rotamer_set

Bindings for core::pack::rotamer_set namespace

class pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation

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

Adds in rotamers from a list of Residues,

__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.AddResiduesRotamerSetOperation, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → 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__

Return str(self).

__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).

alter_rotamer_set(self: pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.pack.task.PackerTask, : pyrosetta.rosetta.utility.graph.Graph, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

C++: core::pack::rotamer_set::AddResiduesRotamerSetOperation::alter_rotamer_set(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 core::pack::rotamer_set::RotamerSet &) –> void

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

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

clone(self: pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: core::pack::rotamer_set::AddResiduesRotamerSetOperation::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>

increase_packer_residue_radius(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, the_task: pyrosetta.rosetta.core.pack.task.PackerTask, residue_in: int) → float

C++: core::pack::rotamer_set::RotamerSetOperation::increase_packer_residue_radius(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long) const –> double

class pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation

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

Adds in rotamers from a list of Residues,

__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.DeleteAllRotamerSetOperation) → 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__

Return str(self).

__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).

alter_rotamer_set(self: pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

C++: core::pack::rotamer_set::DeleteAllRotamerSetOperation::alter_rotamer_set(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 core::pack::rotamer_set::RotamerSet &) –> void

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

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

clone(self: pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: core::pack::rotamer_set::DeleteAllRotamerSetOperation::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>

increase_packer_residue_radius(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, the_task: pyrosetta.rosetta.core.pack.task.PackerTask, residue_in: int) → float

C++: core::pack::rotamer_set::RotamerSetOperation::increase_packer_residue_radius(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long) const –> double

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation

Bases: pybind11_builtins.pybind11_object

RotamerSetOperations are able to modify the contents of a RotamerSet within the packer immediately after rotamer creation.

They are handed into the packer through a packer task; each ResidueLevelTask
keeps its own list of rotamer set operations.
Each RotamerSet, within the build_rotamers() method will iterate across
the RotamerSetOperation objects, and call alter_rotamer_set on each element in the ResidueLevelTask’s list of rotamer_set_operations.
RotamerSetOperations are visited in the order in which they are appended
to the ResidueLevelTasks’s operation list.
RotamerSetOperations are unable to correlate changes to rotamer sets across
multiple rotamer sets – they have access to only a single RotamerSet object in their alter_rotamer_set operations. For correlated alterations to rotamer sets, the (as of yet undefined) RotamerSetsOperation class should be used.
__call__(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation, rotamer: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, rtask: pyrosetta.rosetta.core.pack.task.ResidueLevelTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, chi_set: pyrosetta.rosetta.core.pack.dunbrack.ChiSet) → bool

C++: core::pack::rotamer_set::RotamerOperation::operator()(class std::shared_ptr<class core::conformation::Residue>, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::ResidueLevelTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<class core::pack::dunbrack::ChiSet>) –> bool

__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.RotamerOperation) → 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__

Return str(self).

__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).

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

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

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_

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.

__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.RotamerSet_) → 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.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_float) → None

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

C++: core::pack::rotamer_set::RotamerSet_::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.RotamerSet_, : pyrosetta.rosetta.core.pose.Pose) → None
Give the pose a chance to stash any data needed by the _rotset_
need nonconst access to pose

C++: core::pack::rotamer_set::RotamerSet_::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

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

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset

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

Container for a subset of rotamers that have been created by another rotamer set. This subset object copies pointers to the rotamers contained in another set, as opposed to cloning the rotamers. It’s main purpose is to manage the bookkeeping involved in packing with a subset of rotamers (when it might be faster to use a subset and to create an interaction graph specifically for that subset than to simply pass an abreviated list of rotamers to the SimAnnealer with the “rot_to_pack” vector).

__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.RotamerSubset, rotset: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, rotamer_subset: pyrosetta.rosetta.utility.vector1_unsigned_long) → 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.RotamerSubset, rotamer: pyrosetta.rosetta.core.conformation.Residue) → None

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

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

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

begin(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset) → __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::RotamerSubset::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.RotamerSubset, 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

C++: core::pack::rotamer_set::RotamerSubset::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.RotamerSubset, 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.RotamerSubset, 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::RotamerSubset::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

compute_one_and_two_body_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, 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

C++: core::pack::rotamer_set::RotamerSubset::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.RotamerSubset, 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

C++: core::pack::rotamer_set::RotamerSubset::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.RotamerSubset, 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::RotamerSubset::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.RotamerSubset, rot_id: int) → None

removes a single rotamer and causes a rotamer index update

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

drop_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, 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::RotamerSubset::drop_rotamers(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

drop_rotamers_by_index(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, 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::RotamerSubset::drop_rotamers_by_index(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

end(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset) → __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::RotamerSubset::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.RotamerSubset) → int

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

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

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

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

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

get_n_rotamers_for_residue_type(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, which_restype: int) → int

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

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

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

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

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

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

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

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

given a rotamer id, return an int which represents a type for this rotamer.

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

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

C++: core::pack::rotamer_set::RotamerSubset::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.RotamerSubset) → int

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

initialize_pose_for_rotset_creation(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, : pyrosetta.rosetta.core.pose.Pose) → None
Give the pose a chance to stash any data needed by the _rotset_
need nonconst access to pose

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

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

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

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

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

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.RotamerSubset, rot_id: int) → pyrosetta.rosetta.core.conformation.Residue

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

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

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

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

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

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.RotamerSubset, out: pyrosetta.rosetta.std.ostream) → None

C++: core::pack::rotamer_set::RotamerSubset::show(class std::basic_ostream<char> &) const –> void

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

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

class pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation

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

Adds in rotamers from the “unbound” or native structure(s), pulled from one or more PDBs supplied on the command line.

