Container for a set of rotamers for use in packing. Rotamers are sorted into groups of the same residue type. Offsets into these rotamer groups are maintained by this class, as is information concerning the "original rotamer" – the rotamer present on the input pose before packing began. More...

#include <RotamerSet_.hh>

Public Member Functions
	RotamerSet_ ()

virtual	~RotamerSet_ ()

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)
	Build rotamers that depend on positions of rotamers built in a previous pass. More...

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_resgroup) 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
	Rotamers i to i+j of all the same residue type are grouped together. This function returns the index of the residue type in a contiguous block of rotamers. E.g. rotamers 100 to 120 might all be lysine rotamers, and might be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99. If new lysine rotamers are appended to the end of the rotamer set, they are considered to be in a separate residue type block. Lysine rotamers 200 to 210 might be block 15 while lysine rotamers 100 to 120 are still block 7. More...

virtual Size	get_residue_group_index_for_rotamer (Size which_rotamer) const
	Return the index of the rotamer group for a particular rotamer. More...

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
	Computes the packers "one body energies" for the set of rotamers. More...

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...

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...

void	set_extra_samples (task::PackerTask const &task, int num_10A_neighbors, int chi, chemical::ResidueTypeCOP concrete_residue, utility::vector1< Real > &extra_chi_steps) const
	Pushes standard-deviation multiples that should be sampled for this residue – if this residue has more neighbors within 10A than the task-specified cutoff for buriedness, then extra rotamer samples are added to the extra_chi_steps vector, otherwise, the vector is not modified. More...

virtual core::PackerEnergy	bump_check (ResidueCOP rotamer, scoring::ScoreFunction const &sf, pose::Pose const &pose, task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph) const
	Computes the "bump energy" of a rotamer: the bump energy is the sum of rotamer's interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization. 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...

Protected Member Functions
virtual void	build_rotamers_for_concrete_virt (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, graph::GraphCOP packer_neighbor_graph, bool use_neighbor_context=true)
	Creates a set of rotamers for a particular residue type (the concrete residue type) while relying on the rotamer- building instructions within the PackerTask. Use the residue in the input pose at position resid_ as the existing residue. More...

void	build_rotamers_for_concrete (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, graph::GraphCOP packer_neighbor_graph, bool use_neighbor_context=true)
	Creates a set of rotamers for a particular residue type (the concrete residue type) while relying on the rotamer- building instructions within the PackerTask. More...

void	build_dependent_rotamers_for_concrete (RotamerSets const &rotamer_sets, pose::Pose const &pose, scoring::ScoreFunction const &, task::PackerTask const &task, conformation::Residue const &existing_residue, chemical::ResidueTypeCOP concrete_residue, graph::GraphCOP packer_neighbor_graph)
	Build rotamers of a specific type that depend on positions of rotamers built in a previous pass Use an input "existing residue" which may or may not reflect the coordinates of the residue at pose.residue( resid_ );. More...

void	build_optimize_H_rotamers (pose::Pose const &pose, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, graph::GraphCOP packer_neighbor_graph)
	Creates a sets of rotamers for an "optimize H" repacking. More...

Private Member Functions
	RotamerSet_ (RotamerSet_ const &)

void	build_tp3_water_rotamers (pose::Pose const &pose, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, graph::GraphCOP packer_neighbor_graph)
	logic for building TP3 water rotamers 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 set of rotamers for use in packing. Rotamers are sorted into groups of the same residue type. Offsets into these rotamer groups are maintained by this class, as is information concerning the "original rotamer" – the rotamer present on the input pose before packing began.

Member Typedef Documentation

typedef pack::dunbrack::ChiSetOP core::pack::rotamer_set::RotamerSet_::ChiSetOP

typedef conformation::ResidueCOP core::pack::rotamer_set::RotamerSet_::ResidueCOP

typedef conformation::ResidueOP core::pack::rotamer_set::RotamerSet_::ResidueOP

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

Constructor & Destructor Documentation

core::pack::rotamer_set::RotamerSet_::RotamerSet_ ( )

References scoring.

core::pack::rotamer_set::RotamerSet_::~RotamerSet_ ( )

virtual

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

private

Member Function Documentation

void core::pack::rotamer_set::RotamerSet_::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::RotamerSet_::begin ( ) const

inlinevirtual

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

References rotamers_.

void core::pack::rotamer_set::RotamerSet_::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

Build rotamers that depend on positions of rotamers built in a previous pass.

