Rosetta 3.4
Public Types | Public Member Functions
core::pack::rotamer_set::RotamerSubset Class Reference

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>

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

Public Types

typedef conformation::ResidueOP ResidueOP
typedef conformation::ResidueCOP ResidueCOP
typedef
scoring::trie::RotamerTrieBaseOP 
RotamerTrieBaseOP

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

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


Constructor & Destructor Documentation

core::pack::rotamer_set::RotamerSubset::RotamerSubset ( RotamerSet rotset,
utility::vector1< Size > const &  rotamer_subset 
)
core::pack::rotamer_set::RotamerSubset::~RotamerSubset ( ) [virtual]

Member Function Documentation

void core::pack::rotamer_set::RotamerSubset::add_rotamer ( conformation::Residue const &  rotamer) [virtual]
virtual Rotamers::const_iterator core::pack::rotamer_set::RotamerSubset::begin ( ) const [inline, virtual]
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]
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]
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]
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]
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.

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.

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().

virtual Rotamers::const_iterator core::pack::rotamer_set::RotamerSubset::end ( ) const [inline, virtual]
Size core::pack::rotamer_set::RotamerSubset::get_n_residue_types ( ) const [virtual]
Size core::pack::rotamer_set::RotamerSubset::get_n_rotamers_for_residue_type ( Size  which_restype) const [virtual]
Size core::pack::rotamer_set::RotamerSubset::get_residue_type_begin ( Size  which_restype) const [virtual]
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]
Size core::pack::rotamer_set::RotamerSubset::id_for_current_rotamer ( ) const [virtual]
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.

Size core::pack::rotamer_set::RotamerSubset::num_rotamers ( ) const [virtual]
conformation::ResidueCOP core::pack::rotamer_set::RotamerSubset::rotamer ( Size  rot_id) const [virtual]
void core::pack::rotamer_set::RotamerSubset::store_trie ( Size  method_enum_id,
conformation::AbstractRotamerTrieOP  trie 
) [virtual]

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