Sequence numbering matters – rotamers will only be added if sequence numbers match AND the ResidueType is allowed by the PackerTask. By itself, this class does NOT grant a Dunbrack energy bonus to the native rotamer(s).

__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.UnboundRotamersOperation) → 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__

Return str(self).

__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_pose(self: pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation, pose: pyrosetta.rosetta.core.pose.Pose) → None

Adds rotamers from the specified pose to the unbound collection.

C++: core::pack::rotamer_set::UnboundRotamersOperation::add_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

alter_rotamer_set(self: pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

C++: core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(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 core::pack::rotamer_set::RotamerSet &) –> void

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

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

clone(self: pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: core::pack::rotamer_set::UnboundRotamersOperation::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>

increase_packer_residue_radius(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, the_task: pyrosetta.rosetta.core.pack.task.PackerTask, residue_in: int) → float

C++: core::pack::rotamer_set::RotamerSetOperation::increase_packer_residue_radius(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long) const –> double

initialize_from_command_line(self: pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation) → None

Loads poses from the -unboundrot flag.

C++: core::pack::rotamer_set::UnboundRotamersOperation::initialize_from_command_line() –> void

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

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

pyrosetta.rosetta.core.pack.rotamer_set.bb_independent_rotamers(*args, **kwargs)

Overloaded function.

  1. bb_independent_rotamers(rot_restype: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t
  2. bb_independent_rotamers(rot_restype: pyrosetta.rosetta.core.chemical.ResidueType, ignore_cmdline: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t
a crude function to spit out a list of rotamers
given the residue type only, independent of backbone currently there is no proper way of doing this, since the Dunbrack bbind library is not implemented in rosetta. this function tries to circumvent that by constructing a one residue pose and then using the regular dunbrack library, which will use neutral phi/psi for the only residue in the pose the bool ignore_cmdline can be used if someone only wants base inverse rotamers but use the full set in packing

C++: core::pack::rotamer_set::bb_independent_rotamers(class std::shared_ptr<const class core::chemical::ResidueType>, bool) –> class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

pyrosetta.rosetta.core.pack.rotamer_set.build_anchorless_water_rotamers(seqpos: int, h2o_type: pyrosetta.rosetta.core.chemical.ResidueType, pose: pyrosetta.rosetta.core.pose.Pose, new_rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

builds water molecule rotamers on top of cubic lattice in hydrate/SPaDES protocol

C++: core::pack::rotamer_set::build_anchorless_water_rotamers(const unsigned long, const class core::chemical::ResidueType &, const class core::pose::Pose &, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, const class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.build_dependent_water_rotamers(rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, seqpos_water: int, h2o_type: pyrosetta.rosetta.core.chemical.ResidueType, task: pyrosetta.rosetta.core.pack.task.PackerTask, pose: pyrosetta.rosetta.core.pose.Pose, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, new_rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::rotamer_set::build_dependent_water_rotamers(const class core::pack::rotamer_set::RotamerSets &, const unsigned long, const class core::chemical::ResidueType &, const class core::pack::task::PackerTask &, const class core::pose::Pose &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, const class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.build_dna_rotamers(resid: int, pose: pyrosetta.rosetta.core.pose.Pose, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, task: pyrosetta.rosetta.core.pack.task.PackerTask, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::rotamer_set::build_dna_rotamers(const unsigned long, const class core::pose::Pose &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::pack::task::PackerTask &, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.build_independent_water_rotamers(seqpos_water: int, h2o_type: pyrosetta.rosetta.core.chemical.ResidueType, task: pyrosetta.rosetta.core.pack.task.PackerTask, pose: pyrosetta.rosetta.core.pose.Pose, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, new_rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::rotamer_set::build_independent_water_rotamers(const unsigned long, const class core::chemical::ResidueType &, const class core::pack::task::PackerTask &, const class core::pose::Pose &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, const class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.build_random_dna_rotamers(resid: int, pose: pyrosetta.rosetta.core.pose.Pose, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, level: pyrosetta.rosetta.core.pack.task.ExtraRotSample, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::rotamer_set::build_random_dna_rotamers(const unsigned long, const class core::pose::Pose &, class std::shared_ptr<const class core::chemical::ResidueType>, const enum core::pack::task::ExtraRotSample &, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.build_rna_rotamers(resid: int, pose: pyrosetta.rosetta.core.pose.Pose, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, task: pyrosetta.rosetta.core.pack.task.PackerTask, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, id_for_current_rotamer: int) → None

C++: core::pack::rotamer_set::build_rna_rotamers(const unsigned long, const class core::pose::Pose &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::pack::task::PackerTask &, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.build_rotamers_from_rotamer_bins(residue: pyrosetta.rosetta.core.conformation.Residue, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None
Make a rotamer (Residue) for every combination of torsion angle in the rotamer bins listed in the params
file for the given Residue.

C++: core::pack::rotamer_set::build_rotamers_from_rotamer_bins(const class core::conformation::Residue &, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.create_oriented_water_rotamer(h2o_type: pyrosetta.rosetta.core.chemical.ResidueType, xyz_atom1: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz_O: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz_atom2: pyrosetta.rosetta.numeric.xyzVector_double_t, name1: str, name2: str, tp5: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::create_oriented_water_rotamer(const class core::chemical::ResidueType &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class core::conformation::Residue &) –> class std::shared_ptr<class core::conformation::Residue>

pyrosetta.rosetta.core.pack.rotamer_set.debug_dump_rotamers(rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::rotamer_set::debug_dump_rotamers(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) –> void