symmetry

Bindings for core::pack::rotamer_set::symmetry namespace

class pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_

Bases: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_

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_

PackerEnergyAdd(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, energies: pyrosetta.rosetta.utility.vector1_float, add: pyrosetta.rosetta.utility.vector1_float) None

C++: core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergyAdd(class utility::vector1<float, class std::allocator<float> > &, const class utility::vector1<float, class std::allocator<float> > &) const –> void

PackerEnergyMultiply(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, energies: pyrosetta.rosetta.utility.vector1_float, factor: int) None

C++: core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergyMultiply(class utility::vector1<float, class std::allocator<float> > &, unsigned long) const –> void

PackerEnergySubtract(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, energies: pyrosetta.rosetta.utility.vector1_float, subtract: pyrosetta.rosetta.utility.vector1_float) None

C++: core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergySubtract(class utility::vector1<float, class std::allocator<float> > &, const class utility::vector1<float, class std::allocator<float> > &) const –> void

add_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rotamer: pyrosetta.rosetta.core.conformation.Residue) None

C++: core::pack::rotamer_set::RotamerSet_::add_rotamer(const class core::conformation::Residue &) –> void

add_rotamer_into_existing_group(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rotamer: pyrosetta.rosetta.core.conformation.Residue) None

C++: core::pack::rotamer_set::RotamerSet_::add_rotamer_into_existing_group(const class core::conformation::Residue &) –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

C++: core::pack::rotamer_set::RotamerSet::operator=(const class core::pack::rotamer_set::RotamerSet &) –> class core::pack::rotamer_set::RotamerSet &

begin(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_) __gnu_cxx::__normal_iterator<std::shared_ptr<core::conformation::Residue> const*, std::vector<std::shared_ptr<core::conformation::Residue>, std::allocator<std::shared_ptr<core::conformation::Residue> > > >

C++: core::pack::rotamer_set::RotamerSet_::begin() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class core::conformation::Residue> *, class std::vector<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > >

build_dependent_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) None

Build rotamers that depend on positions of rotamers built in a previous pass

C++: core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers(const class core::pack::rotamer_set::RotamerSets &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) –> void

build_rotamers(*args, **kwargs)

Overloaded function.

  1. build_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, the_pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) -> None

  2. build_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, the_pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, use_neighbor_context: bool) -> None

C++: core::pack::rotamer_set::RotamerSet_::build_rotamers(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, bool) –> void

bump_check(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rotamer: pyrosetta.rosetta.core.conformation.Residue, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) float
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.

C++: core::pack::rotamer_set::RotamerSet_::bump_check(class std::shared_ptr<const class core::conformation::Residue>, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

compute_one_and_two_body_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, one_body_energies: pyrosetta.rosetta.utility.vector1_float, two_body_energies: pyrosetta.rosetta.utility.vector1_utility_vector1_float_std_allocator_float_t, packable_neighbors: pyrosetta.rosetta.utility.vector1_unsigned_long) None
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.

C++: core::pack::rotamer_set::RotamerSet_::compute_one_and_two_body_energies(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<float, class std::allocator<float> > &, class utility::vector1<class utility::vector1<float, class std::allocator<float> >, class std::allocator<class utility::vector1<float, class std::allocator<float> > > > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

compute_one_body_energies(*args, **kwargs)

Overloaded function.

  1. compute_one_body_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_float) -> None

  2. compute_one_body_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_float, no_update: bool) -> None

Computes the packers “one body energies” for the set of rotamers.

C++: core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<float, class std::allocator<float> > &, const bool) const –> void

compute_one_body_energy_maps(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) None

for OPTE

C++: core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<class core::scoring::EMapVector, class std::allocator<class core::scoring::EMapVector> > &) const –> void

data(self: pyrosetta.rosetta.core.conformation.RotamerSetBase) pyrosetta.rosetta.basic.datacache.BasicDataCache

BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh

C++: core::conformation::RotamerSetBase::data() –> class basic::datacache::BasicDataCache &

drop_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rot_id: int) None

removes a single rotamer and causes a rotamer index update

C++: core::pack::rotamer_set::RotamerSet_::drop_rotamer(unsigned long) –> void

drop_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rotamers_to_delete: pyrosetta.rosetta.utility.vector1_bool) None
rotamers_to_delete must be of size nrotmaers – each position

in the array that’s “true” is removed from the set of rotamers

C++: core::pack::rotamer_set::RotamerSet_::drop_rotamers(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

drop_rotamers_by_index(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rotamer_indices_to_delete: pyrosetta.rosetta.utility.vector1_unsigned_long) None
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.

