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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

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(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

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 –> 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>

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(class std::basic_ostream<char> &) const –> void

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