#include <RotamerSet.hh>

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

Collaboration diagram for core::pack::rotamer_set::RotamerSet:

Public Member Functions
	RotamerSet ()

virtual	~RotamerSet ()

void	set_resid (Size resid)

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)=0

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)=0

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

virtual Size	get_n_residue_types () const =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...

virtual Size	get_residue_type_begin (Size which_restype) const =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...

virtual Size	get_n_rotamers_for_residue_type (Size which_restype) const =0

virtual Size	get_n_rotamers_for_residue_group (Size which_resgroup) const =0

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

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 =0
	for OptE More...

virtual Size	num_rotamers () const =0

virtual Size	id_for_current_rotamer () const =0

virtual Size	resid () const

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

virtual Rotamers::const_iterator	begin () const =0

virtual Rotamers::const_iterator	end () const =0

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

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

virtual conformation::AbstractRotamerTrieCOP	get_trie (Size method_enum_id) const =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...

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 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

Detailed Description

Definition at line 60 of file RotamerSet.hh.

Member Typedef Documentation

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

private

Definition at line 64 of file RotamerSet.hh.

Constructor & Destructor Documentation

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

Definition at line 26 of file RotamerSet.cc.

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

virtual

Definition at line 31 of file RotamerSet.cc.

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

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

Referenced by protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO::alter_rotamer_set(), core::pack::rotamer_set::UnboundRotamersOperation::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::task_operations::LimitAromaChi2_RotamerSetOperation::alter_rotamer_set(), and protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set().

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,
		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,
		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_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

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,
		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 protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO::alter_rotamer_set(), and protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation::alter_rotamer_set().

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::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation::alter_rotamer_set().

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.

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

pure 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.

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

pure 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.

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.

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

pure 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().

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

pure 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.

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

pure 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

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

Referenced by protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation::alter_rotamer_set(), and core::pack::rotamer_set::RotamerSubset::RotamerSubset().

virtual conformation::ResidueOP core::pack::rotamer_set::RotamerSet::nonconst_rotamer ( Size rot_id)

pure virtual