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

References core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), build_dependent_rotamers_for_concrete(), chemical, core::pack::rotamer_set::RotamerSet::resid(), core::pose::Pose::residue(), and core::pack::task::PackerTask::residue_task().

void core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers_for_concrete	(	RotamerSets const &	rotamer_sets,
		pose::Pose const &	pose,
		scoring::ScoreFunction const &	,
		task::PackerTask const &	task,
		conformation::Residue const &	existing_residue,
		chemical::ResidueTypeCOP	concrete_residue,
		graph::GraphCOP	packer_neighbor_graph
	)

protected

Build rotamers of a specific type that depend on positions of rotamers built in a previous pass Use an input "existing residue" which may or may not reflect the coordinates of the residue at pose.residue( resid_ );.

References core::pack::rotamer_set::build_dependent_water_rotamers(), core::conformation::Residue::chain(), prepare_for_new_residue_type(), push_back_rotamer(), core::pack::rotamer_set::RotamerSet::resid(), and utility_exit_with_message.

Referenced by build_dependent_rotamers().

void core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers	(	pose::Pose const &	pose,
		task::PackerTask const &	task,
		chemical::ResidueTypeCOP	concrete_residue,
		conformation::Residue const &	existing_residue,
		graph::GraphCOP	packer_neighbor_graph
	)

protected

Creates a sets of rotamers for an "optimize H" repacking.

Creates a sets of rotamers for an "optimize H" repacking: optimize H repositions hydroxyl hydrogens and resolve protonation ambiguity and if the task's flip_HNQ flag is set, it will flip amide groups ( ASN (N) and GLN (Q) ) and the ring orientation in histidine (H).

Referenced by build_rotamers_for_concrete().

void core::pack::rotamer_set::RotamerSet_::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.

References core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), build_rotamers_for_concrete_virt(), chemical, core::conformation::Residue::create_rotamer(), id_for_current_rotamer_, core::conformation::Residue::name(), num_rotamers(), prepare_for_new_residue_type(), push_back_rotamer(), core::pack::rotamer_set::RotamerSet::resid(), core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), core::pose::Pose::residue_type(), core::pack::task::ResidueLevelTask::rotamer_set_operation_begin(), core::pack::task::ResidueLevelTask::rotamer_set_operation_end(), and core::pack::rotamer_set::tt.

void core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scorefxn,
		task::PackerTask const &	task,
		chemical::ResidueTypeCOP	concrete_residue,
		conformation::Residue const &	existing_residue,
		graph::GraphCOP	packer_neighbor_graph,
		bool	use_neighbor_context = `true`
	)

protected

Creates a set of rotamers for a particular residue type (the concrete residue type) while relying on the rotamer- building instructions within the PackerTask.

Referenced by build_rotamers_for_concrete_virt().

void core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete_virt	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scorefxn,
		task::PackerTask const &	task,
		chemical::ResidueTypeCOP	concrete_residue,
		graph::GraphCOP	packer_neighbor_graph,
		bool	use_neighbor_context = `true`
	)

protectedvirtual

Creates a set of rotamers for a particular residue type (the concrete residue type) while relying on the rotamer- building instructions within the PackerTask. Use the residue in the input pose at position resid_ as the existing residue.

This will check for rotamer/background collisions if the PackerTask's bump_check boolean is true – it uses the bump_check_{sidechain/full} methods defined by the energy methods contained in the scorefxn object

References build_rotamers_for_concrete(), core::pack::rotamer_set::RotamerSet::resid(), and core::pose::Pose::residue().

Referenced by build_rotamers().

void core::pack::rotamer_set::RotamerSet_::build_tp3_water_rotamers	(	pose::Pose const &	pose,
		task::PackerTask const &	task,
		chemical::ResidueTypeCOP	concrete_residue,
		conformation::Residue const &	existing_residue,
		graph::GraphCOP	packer_neighbor_graph
	)

private

logic for building TP3 water rotamers

refactored into its own method so that it could be used in both regular packing and also in optimizeH.

