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protocols::flexpack::rotamer_set::FlexbbRotamerSet Class Reference

#include <FlexbbRotamerSet.hh>

Inheritance diagram for protocols::flexpack::rotamer_set::FlexbbRotamerSet:
Inheritance graph
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Public Types

typedef
core::pack::rotamer_set::RotamerSet_ 
parent
 
- 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

 FlexbbRotamerSet ()
 
 ~FlexbbRotamerSet () override
 
void set_owner (FlexbbRotamerSetsCAP owner)
 
void build_dependent_rotamers (core::pack::rotamer_set::RotamerSets const &rotamer_sets, core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn, core::pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph) override
 Build rotamers that depend on positions of rotamers built in a previous pass This function won't work... More...
 
void set_existing_residue (core::conformation::ResidueCOP residue)
 
- Public Member Functions inherited from core::pack::rotamer_set::RotamerSet_
 RotamerSet_ ()
 
 ~RotamerSet_ () override
 
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) override
 
void add_rotamer (conformation::Residue const &rotamer) override
 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...
 
void add_rotamer_into_existing_group (conformation::Residue const &rotamer) override
 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
 Return the number of different residue types; two residue types are considered different if they have a different address. More...
 
Size get_n_residue_groups () const override
 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
 Return the first rotamer of a particular residue type. More...
 
Size get_residue_group_begin (Size which_resgroup) const override
 Return the first rotamer that belongs to a particular rotamer group. More...
 
Size get_n_rotamers_for_residue_type (Size which_resgroup) const override
 
Size get_n_rotamers_for_residue_group (Size which_resgroup) const override
 
Size get_residue_type_index_for_rotamer (Size which_rotamer) const override
 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...
 
Size get_residue_group_index_for_rotamer (Size which_rotamer) const override
 Return the index of the rotamer group for a particular rotamer. More...
 
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 override
 Computes the packers "one body energies" for the set of rotamers. More...
 
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 override
 Computes the packers one body energies for the set of rotamers as well as two body energies for neighboring positions defined as packable by the task. More...
 
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 override
 for OPTE More...
 
Size num_rotamers () const override
 
Size id_for_current_rotamer () const override
 Return the index in the RotamerSet for the current rotamer. More...
 
conformation::ResidueCOP rotamer (Size rot_id) const override
 
basic::datacache::BasicDataCache & rotamer_data_cache (Size rot_id) const override
 
conformation::Residue const & rotamer_ref (Size rot_id) const override
 
Rotamers::const_iterator begin () const override
 
Rotamers::const_iterator end () const override
 
conformation::ResidueOP nonconst_rotamer (Size rot_id) override
 mutatable access to a single rotamer in the set. More...
 
void store_trie (Size method_enum_id, conformation::AbstractRotamerTrieOP trie) override
 
conformation::AbstractRotamerTrieCOP get_trie (Size method_enum_id) const override
 
void drop_rotamer (Size rot_id) override
 removes a single rotamer and causes a rotamer index update More...
 
void drop_rotamers (utility::vector1< bool > const &rotamers_to_delete) override
 rotamers_to_delete must be of size nrotmaers – each position in the array that's "true" is removed from the set of rotamers More...
 
void drop_rotamers_by_index (utility::vector1< Size > const &rotamer_indices_to_delete) override
 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 initialize_pose_for_rotset_creation (pose::Pose &) const override
 Give the pose a chance to stash any data needed by the rotset need nonconst access to pose. 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...
 
void show (std::ostream &out) const override
 
void update_rotamer_offsets () const override
 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::pack::rotamer_set::RotamerSet
 RotamerSet ()
 
 ~RotamerSet () override
 
void set_resid (Size resid)
 
Size resid () const override
 
- Public Member Functions inherited from core::conformation::RotamerSetBase
 RotamerSetBase ()
 
 ~RotamerSetBase () override
 
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...
 

Protected Member Functions

void build_rotamers_for_concrete_virt (core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn, core::pack::task::PackerTask const &task, core::chemical::ResidueTypeCOP concrete_residue, utility::graph::GraphCOP packer_neighbor_graph, bool use_neighbor_context=true) override
 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...
 
core::PackerEnergy bump_check (core::conformation::ResidueCOP rotamer, core::scoring::ScoreFunction const &sf, core::pose::Pose const &pose, core::pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph) const override
 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...
 
- Protected Member Functions inherited from core::pack::rotamer_set::RotamerSet_
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, utility::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 filter_water_rotamers (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > const &new_rotamers, utility::vector1< conformation::ResidueOP > &filtered_rotamers)
 , Filter water rotamers by eliminating rotamers with overlaps and uniformly only keeping a maximum number of rotamers (water_rotamers_cap, def=500) 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, utility::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, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &scorefxn)
 Creates a sets of rotamers for an "optimize H" repacking. More...
 

Private Attributes

ResidueCOP existing_residue_
 
FlexbbRotamerSetsCAP owner_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::flexpack::rotamer_set::FlexbbRotamerSet::FlexbbRotamerSet ( )
protocols::flexpack::rotamer_set::FlexbbRotamerSet::~FlexbbRotamerSet ( )
overridedefault

Member Function Documentation

void protocols::flexpack::rotamer_set::FlexbbRotamerSet::build_dependent_rotamers ( core::pack::rotamer_set::RotamerSets const &  rotamer_sets,
core::pose::Pose const &  pose,
core::scoring::ScoreFunction const &  scorefxn,
core::pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph 
)
overridevirtual

Build rotamers that depend on positions of rotamers built in a previous pass This function won't work...

Reimplemented from core::pack::rotamer_set::RotamerSet_.

void protocols::flexpack::rotamer_set::FlexbbRotamerSet::build_rotamers_for_concrete_virt ( core::pose::Pose const &  pose,
core::scoring::ScoreFunction const &  scorefxn,
core::pack::task::PackerTask const &  task,
core::chemical::ResidueTypeCOP  concrete_residue,
utility::graph::GraphCOP  packer_neighbor_graph,
bool  use_neighbor_context = true 
)
overrideprotectedvirtual

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.

Reimplemented from core::pack::rotamer_set::RotamerSet_.

References core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), and existing_residue_.

core::PackerEnergy protocols::flexpack::rotamer_set::FlexbbRotamerSet::bump_check ( core::conformation::ResidueCOP  rotamer,
core::scoring::ScoreFunction const &  sf,
core::pose::Pose const &  pose,
core::pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph 
) const
overrideprotectedvirtual

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.

Reimplemented from core::pack::rotamer_set::RotamerSet_.

References core::scoring::ScoreFunction::bump_check_backbone(), core::scoring::ScoreFunction::bump_check_full(), core::scoring::EMapVector::dot(), owner_, core::pack::task::PackerTask::pack_residue(), core::pack::rotamer_set::RotamerSet::resid(), core::pose::Pose::residue(), and core::scoring::ScoreFunction::weights().

void protocols::flexpack::rotamer_set::FlexbbRotamerSet::set_existing_residue ( core::conformation::ResidueCOP  residue)

References existing_residue_.

void protocols::flexpack::rotamer_set::FlexbbRotamerSet::set_owner ( FlexbbRotamerSetsCAP  owner)

References owner_.

Member Data Documentation

ResidueCOP protocols::flexpack::rotamer_set::FlexbbRotamerSet::existing_residue_
private
FlexbbRotamerSetsCAP protocols::flexpack::rotamer_set::FlexbbRotamerSet::owner_
private

Referenced by bump_check(), and set_owner().


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