Rosetta 3.4
Public Member Functions
core::pack::rotamer_set::RotamerSet Class Reference

#include <RotamerSet.hh>

Inheritance diagram for core::pack::rotamer_set::RotamerSet:
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Collaboration diagram for core::pack::rotamer_set::RotamerSet:
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List of all members.

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
virtual Size get_residue_type_begin (Size which_restype) const =0
virtual Size get_n_rotamers_for_residue_type (Size which_restype) 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.
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
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.
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
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
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.

Constructor & Destructor Documentation

core::pack::rotamer_set::RotamerSet::RotamerSet ( )
core::pack::rotamer_set::RotamerSet::~RotamerSet ( ) [virtual]

Member Function Documentation

virtual void core::pack::rotamer_set::RotamerSet::add_rotamer ( conformation::Residue const &  rotamer) [pure virtual]
virtual Rotamers::const_iterator core::pack::rotamer_set::RotamerSet::begin ( ) const [pure virtual]
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]
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]
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]
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]
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::task_operations::LimitAromaChi2_RotamerSetOperation::alter_rotamer_set(), and protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO::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]
virtual Size core::pack::rotamer_set::RotamerSet::get_n_residue_types ( ) const [pure virtual]
virtual Size core::pack::rotamer_set::RotamerSet::get_n_rotamers_for_residue_type ( Size  which_restype) const [pure virtual]
virtual Size core::pack::rotamer_set::RotamerSet::get_residue_type_begin ( Size  which_restype) const [pure virtual]
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]
virtual Size core::pack::rotamer_set::RotamerSet::id_for_current_rotamer ( ) const [pure virtual]
virtual conformation::ResidueOP core::pack::rotamer_set::RotamerSet::nonconst_rotamer ( Size  rot_id) [pure virtual]
virtual Size core::pack::rotamer_set::RotamerSet::num_rotamers ( ) const [pure virtual]
virtual Size core::pack::rotamer_set::RotamerSet::resid ( ) const [inline, virtual]
virtual conformation::ResidueCOP core::pack::rotamer_set::RotamerSet::rotamer ( Size  rot_id) const [pure virtual]
void core::pack::rotamer_set::RotamerSet::set_resid ( Size  resid)

References resid().

virtual void core::pack::rotamer_set::RotamerSet::store_trie ( Size  method_enum_id,
conformation::AbstractRotamerTrieOP  trie 
) [pure virtual]

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