RotamerSet.

References n_residue_groups_, residue_group_rotamers_begin_, and update_rotamer_offsets().

Size core::pack::rotamer_set::RotamerSubset::get_residue_group_index_for_rotamer ( Size which_rotamer ) const

overridevirtual

given a rotamer id, return an int which represents a type for this rotamer. INCOMPLETELY IMPLEMENTED. ANDREW: FIX THIS.

Implements core::pack::rotamer_set::RotamerSet.

Size core::pack::rotamer_set::RotamerSubset::get_residue_type_begin ( Size which_restype ) const

overridevirtual

Return the first rotamer of a particular residue type.

Implements core::pack::rotamer_set::RotamerSet.

References n_residue_types_, residue_type_rotamers_begin_, and update_rotamer_offsets().

Size core::pack::rotamer_set::RotamerSubset::get_residue_type_index_for_rotamer ( Size which_rotamer ) const

overridevirtual

given a rotamer id, return an int which represents a type for this rotamer.

given a rotamer id, return an int which represents a type for this rotamer. INCOMPLETELY IMPLEMENTED. ANDREW: FIX THIS.

Implements core::pack::rotamer_set::RotamerSet.

conformation::AbstractRotamerTrieCOP core::pack::rotamer_set::RotamerSubset::get_trie ( Size method_enum_id ) const

overridevirtual

Implements core::pack::rotamer_set::RotamerSet.

References cached_tries_.

Size core::pack::rotamer_set::RotamerSubset::id_for_current_rotamer ( ) const

overridevirtual

Return the index in the RotamerSet for the current rotamer.

Implements core::pack::rotamer_set::RotamerSet.

References id_for_current_rotamer_.

void core::pack::rotamer_set::RotamerSubset::initialize_pose_for_rotset_creation ( pose::Pose & ) const

inlineoverridevirtual

Give the pose a chance to stash any data needed by the rotset need nonconst access to pose.

Implements core::pack::rotamer_set::RotamerSet.

void core::pack::rotamer_set::RotamerSubset::new_residue_group ( )

private

This function should not be called directly – it ought to be called only from prepare_for_new_residue_type.

References n_residue_groups_, n_rotamers_for_resgroup_, num_rotamers(), and residue_group_rotamers_begin_.

Referenced by prepare_for_new_residue_type().

void core::pack::rotamer_set::RotamerSubset::new_residue_type ( )

private

This function should not be called directly – it ought to be called only from prepare_for_new_residue_type.

References n_residue_types_, n_rotamers_for_restype_, num_rotamers(), and residue_type_rotamers_begin_.

Referenced by prepare_for_new_residue_type().

conformation::ResidueOP core::pack::rotamer_set::RotamerSubset::nonconst_rotamer ( Size rot_id )

overridevirtual

In handing out non-const data, the guarantee of rotamer-type contiguity within the rotamers_ array, and the correspondence of the rotamer offset data is lost. Future access to rotamer offset data first requires an update of the rotamer offset arrays.

Implements core::pack::rotamer_set::RotamerSet.

References rotamer_offsets_require_update_, and rotamers_.

Size core::pack::rotamer_set::RotamerSubset::num_rotamers ( ) const

overridevirtual

Implements core::pack::rotamer_set::RotamerSet.

References rotamers_.

Referenced by new_residue_group(), new_residue_type(), prepare_for_new_residue_type(), and show().

void core::pack::rotamer_set::RotamerSubset::prepare_for_new_residue_type ( core::chemical::ResidueType const & restype )

private

declare that a new block of residue types has begun, and that new residues are about to be pushed back.

References different_resgroup(), different_restype(), n_residue_types_, new_residue_group(), new_residue_type(), num_rotamers(), and rotamers_.

Referenced by add_rotamer().

void core::pack::rotamer_set::RotamerSubset::push_back_rotamer ( conformation::ResidueOP rotamer )

private

appends a rotamer to the list of rotamers, and increments the count for the number of rotamers for the current value of n_residue_types.

References n_residue_types_, n_rotamers_for_restype_, residue_type_for_rotamers_, and rotamers_.

Referenced by add_rotamer().

conformation::ResidueCOP core::pack::rotamer_set::RotamerSubset::rotamer ( Size rot_id ) const

overridevirtual

Implements core::pack::rotamer_set::RotamerSet.

References rotamers_.

basic::datacache::BasicDataCache & core::pack::rotamer_set::RotamerSubset::rotamer_data_cache ( Size rot_id ) const

overridevirtual

Implements core::pack::rotamer_set::RotamerSet.

References rotamers_.

conformation::Residue const & core::pack::rotamer_set::RotamerSubset::rotamer_ref ( Size rot_id ) const

overridevirtual

Implements core::conformation::RotamerSetBase.

References rotamers_.

void core::pack::rotamer_set::RotamerSubset::show ( std::ostream & out ) const

overridevirtual

Implements core::pack::rotamer_set::RotamerSet.

References core::conformation::Residue::chi(), get_n_residue_groups(), get_n_residue_types(), core::conformation::Residue::mainchain_torsions(), core::conformation::Residue::name(), num_rotamers(), core::conformation::Residue::nus(), core::pack::rotamer_set::RotamerSet::resid(), rot(), and rotamers_.

void core::pack::rotamer_set::RotamerSubset::steal_rotamer ( conformation::ResidueOP rotamer )

private

declare that a new block of residue types has begun, and that new residues are about to be pushed back. NOT IMPLEMENTED.

declare that a new block of residue types has begun, and that new residues are about to be pushed back.

appends a rotamer to the list of rotamers, and increments the count for the number of rotamers for the current value of n_residue_types. NOT IMPLEMENTED. Borrow (steal) a rotamer held by another RotamerSet without cloning that rotamer. That is, both sets will now point at the same rotamer object, so if that rotamer changes for one set, it changes for both.

appends a rotamer to the list of rotamers, and increments the count for the number of rotamers for the current value of n_residue_types.