References core::pack::rotamer_set::build_independent_water_rotamers(), core::conformation::Residue::chain(), core::conformation::Residue::create_rotamer(), id_for_current_rotamer_, core::pack::task::PackerTask::include_current(), core::conformation::Residue::name(), num_rotamers(), push_back_rotamer(), and core::pack::rotamer_set::RotamerSet::resid().

Referenced by build_optimize_H_rotamers(), and build_rotamers_for_concrete().

core::PackerEnergy core::pack::rotamer_set::RotamerSet_::bump_check	(	ResidueCOP	rotamer,
		scoring::ScoreFunction const &	sf,
		pose::Pose const &	pose,
		task::PackerTask const &	task,
		graph::GraphCOP	packer_neighbor_graph
	)		const

virtual

Computes the "bump energy" of a rotamer: the bump energy is the sum of rotamer's interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

Bump check does not include long range energies, though, maybe this should change.

References core::scoring::ScoreFunction::bump_check_backbone(), core::scoring::ScoreFunction::bump_check_full(), core::scoring::EMapVector::dot(), core::pack::task::PackerTask::pack_residue(), core::pack::rotamer_set::RotamerSet::resid(), core::pose::Pose::residue(), scoring, and core::scoring::ScoreFunction::weights().

Referenced by build_rotamers_for_concrete().

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

virtual

Computes the packers "one body energies" for the set of rotamers.

The packer's 1-body is a combination of the rotamer internal energies (the context dependent and independent one body energies), the intra-residue energies defined by the two body energies, and the sum of the two body energies with the background residues in this repacking. The PackerTask tells the RotamerSet_ what residues are part of the background and which are being repacked.

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

Reimplemented in core::pack::rotamer_set::symmetry::SymmetricRotamerSet_.

References core::scoring::EMapVector::dot(), core::pose::Pose::energies(), core::scoring::ScoreFunction::eval_cd_1b(), core::scoring::ScoreFunction::eval_ci_1b(), core::scoring::ScoreFunction::evaluate_rotamer_background_energies(), core::scoring::ScoreFunction::evaluate_rotamer_intrares_energies(), core::scoring::Energies::long_range_container(), core::scoring::ScoreFunction::long_range_energies_begin(), core::scoring::ScoreFunction::long_range_energies_end(), num_rotamers(), core::pack::task::PackerTask::pack_residue(), core::pack::rotamer_set::RotamerSet::resid(), core::pose::Pose::residue(), rotamers_, scoring, and core::scoring::ScoreFunction::weights().

Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies().

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

virtual

for OPTE

Used in OptE. Based on the function compute_one_body_energies(). OptE needs to store the energies for all score terms for each rotamer separately. In this context there are only rotamers at a single position, with all other positions fixed.

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

bool core::pack::rotamer_set::RotamerSet_::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::RotamerSet_::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::RotamerSet_::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::RotamerSet_::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::RotamerSet_::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::RotamerSet_::end ( ) const

inlinevirtual

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

References rotamers_.

Size core::pack::rotamer_set::RotamerSet_::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::RotamerSet_::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::RotamerSet_::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::RotamerSet_::get_n_rotamers_for_residue_type ( Size which_resgroup ) 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::RotamerSet_::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::RotamerSet_::get_residue_group_index_for_rotamer ( Size which_rotamer ) const

virtual

Return the index of the rotamer group for a particular rotamer.

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

References residue_group_for_rotamers_.

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

virtual

Rotamers i to i+j of all the same residue type are grouped together. This function returns the index of the residue type in a contiguous block of rotamers. E.g. rotamers 100 to 120 might all be lysine rotamers, and might be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99. If new lysine rotamers are appended to the end of the rotamer set, they are considered to be in a separate residue type block. Lysine rotamers 200 to 210 might be block 15 while lysine rotamers 100 to 120 are still block 7.

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

References residue_type_for_rotamers_.

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

virtual

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

References cached_tries_.