C++: core::pack::rotamer_set::RotamerSet_::drop_rotamers_by_index(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

end(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_) __gnu_cxx::__normal_iterator<std::shared_ptr<core::conformation::Residue> const*, std::vector<std::shared_ptr<core::conformation::Residue>, std::allocator<std::shared_ptr<core::conformation::Residue> > > >

C++: core::pack::rotamer_set::RotamerSet_::end() const –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class core::conformation::Residue> *, class std::vector<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > >

get_n_residue_groups(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_) int

C++: core::pack::rotamer_set::RotamerSet_::get_n_residue_groups() const –> unsigned long

get_n_residue_types(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_) int

C++: core::pack::rotamer_set::RotamerSet_::get_n_residue_types() const –> unsigned long

get_n_rotamers_for_residue_group(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, which_resgroup: int) int

C++: core::pack::rotamer_set::RotamerSet_::get_n_rotamers_for_residue_group(unsigned long) const –> unsigned long

get_n_rotamers_for_residue_type(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, which_resgroup: int) int

C++: core::pack::rotamer_set::RotamerSet_::get_n_rotamers_for_residue_type(unsigned long) const –> unsigned long

get_residue_group_begin(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, which_resgroup: int) int

C++: core::pack::rotamer_set::RotamerSet_::get_residue_group_begin(unsigned long) const –> unsigned long

get_residue_group_index_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, which_rotamer: int) int

C++: core::pack::rotamer_set::RotamerSet_::get_residue_group_index_for_rotamer(unsigned long) const –> unsigned long

get_residue_type_begin(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, which_restype: int) int

C++: core::pack::rotamer_set::RotamerSet_::get_residue_type_begin(unsigned long) const –> unsigned long

get_residue_type_index_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, which_rotamer: int) int

C++: core::pack::rotamer_set::RotamerSet_::get_residue_type_index_for_rotamer(unsigned long) const –> unsigned long

get_trie(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, method_enum_id: int) pyrosetta.rosetta.core.conformation.AbstractRotamerTrie

C++: core::pack::rotamer_set::RotamerSet_::get_trie(unsigned long) const –> class std::shared_ptr<const class core::conformation::AbstractRotamerTrie>

id_for_current_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_) int

C++: core::pack::rotamer_set::RotamerSet_::id_for_current_rotamer() const –> unsigned long

initialize_pose_for_rotset_creation(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::initialize_pose_for_rotset_creation(class core::pose::Pose &) const –> void

nonconst_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rot_id: int) pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSet_::nonconst_rotamer(unsigned long) –> class std::shared_ptr<class core::conformation::Residue>

num_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_) int

C++: core::pack::rotamer_set::RotamerSet_::num_rotamers() const –> unsigned long

orient_rotamer_set_to_symmetric_partner(*args, **kwargs)

Overloaded function.

  1. orient_rotamer_set_to_symmetric_partner(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, pose: pyrosetta.rosetta.core.pose.Pose, residue_in: pyrosetta.rosetta.core.conformation.Residue, sympos: int, rotset_in: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

  2. orient_rotamer_set_to_symmetric_partner(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, pose: pyrosetta.rosetta.core.pose.Pose, residue_in: pyrosetta.rosetta.core.conformation.Residue, sympos: int, rotset_in: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, set_up_mirror_types_if_has_mirror_symmetry: bool) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

C++: core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_set_to_symmetric_partner(const class core::pose::Pose &, const class core::conformation::Residue &, const int &, const class core::pack::rotamer_set::RotamerSet &, const bool) const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>

orient_rotamer_to_symmetric_partner(*args, **kwargs)

Overloaded function.

  1. orient_rotamer_to_symmetric_partner(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, pose: pyrosetta.rosetta.core.pose.Pose, residue_in: pyrosetta.rosetta.core.conformation.Residue, sympos: int) -> pyrosetta.rosetta.core.conformation.Residue

  2. orient_rotamer_to_symmetric_partner(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, pose: pyrosetta.rosetta.core.pose.Pose, residue_in: pyrosetta.rosetta.core.conformation.Residue, sympos: int, set_up_mirror_types_if_has_mirror_symmetry: bool) -> pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner(const class core::pose::Pose &, const class core::conformation::Residue &, const int &, const bool) const –> class std::shared_ptr<class core::conformation::Residue>

resid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) int

C++: core::pack::rotamer_set::RotamerSet::resid() const –> unsigned long

rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rot_id: int) pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSet_::rotamer(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

rotamer_data_cache(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rot_id: int) pyrosetta.rosetta.basic.datacache.BasicDataCache

C++: core::pack::rotamer_set::RotamerSet_::rotamer_data_cache(unsigned long) const –> class basic::datacache::BasicDataCache &

rotamer_ref(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rot_id: int) pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSet_::rotamer_ref(unsigned long) const –> const class core::conformation::Residue &

set_extra_samples(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, task: pyrosetta.rosetta.core.pack.task.PackerTask, num_10A_neighbors: int, chi: int, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, extra_chi_steps: pyrosetta.rosetta.utility.vector1_double) None
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.