References rotamer_offsets_require_update_, and rotamers_.

Referenced by RotamerSubset().

void core::pack::rotamer_set::RotamerSubset::store_trie	(	Size	method_enum_id,
		conformation::AbstractRotamerTrieOP	trie
	)

overridevirtual

Implements core::pack::rotamer_set::RotamerSet.

References cached_tries_.

void core::pack::rotamer_set::RotamerSubset::update_rotamer_offsets ( ) const

overrideprivatevirtual

Lazy update of rotamer indices and offsets and integration of those rotamers in the rotamers_waiting_for_sort_ list.

Implements core::pack::rotamer_set::RotamerSet.

References different_resgroup(), different_restype(), id_for_current_rotamer_, n_residue_groups_, n_residue_types_, n_rotamers_for_resgroup_, n_rotamers_for_restype_, residue_group_for_rotamers_, residue_group_rotamers_begin_, residue_type_for_rotamers_, residue_type_rotamers_begin_, rotamer_offsets_require_update_, rotamers_, rotamers_waiting_for_sort_, and core::pack::rotamer_set::sort_new_rotamers_into_rotset_vector().

Referenced by drop_rotamer(), drop_rotamers(), get_n_residue_groups(), get_n_residue_types(), get_n_rotamers_for_residue_group(), get_n_rotamers_for_residue_type(), get_residue_group_begin(), and get_residue_type_begin().

Member Data Documentation

utility::vector1< conformation::AbstractRotamerTrieOP > core::pack::rotamer_set::RotamerSubset::cached_tries_

private

Referenced by get_trie(), and store_trie().

ResidueOP core::pack::rotamer_set::RotamerSubset::current_rotamer_copy_

private

Referenced by drop_rotamers().

Size core::pack::rotamer_set::RotamerSubset::id_for_current_rotamer_

mutableprivate

Referenced by drop_rotamer(), drop_rotamers(), id_for_current_rotamer(), RotamerSubset(), and update_rotamer_offsets().

Size core::pack::rotamer_set::RotamerSubset::n_residue_groups_

mutableprivate

Referenced by get_n_residue_groups(), get_n_rotamers_for_residue_group(), get_residue_group_begin(), new_residue_group(), and update_rotamer_offsets().

Size core::pack::rotamer_set::RotamerSubset::n_residue_types_

mutableprivate

Referenced by get_n_residue_types(), get_n_rotamers_for_residue_type(), get_residue_type_begin(), new_residue_type(), prepare_for_new_residue_type(), push_back_rotamer(), and update_rotamer_offsets().

utility::vector1< Size > core::pack::rotamer_set::RotamerSubset::n_rotamers_for_resgroup_

mutableprivate

Referenced by get_n_rotamers_for_residue_group(), new_residue_group(), and update_rotamer_offsets().

utility::vector1< Size > core::pack::rotamer_set::RotamerSubset::n_rotamers_for_restype_

mutableprivate

Referenced by get_n_rotamers_for_residue_type(), new_residue_type(), push_back_rotamer(), and update_rotamer_offsets().

utility::vector1< Size > core::pack::rotamer_set::RotamerSubset::residue_group_for_rotamers_

mutableprivate

Referenced by update_rotamer_offsets().

utility::vector1< Size > core::pack::rotamer_set::RotamerSubset::residue_group_rotamers_begin_

mutableprivate

Referenced by get_residue_group_begin(), new_residue_group(), and update_rotamer_offsets().

utility::vector1< Size > core::pack::rotamer_set::RotamerSubset::residue_type_for_rotamers_

mutableprivate

Referenced by push_back_rotamer(), and update_rotamer_offsets().

utility::vector1< Size > core::pack::rotamer_set::RotamerSubset::residue_type_rotamers_begin_

mutableprivate

Referenced by get_residue_type_begin(), new_residue_type(), and update_rotamer_offsets().

bool core::pack::rotamer_set::RotamerSubset::rotamer_offsets_require_update_

mutableprivate

Referenced by add_rotamer_into_existing_group(), drop_rotamer(), drop_rotamers(), nonconst_rotamer(), steal_rotamer(), and update_rotamer_offsets().

Rotamers core::pack::rotamer_set::RotamerSubset::rotamers_

mutableprivate

Referenced by begin(), drop_rotamer(), drop_rotamers(), drop_rotamers_by_index(), end(), nonconst_rotamer(), num_rotamers(), prepare_for_new_residue_type(), push_back_rotamer(), rotamer(), rotamer_data_cache(), rotamer_ref(), RotamerSubset(), show(), steal_rotamer(), and update_rotamer_offsets().

std::list< ResidueOP > core::pack::rotamer_set::RotamerSubset::rotamers_waiting_for_sort_

mutableprivate

Referenced by add_rotamer_into_existing_group(), and update_rotamer_offsets().

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

src/core/pack/rotamer_set/RotamerSubset.hh
src/core/pack/rotamer_set/RotamerSubset.cc

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