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

virtual

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

References id_for_current_rotamer_.

void core::pack::rotamer_set::RotamerSet_::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::RotamerSet_::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::RotamerSet_::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::RotamerSet_::num_rotamers ( ) const

virtual

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

References rotamers_.

Referenced by build_rotamers(), build_rotamers_for_concrete(), build_tp3_water_rotamers(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), compute_one_body_energies(), compute_one_body_energy_maps(), new_residue_group(), new_residue_type(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergyAdd(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergyMultiply(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergySubtract(), and prepare_for_new_residue_type().

void core::pack::rotamer_set::RotamerSet_::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(), build_dependent_rotamers_for_concrete(), build_rotamers(), and build_rotamers_for_concrete().

void core::pack::rotamer_set::RotamerSet_::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_groups_, n_residue_types_, n_rotamers_for_resgroup_, n_rotamers_for_restype_, residue_group_for_rotamers_, residue_type_for_rotamers_, and rotamers_.

Referenced by add_rotamer(), build_dependent_rotamers_for_concrete(), build_optimize_H_rotamers(), build_rotamers(), build_rotamers_for_concrete(), and build_tp3_water_rotamers().

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

virtual

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

References rotamers_.

Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies().

void core::pack::rotamer_set::RotamerSet_::set_extra_samples	(	task::PackerTask const &	task,
		int	num_10A_neighbors,
		int	chi,
		chemical::ResidueTypeCOP	concrete_residue,
		utility::vector1< Real > &	extra_chi_steps
	)		const

Pushes standard-deviation multiples that should be sampled for this residue – if this residue has more neighbors within 10A than the task-specified cutoff for buriedness, then extra rotamer samples are added to the extra_chi_steps vector, otherwise, the vector is not modified.

Referenced by build_rotamers_for_concrete().

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

virtual

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

References cached_tries_.

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

private

Member Data Documentation

BumpSelector core::pack::rotamer_set::RotamerSet_::bump_selector_

private

Referenced by build_rotamers_for_concrete().

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

private

Referenced by get_trie(), and store_trie().

ResidueOP core::pack::rotamer_set::RotamerSet_::current_rotamer_copy_

private

Referenced by drop_rotamers().

Size core::pack::rotamer_set::RotamerSet_::id_for_current_rotamer_

mutableprivate

Referenced by build_optimize_H_rotamers(), build_rotamers(), build_rotamers_for_concrete(), build_tp3_water_rotamers(), drop_rotamer(), drop_rotamers(), and id_for_current_rotamer().

Size core::pack::rotamer_set::RotamerSet_::n_residue_groups_

mutableprivate

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

Size core::pack::rotamer_set::RotamerSet_::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::RotamerSet_::n_rotamers_for_resgroup_

mutableprivate

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

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

mutableprivate

Referenced by get_residue_group_index_for_rotamer(), push_back_rotamer(), and update_rotamer_offsets().

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

mutableprivate

Referenced by get_residue_type_index_for_rotamer(), push_back_rotamer(), and update_rotamer_offsets().

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

mutableprivate

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

bool core::pack::rotamer_set::RotamerSet_::rotamer_offsets_require_update_

mutableprivate

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

Rotamers core::pack::rotamer_set::RotamerSet_::rotamers_

private

Referenced by begin(), build_optimize_H_rotamers(), build_rotamers_for_concrete(), compute_one_body_energies(), compute_one_body_energy_maps(), drop_rotamer(), drop_rotamers(), drop_rotamers_by_index(), end(), nonconst_rotamer(), num_rotamers(), prepare_for_new_residue_type(), push_back_rotamer(), rotamer(), and update_rotamer_offsets().

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

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

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

Public Types
typedef conformation::ResidueOP	ResidueOP

typedef conformation::ResidueCOP	ResidueCOP

typedef pack::dunbrack::ChiSetOP	ChiSetOP

typedef scoring::trie::RotamerTrieBaseOP	RotamerTrieBaseOP

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

typedef basic::datacache::BasicDataCacheOP	BasicDataCacheOP

Private Attributes
BumpSelector	bump_selector_

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_