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>

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)

virtual	~RotamerSubset ()

virtual void	add_rotamer (conformation::Residue const &rotamer)

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

virtual Size	get_n_residue_groups () const
	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...

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

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

virtual Size	get_n_rotamers_for_residue_type (Size which_restype) const

virtual Size	get_n_rotamers_for_residue_group (Size which_resgroup) const

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

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

virtual Size	num_rotamers () const

virtual Size	id_for_current_rotamer () const

virtual conformation::ResidueCOP	rotamer (Size rot_id) const

virtual Rotamers::const_iterator	begin () const

virtual Rotamers::const_iterator	end () const

virtual conformation::ResidueOP	nonconst_rotamer (Size rot_id)

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

virtual conformation::AbstractRotamerTrieCOP	get_trie (Size method_enum_id) const

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

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

virtual void	drop_rotamers_by_index (utility::vector1< Size > const &rotamer_indices_to_delete)
	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...

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

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

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

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

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

virtual	~RotamerSet ()

void	set_resid (Size resid)

virtual Size	resid () const

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

virtual	~RotamerSetBase ()

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

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_, scoring, and steal_rotamer().

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

virtual

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 )

virtual

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

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

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

inlinevirtual

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,
		graph::GraphCOP	packer_neighbor_graph
	)

virtual

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

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

virtual

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,
		graph::GraphCOP	packer_neighbor_graph,
		utility::vector1< core::PackerEnergy > &	energies
	)		const

virtual

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,
		graph::GraphCOP	packer_neighbor_graph,
		utility::vector1< scoring::EnergyMap > &	energies
	)		const

virtual

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::ResidueType::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 )

virtual

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 )

virtual

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_, update_rotamer_offsets(), and utility_exit_with_message.

Referenced by drop_rotamers_by_index().

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

virtual

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_.

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

inlinevirtual

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

References rotamers_.

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

virtual

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().

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

virtual

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().

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

virtual

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

virtual

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

virtual

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

virtual

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

virtual

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

virtual

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

virtual

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

References cached_tries_.

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

virtual

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

References id_for_current_rotamer_.

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 )

virtual

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

virtual

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

References rotamers_.

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

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(), rotamers_, and type.

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

virtual

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

References 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
	)

virtual

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

References cached_tries_.

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

private

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(), and RotamerSubset().

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 drop_rotamer(), drop_rotamers(), nonconst_rotamer(), steal_rotamer(), and update_rotamer_offsets().

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

private

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(), RotamerSubset(), steal_rotamer(), 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

Private Attributes
Rotamers	rotamers_

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_

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation