#include <RotamerSet.hh>

Inheritance diagram for core::pack::rotamer_set::RotamerSet:

Public Member Functions
	RotamerSet ()

	~RotamerSet () override

void	set_resid (Size resid)

virtual 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)=0

virtual 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)=0

virtual void	add_rotamer (conformation::Residue const &rotamer)=0
	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...

virtual void	add_rotamer_into_existing_group (conformation::Residue const &rotamer)=0
	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=0
	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 =0
	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=0
	Return the first rotamer of a particular residue type. More...

virtual Size	get_residue_group_begin (Size which_resgroup) const =0
	Return the first rotamer that belongs to a particular rotamer group. More...

Size	get_n_rotamers_for_residue_type (Size which_restype) const override=0

virtual Size	get_n_rotamers_for_residue_group (Size which_resgroup) const =0

Size	get_residue_type_index_for_rotamer (Size which_rotamer) const override=0
	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 =0
	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, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< core::PackerEnergy > &energies, bool const no_update=false) const =0

virtual 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 =0

virtual 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 =0
	for OptE More...

Size	num_rotamers () const override=0

virtual Size	id_for_current_rotamer () const =0
	Return the index in the RotamerSet for the current rotamer. More...

Size	resid () const override

conformation::ResidueCOP	rotamer (Size rot_id) const override=0

virtual basic::datacache::BasicDataCache &	rotamer_data_cache (Size rot_id) const =0

virtual Rotamers::const_iterator	begin () const =0

virtual Rotamers::const_iterator	end () const =0

conformation::ResidueOP	nonconst_rotamer (Size rot_id) override=0
	mutatable access to a single rotamer in the set. More...

void	store_trie (Size method_enum_id, conformation::AbstractRotamerTrieOP trie) override=0

conformation::AbstractRotamerTrieCOP	get_trie (Size method_enum_id) const override=0

virtual void	drop_rotamer (Size rot_id)=0
	removes a single rotamer and causes a rotamer index update More...

virtual void	drop_rotamers (utility::vector1< bool > const &rotamers_to_delete)=0
	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)=0
	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	show (std::ostream &out) const =0

virtual void	initialize_pose_for_rotset_creation (pose::Pose &pose) const =0

virtual void	update_rotamer_offsets () const =0
	Lazy update of rotamer indices and offsets and integration of those rotamers in the rotamers_waiting_for_sort_ list. More...

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

	~RotamerSetBase () override

virtual conformation::Residue const &	rotamer_ref (Size rot_id) const =0

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 Types
typedef conformation::RotamerSetBase	parent

Private Member Functions
	RotamerSet (RotamerSet const &)

Private Attributes
Size	resid_

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

typedef basic::datacache::BasicDataCacheOP	BasicDataCacheOP

Member Typedef Documentation

typedef conformation::RotamerSetBase core::pack::rotamer_set::RotamerSet::parent

private

Constructor & Destructor Documentation

core::pack::rotamer_set::RotamerSet::RotamerSet ( )

core::pack::rotamer_set::RotamerSet::~RotamerSet ( )

overridedefault

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

private

Member Function Documentation

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

pure virtual

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.

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

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

pure virtual

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.

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

Referenced by protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_to_rotamer_set(), core::pack::rotamer_set::AddResiduesRotamerSetOperation::alter_rotamer_set(), protocols::matdes::MotifHitsRotamersOperation::alter_rotamer_set(), protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO::alter_rotamer_set(), core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::alter_rotamer_set(), and protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set().

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

pure virtual

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

Referenced by protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), and protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb().

virtual 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,
		utility::graph::GraphCOP	packer_neighbor_graph
	)

pure virtual

Implemented in core::pack::rotamer_set::RotamerSubset, core::pack::rotamer_set::RotamerSet_, and protocols::flexpack::rotamer_set::FlexbbRotamerSet.

virtual void core::pack::rotamer_set::RotamerSet::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`
	)

pure virtual

Implemented in core::pack::rotamer_set::RotamerSubset, and core::pack::rotamer_set::RotamerSet_.

virtual void core::pack::rotamer_set::RotamerSet::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

pure virtual

Implemented in core::pack::rotamer_set::RotamerSubset, and core::pack::rotamer_set::RotamerSet_.

virtual void core::pack::rotamer_set::RotamerSet::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

pure virtual

Implemented in core::pack::rotamer_set::RotamerSubset, core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::symmetry::SymmetricRotamerSet_.

virtual void core::pack::rotamer_set::RotamerSet::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

pure virtual

for OptE

Implemented in core::pack::rotamer_set::RotamerSubset, and core::pack::rotamer_set::RotamerSet_.

virtual void core::pack::rotamer_set::RotamerSet::drop_rotamer ( Size rot_id )

pure virtual

removes a single rotamer and causes a rotamer index update

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

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

pure virtual

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

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

Referenced by core::pack::rotamer_set::DeleteAllRotamerSetOperation::alter_rotamer_set(), protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO::alter_rotamer_set(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), and protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb().

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

pure 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.

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

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

pure virtual

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

Referenced by protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), and protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb().

virtual Size core::pack::rotamer_set::RotamerSet::get_n_residue_groups ( ) const

pure 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.

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

Referenced by protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::alter_rotamer_set(), and protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::rotamer_set_contains_rotamer().

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

overridepure virtual

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

Implements core::conformation::RotamerSetBase.

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

Referenced by protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), and core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection().

virtual Size core::pack::rotamer_set::RotamerSet::get_n_rotamers_for_residue_group ( Size which_resgroup ) const

pure virtual

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

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

overridepure virtual

Implements core::conformation::RotamerSetBase.

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

virtual Size core::pack::rotamer_set::RotamerSet::get_residue_group_begin ( Size which_resgroup ) const

pure virtual

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

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

Referenced by protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::rotamer_set_contains_rotamer().

virtual Size core::pack::rotamer_set::RotamerSet::get_residue_group_index_for_rotamer ( Size which_rotamer ) const

pure virtual

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

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

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

overridepure virtual

Return the first rotamer of a particular residue type.

Implements core::conformation::RotamerSetBase.

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

Referenced by core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection().

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

overridepure 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::conformation::RotamerSetBase.

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

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

overridepure virtual

Implements core::conformation::RotamerSetBase.

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

virtual Size core::pack::rotamer_set::RotamerSet::id_for_current_rotamer ( ) const

pure virtual

Return the index in the RotamerSet for the current rotamer.

Implemented in core::pack::rotamer_set::RotamerSet_, and core::pack::rotamer_set::RotamerSubset.

Referenced by protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), and core::pack::rotamer_set::RotamerSubset::RotamerSubset().

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