C++: core::pack::rotamer_set::RotamerSet_::set_extra_samples(const class core::pack::task::PackerTask &, int, int, class std::shared_ptr<const class core::chemical::ResidueType>, class utility::vector1<double, class std::allocator<double> > &) const –> void

set_resid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, resid: int) None

C++: core::pack::rotamer_set::RotamerSet::set_resid(unsigned long) –> void

show(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, out: pyrosetta.rosetta.std.ostream) None

C++: core::pack::rotamer_set::RotamerSet_::show(std::ostream &) const –> void

single_rotamer_rotset_original_rotmer_index(*args, **kwargs)

Overloaded function.

  1. single_rotamer_rotset_original_rotmer_index(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_, setting: int) -> None

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.

C++: core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::single_rotamer_rotset_original_rotmer_index(const unsigned long) –> void

  1. single_rotamer_rotset_original_rotmer_index(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_) -> int

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.

C++: core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::single_rotamer_rotset_original_rotmer_index() const –> unsigned long

store_trie(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, method_enum_id: int, trie: pyrosetta.rosetta.core.conformation.AbstractRotamerTrie) None

C++: core::pack::rotamer_set::RotamerSet_::store_trie(unsigned long, class std::shared_ptr<class core::conformation::AbstractRotamerTrie>) –> void

update_rotamer_offsets(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_) None
Lazy update of rotamer indices and offsets and integration of those rotamers

in the rotamers_waiting_for_sort_ list.

C++: core::pack::rotamer_set::RotamerSet_::update_rotamer_offsets() const –> void

class pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets

Bases: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets, : pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets) pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets

C++: core::pack::rotamer_set::symmetry::SymmetricRotamerSets::operator=(const class core::pack::rotamer_set::symmetry::SymmetricRotamerSets &) –> class core::pack::rotamer_set::symmetry::SymmetricRotamerSets &

begin(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) __gnu_cxx::__normal_iterator<std::shared_ptr<core::pack::rotamer_set::RotamerSet> const*, std::vector<std::shared_ptr<core::pack::rotamer_set::RotamerSet>, std::allocator<std::shared_ptr<core::pack::rotamer_set::RotamerSet> > > >

C++: core::pack::rotamer_set::RotamerSets::begin() –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class core::pack::rotamer_set::RotamerSet> *, class std::vector<class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>, class std::allocator<class std::shared_ptr<class core::pack::rotamer_set::RotamerSet> > > >

build_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) None

C++: core::pack::rotamer_set::RotamerSets::build_rotamers(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class utility::graph::Graph>) –> void

compute_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, ig: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, threads_to_request: int) None

C++: core::pack::rotamer_set::symmetry::SymmetricRotamerSets::compute_energies(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<class core::pack::interaction_graph::InteractionGraphBase>, const unsigned long) –> void

drop_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, rotamers_to_delete: pyrosetta.rosetta.utility.vector1_bool) None
rotamers_to_delete must be of size nrotmaers – each position

in the array that’s “true” is removed from the set of rotamers

C++: core::pack::rotamer_set::RotamerSets::drop_rotamers(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

dump_pdb(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, filename: str) None

C++: core::pack::rotamer_set::RotamerSets::dump_pdb(const class core::pose::Pose &, const std::string &) const –> void

end(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) __gnu_cxx::__normal_iterator<std::shared_ptr<core::pack::rotamer_set::RotamerSet> const*, std::vector<std::shared_ptr<core::pack::rotamer_set::RotamerSet>, std::allocator<std::shared_ptr<core::pack::rotamer_set::RotamerSet> > > >

C++: core::pack::rotamer_set::RotamerSets::end() –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<class core::pack::rotamer_set::RotamerSet> *, class std::vector<class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>, class std::allocator<class std::shared_ptr<class core::pack::rotamer_set::RotamerSet> > > >

static get_bb_bbE(pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue) float

C++: core::pack::rotamer_set::RotamerSets::get_bb_bbE(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::conformation::Residue &, const class core::conformation::Residue &) –> float

static get_sc_bbE(pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue) float

C++: core::pack::rotamer_set::RotamerSets::get_sc_bbE(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::conformation::Residue &, const class core::conformation::Residue &) –> float

has_rotamer_set_for_residue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, resid: int) bool
Does this RotamerSets object store a rotamer set for a residue at position resid

in the pose?

