Rosetta Core  2014.35
Public Types | Public Member Functions | List of all members
core::pack::rotamer_set::symmetry::SymmetricRotamerSet_ Class Reference

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. symmetrical version of RotamerSet_. More...

#include <SymmetricRotamerSet_.hh>

Public Types

typedef
conformation::symmetry::SymmetricConformation 
SymmetricConformation
 
typedef
conformation::symmetry::SymmetryInfoCOP 
SymmetryInfoCOP
 
- Public Types inherited from core::pack::rotamer_set::RotamerSet_
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
 

Public Member Functions

 SymmetricRotamerSet_ ()
 
virtual ~SymmetricRotamerSet_ ()
 
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...
 
void PackerEnergyMultiply (utility::vector1< core::PackerEnergy > &energies, core::Size factor) const
 
void PackerEnergyAdd (utility::vector1< core::PackerEnergy > &energies, utility::vector1< core::PackerEnergy > const &add) const
 
void PackerEnergySubtract (utility::vector1< core::PackerEnergy > &energies, utility::vector1< core::PackerEnergy > const &subtract) const
 
RotamerSetOP orient_rotamer_set_to_symmetric_partner (pose::Pose const &pose, conformation::ResidueOP residue_in, int const &sympos, RotamerSetOP rotset_in) const
 
- Public Member Functions inherited from core::pack::rotamer_set::RotamerSet_
 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_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 ()
 
BasicDataCachedata ()
 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...
 

Additional Inherited Members

- Protected Member Functions inherited from core::pack::rotamer_set::RotamerSet_
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...
 

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. symmetrical version of RotamerSet_.

Member Typedef Documentation

Constructor & Destructor Documentation

core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::SymmetricRotamerSet_ ( )
core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::~SymmetricRotamerSet_ ( )
virtual

Member Function Documentation

void core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::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
RotamerSetOP core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_set_to_symmetric_partner ( pose::Pose const &  pose,
conformation::ResidueOP  residue_in,
int const &  sympos,
RotamerSetOP  rotset_in 
) const
void core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergyAdd ( utility::vector1< core::PackerEnergy > &  energies,
utility::vector1< core::PackerEnergy > const &  add 
) const
void core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergyMultiply ( utility::vector1< core::PackerEnergy > &  energies,
core::Size  factor 
) const
void core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergySubtract ( utility::vector1< core::PackerEnergy > &  energies,
utility::vector1< core::PackerEnergy > const &  subtract 
) const

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