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>
Inheritance diagram for core::pack::rotamer_set::symmetry::SymmetricRotamerSet_:
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_ () | |
| ~SymmetricRotamerSet_ () override | |
| 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 | 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::Residue const &residue_in, int const &sympos, RotamerSet const &rotset_in, bool const set_up_mirror_types_if_has_mirror_symmetry=false) const |
| core::conformation::ResidueOP | orient_rotamer_to_symmetric_partner (pose::Pose const &pose, conformation::Residue const &residue_in, int const &sympos, bool const set_up_mirror_types_if_has_mirror_symmetry=false) const |
| void | initialize_pose_for_rotset_creation (pose::Pose &pose) const override |
| Give the pose a chance to stash any data needed by the rotset need nonconst access to pose. More... | |
| void | single_rotamer_rotset_original_rotmer_index (core::Size const setting) |
| Symmetric rotamer sets are used in a funny way for self interactions. In the case of using a symmetric rotamer set to store a single rotamer, this is the index of the single rotamer. This function stores the value. More... | |
| core::Size | single_rotamer_rotset_original_rotmer_index () const |
| Symmetric rotamer sets are used in a funny way for self interactions. In the case of using a symmetric rotamer set to store a single rotamer, this is the index of the single rotamer. This function retrieves the value. More... | |
| 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 | build_dependent_rotamers (RotamerSets const &rotamer_sets, pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph) override |
| Build rotamers that depend on positions of rotamers built in a previous pass. More... | |
| 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_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 | 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, utility::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... | |
| 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 | |
| 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 Attributes | |
| core::Size | single_rotamer_rotset_original_rotmer_index_ = 0 |
| Symmetric rotamer sets are used in a funny way for self interactions. In the case of using a symmetric rotamer set to store a single rotamer, this is the index of the single rotamer. 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, 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. 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, 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... | |
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
◆ SymmetricConformation
| typedef conformation::symmetry::SymmetricConformation core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::SymmetricConformation |
◆ SymmetryInfoCOP
| typedef conformation::symmetry::SymmetryInfoCOP core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::SymmetryInfoCOP |
Constructor & Destructor Documentation
◆ SymmetricRotamerSet_()
| core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::SymmetricRotamerSet_ | ( | ) |
◆ ~SymmetricRotamerSet_()
|
overridedefault |
Member Function Documentation
◆ compute_one_body_energies()
|
overridevirtual |
Computes the packers "one body energies" for the set of rotamers.
Reimplemented from core::pack::rotamer_set::RotamerSet_.
References core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), core::pose::Pose::conformation(), core::scoring::EMapVector::dot(), core::pose::Pose::energies(), core::scoring::ScoreFunction::eval_cd_1b(), core::scoring::ScoreFunction::eval_ci_1b(), core::scoring::ScoreFunction::evaluate_rotamer_background_energies(), core::scoring::ScoreFunction::evaluate_rotamer_intrares_energies(), core::scoring::ScoreFunction::evaluate_rotamer_pair_energies(), core::pose::symmetry::is_symmetric(), core::scoring::Energies::long_range_container(), core::scoring::ScoreFunction::long_range_energies_begin(), core::scoring::ScoreFunction::long_range_energies_end(), core::pack::rotamer_set::RotamerSet_::num_rotamers(), orient_rotamer_set_to_symmetric_partner(), core::pack::task::PackerTask::pack_residue(), PackerEnergyAdd(), PackerEnergyMultiply(), core::scoring::ScoreFunction::prepare_rotamers_for_packing(), core::pack::rotamer_set::RotamerSet::resid(), core::pose::Pose::residue(), core::pack::rotamer_set::RotamerSet_::rotamer(), and core::scoring::ScoreFunction::weights().
◆ initialize_pose_for_rotset_creation()
|
overridevirtual |
Give the pose a chance to stash any data needed by the rotset need nonconst access to pose.
Reimplemented from core::pack::rotamer_set::RotamerSet_.
References core::pose::Pose::conformation().
◆ orient_rotamer_set_to_symmetric_partner()
| RotamerSetOP core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_set_to_symmetric_partner | ( | pose::Pose const & | pose, |
| conformation::Residue const & | residue_in, | ||
| int const & | sympos, | ||
| RotamerSet const & | rotset_in, | ||
| bool const | set_up_mirror_types_if_has_mirror_symmetry = false |
||
| ) | const |
translate a rotamer_set to a different sequence position
- Note
- If set_up_mirror_symmetry_if_has_mirror_symmetry_ is true, then residues in mirrored subunits have their ResidueTypes switched to the types of the opposite chirality. If false (the default), then they keep the same types, and only have their geometry mirrored. The default is false, which is computationally less expensive at the expense of having the incorrect types in mirrored subunits.
References core::pose::Pose::conformation(), core::pose::Pose::conformation_ptr(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), and rot().
Referenced by compute_one_body_energies().
◆ orient_rotamer_to_symmetric_partner()
| conformation::ResidueOP core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner | ( | pose::Pose const & | pose, |
| conformation::Residue const & | residue_in, | ||
| int const & | sympos, | ||
| bool const | set_up_mirror_types_if_has_mirror_symmetry = false |
||
| ) | const |
References core::conformation::Residue::clone(), core::conformation::Residue::clone_flipping_chirality(), core::pose::Pose::conformation(), core::pose::Pose::conformation_ptr(), core::chemical::ResidueTypeBase::mode(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), and core::conformation::Residue::type().
Referenced by core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_for_symmetry().
◆ PackerEnergyAdd()
| void core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergyAdd | ( | utility::vector1< core::PackerEnergy > & | energies, |
| utility::vector1< core::PackerEnergy > const & | add | ||
| ) | const |
References protocols::mean_field::add(), and core::pack::rotamer_set::RotamerSet_::num_rotamers().
Referenced by compute_one_body_energies().
◆ PackerEnergyMultiply()
| void core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergyMultiply | ( | utility::vector1< core::PackerEnergy > & | energies, |
| core::Size | factor | ||
| ) | const |
References core::pack::rotamer_set::RotamerSet_::num_rotamers().
Referenced by compute_one_body_energies().
◆ PackerEnergySubtract()
| void core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergySubtract | ( | utility::vector1< core::PackerEnergy > & | energies, |
| utility::vector1< core::PackerEnergy > const & | subtract | ||
| ) | const |
◆ single_rotamer_rotset_original_rotmer_index() [1/2]
|
inline |
Symmetric rotamer sets are used in a funny way for self interactions. In the case of using a symmetric rotamer set to store a single rotamer, this is the index of the single rotamer. This function retrieves the value.
References single_rotamer_rotset_original_rotmer_index_.
◆ single_rotamer_rotset_original_rotmer_index() [2/2]
|
inline |
Symmetric rotamer sets are used in a funny way for self interactions. In the case of using a symmetric rotamer set to store a single rotamer, this is the index of the single rotamer. This function stores the value.
References single_rotamer_rotset_original_rotmer_index_.
Referenced by core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::evaluate_rotamer_pair_energies().
Member Data Documentation
◆ single_rotamer_rotset_original_rotmer_index_
|
private |
Symmetric rotamer sets are used in a funny way for self interactions. In the case of using a symmetric rotamer set to store a single rotamer, this is the index of the single rotamer.
Referenced by single_rotamer_rotset_original_rotmer_index().
The documentation for this class was generated from the following files:
- src/core/pack/rotamer_set/symmetry/SymmetricRotamerSet_.hh
- src/core/pack/rotamer_set/symmetry/SymmetricRotamerSet_.cc