Rotamer sets for non-packable residues aren’t generated, but could conceivably be queried by protocols or energy functions.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::rotamer_set::RotamerSets::has_rotamer_set_for_residue(const unsigned long) const –> bool

initialize_pose_for_rotsets_creation(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::pack::rotamer_set::symmetry::SymmetricRotamerSets::initialize_pose_for_rotsets_creation(class core::pose::Pose &) const –> void

moltenres_2_resid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) int

C++: core::pack::rotamer_set::RotamerSets::moltenres_2_resid(unsigned long) const –> unsigned long

moltenres_2_resid_vector(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::rotamer_set::RotamerSets::moltenres_2_resid_vector() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

moltenres_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) int

C++: core::pack::rotamer_set::RotamerSets::moltenres_for_rotamer(unsigned long) const –> unsigned long

moltenres_rotid_2_rotid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, moltenres: int, moltenresrotid: int) int

convert moltenres rotid to id in full rotamer enumeration

C++: core::pack::rotamer_set::RotamerSets::moltenres_rotid_2_rotid(unsigned long, unsigned long) const –> unsigned long

nmoltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) int

C++: core::pack::rotamer_set::RotamerSets::nmoltenres() const –> unsigned long

nrotamer_offset_for_moltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) int

C++: core::pack::rotamer_set::RotamerSets::nrotamer_offset_for_moltenres(unsigned long) const –> unsigned long

nrotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) int

C++: core::pack::rotamer_set::RotamerSets::nrotamers() const –> unsigned long

nrotamers_for_moltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) int

C++: core::pack::rotamer_set::RotamerSets::nrotamers_for_moltenres(unsigned long) const –> unsigned long

offset_data_up_to_date(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) bool

Used as a debug assert to ensure that RotamerSetsOperations call update_offset_data()

Without this check, rotamer sets operations could potentially introduce very-hard-to-debug

glitches if they don’t call update_offset_data().

C++: core::pack::rotamer_set::RotamerSets::offset_data_up_to_date() –> bool

static orient_rotamer_set_to_symmetric_partner(*args, **kwargs)

Overloaded function.

  1. orient_rotamer_set_to_symmetric_partner(pose: pyrosetta.rosetta.core.pose.Pose, rotset_for_seqpos: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, symmpos: int) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

  2. orient_rotamer_set_to_symmetric_partner(pose: pyrosetta.rosetta.core.pose.Pose, rotset_for_seqpos: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, symmpos: int, set_up_mirror_types_if_has_mirror_symmetry: bool) -> pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

Generate a new rotamer set oriented onto a reference rotamer set by cloning the reference set and reorienting

using symmetry information. Return an owning pointer to the new, reoriented rotamer set.

Orients all rotamers in a rotamer_set to a different (symmetrical) position

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.

C++: core::pack::rotamer_set::symmetry::SymmetricRotamerSets::orient_rotamer_set_to_symmetric_partner(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>, const unsigned long &, const bool) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>

prepare_sets_for_packing(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::pack::rotamer_set::RotamerSets::prepare_sets_for_packing(const class core::pose::Pose &, const class core::scoring::ScoreFunction &) –> void

res_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) int

C++: core::pack::rotamer_set::RotamerSets::res_for_rotamer(unsigned long) const –> unsigned long

resid_2_moltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) int

C++: core::pack::rotamer_set::RotamerSets::resid_2_moltenres(unsigned long) const –> unsigned long

resid_2_moltenres_vector(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::rotamer_set::RotamerSets::resid_2_moltenres_vector() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSets::rotamer(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

rotamer_for_moltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, moltenres_id: int, rotamerid: int) pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSets::rotamer_for_moltenres(unsigned long, unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

rotamer_set_for_moltenresidue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, moltenresid: int) core::pack::rotamer_set::RotamerSet

C++: core::pack::rotamer_set::RotamerSets::rotamer_set_for_moltenresidue(unsigned long) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>

rotamer_set_for_residue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, resid: int) core::pack::rotamer_set::RotamerSet

C++: core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(unsigned long) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>

rotid_on_moltenresidue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, rotid: int) int

convert rotid in full rotamer enumeration into rotamer id on its source residue

C++: core::pack::rotamer_set::RotamerSets::rotid_on_moltenresidue(unsigned long) const –> unsigned long

set_explicit_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, moltenresid: int, rotamers: core::pack::rotamer_set::RotamerSet) None

C++: core::pack::rotamer_set::RotamerSets::set_explicit_rotamers(unsigned long, class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>) –> void

set_task(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, task: pyrosetta.rosetta.core.pack.task.PackerTask) None

C++: core::pack::rotamer_set::RotamerSets::set_task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

show(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, out: pyrosetta.rosetta.std.ostream) None

C++: core::pack::rotamer_set::RotamerSets::show(std::ostream &) const –> void

task(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) pyrosetta.rosetta.core.pack.task.PackerTask

access to packer_task_

C++: core::pack::rotamer_set::RotamerSets::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

total_residue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) int

C++: core::pack::rotamer_set::RotamerSets::total_residue() const –> unsigned long

update_offset_data(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) None
fd: make this public

the reason? we now can update rotamersets interactively from code, so this should be exposed

C++: core::pack::rotamer_set::RotamerSets::update_offset_data() –> void