libraries¶

Bindings for protocols::rna::denovo::libraries namespace

class pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary¶

Bases: pybind11_builtins.pybind11_object

__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__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary, canonical: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary, arg0: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary) -> 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).

canonical(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary) → bool¶: C++: protocols::rna::denovo::libraries::BasePairStepLibrary::canonical() const –> bool

database_dir(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary) → str¶: C++: protocols::rna::denovo::libraries::BasePairStepLibrary::database_dir() const –> std::string

has_value(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary, base_pair_step_sequence: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence) → bool¶: C++: protocols::rna::denovo::libraries::BasePairStepLibrary::has_value(const class protocols::rna::denovo::libraries::BasePairStepSequence &) const –> bool

mini_pose_list(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary, base_pair_step_sequence: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_MiniPose_t¶: C++: protocols::rna::denovo::libraries::BasePairStepLibrary::mini_pose_list(const class protocols::rna::denovo::libraries::BasePairStepSequence &) const –> const class utility::vector1<class std::shared_ptr<class core::pose::MiniPose>, class std::allocator<class std::shared_ptr<class core::pose::MiniPose> > > &

scratch_pose(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary, base_pair_step_sequence: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::rna::denovo::libraries::BasePairStepLibrary::scratch_pose(const class protocols::rna::denovo::libraries::BasePairStepSequence &) const –> const class std::shared_ptr<const class core::pose::Pose> &

class pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence¶

Bases: pybind11_builtins.pybind11_object

__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__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence, arg0: str, arg1: str, arg2: str, arg3: str) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence, nt_i: str, nt_i_next: str, nt_j: str, nt_j_next: str, num_bulge: int) -> None
__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence, sequence: str, i: int, i_next: int, j: int, j_next: int) -> None
__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence, sequence: str, base_pair_step: pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep) -> 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.protocols.rna.denovo.libraries.BasePairStepSequence) → 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).

assign(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence, : pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence) → pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence¶: C++: protocols::rna::denovo::libraries::BasePairStepSequence::operator=(const class protocols::rna::denovo::libraries::BasePairStepSequence &) –> class protocols::rna::denovo::libraries::BasePairStepSequence &

num_bulge(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence) → int¶: C++: protocols::rna::denovo::libraries::BasePairStepSequence::num_bulge() const –> const int &

subdir(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence) → str¶: C++: protocols::rna::denovo::libraries::BasePairStepSequence::subdir() const –> std::string

tag(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence) → str¶: C++: protocols::rna::denovo::libraries::BasePairStepSequence::tag() const –> std::string

class pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType¶

Bases: pybind11_builtins.pybind11_object

__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.protocols.rna.denovo.libraries.BasePairType, aa1_in: str, aa2_in: str, edge1_in: pyrosetta.rosetta.core.chemical.rna.BaseEdge, edge2_in: pyrosetta.rosetta.core.chemical.rna.BaseEdge, orientation_in: pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation) → 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).

tag(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType) → str¶: C++: protocols::rna::denovo::libraries::BasePairType::tag() const –> std::string

class pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary¶

Bases: pybind11_builtins.pybind11_object

__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__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary) -> None
__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, arg0: pyrosetta.rosetta.utility.vector1_std_string, arg1: pyrosetta.rosetta.utility.vector1_std_string, arg2: pyrosetta.rosetta.core.pose.Pose, arg3: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, pdb_files: pyrosetta.rosetta.utility.vector1_std_string, silent_files: pyrosetta.rosetta.utility.vector1_std_string, pose: pyrosetta.rosetta.core.pose.Pose, input_res: pyrosetta.rosetta.utility.vector1_unsigned_long, allow_insert_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, silent_files: pyrosetta.rosetta.utility.vector1_std_string, pose: pyrosetta.rosetta.core.pose.Pose, input_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose) -> None
__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, arg0: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary) -> 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_chunk_set(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, silent_file: str, res_map: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, big_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::add_chunk_set(const class std::basic_string<char> &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, : pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary) → pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::operator=(const class protocols::rna::denovo::libraries::RNA_ChunkLibrary &) –> class protocols::rna::denovo::libraries::RNA_ChunkLibrary &

atom_level_domain_map(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary) → pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::atom_level_domain_map() const –> class std::shared_ptr<class protocols::toolbox::AtomLevelDomainMap>

check_fold_tree_OK(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::check_fold_tree_OK(const class core::pose::Pose &) const –> bool

chunk_coverage(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary) → float¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::chunk_coverage() const –> const double &

chunk_set(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, n: int) → pyrosetta.rosetta.protocols.rna.denovo.libraries.ChunkSet¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::chunk_set(const unsigned long) const –> class std::shared_ptr<class protocols::rna::denovo::libraries::ChunkSet>

clone(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary) → pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary¶

clone the ChunkLibrary

C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::clone() const –> class std::shared_ptr<class protocols::rna::denovo::libraries::RNA_ChunkLibrary>

get_alignment_domain(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::get_alignment_domain(const class core::pose::Pose &) const –> unsigned long

get_indices_of_moving_chunks(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::get_indices_of_moving_chunks() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

initialize_random_chunks(*args, **kwargs)¶

Overloaded function.

initialize_random_chunks(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose) -> None
initialize_random_chunks(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose, dump_pdb: bool) -> None

C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::initialize_random_chunks(class core::pose::Pose &, const bool) const –> void

initialize_rna_chunk_library(*args, **kwargs)¶

Overloaded function.

initialize_rna_chunk_library(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, pdb_files: pyrosetta.rosetta.utility.vector1_std_string, silent_files: pyrosetta.rosetta.utility.vector1_std_string, pose: pyrosetta.rosetta.core.pose.Pose, input_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
initialize_rna_chunk_library(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, pdb_files: pyrosetta.rosetta.utility.vector1_std_string, silent_files: pyrosetta.rosetta.utility.vector1_std_string, pose: pyrosetta.rosetta.core.pose.Pose, input_res: pyrosetta.rosetta.utility.vector1_unsigned_long, allow_insert_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::initialize_rna_chunk_library(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

insert_chunk_into_pose(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose, chunk_list_index: int, chunk_pose_index: int) → None¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::insert_chunk_into_pose(class core::pose::Pose &, const unsigned long &, const unsigned long &) const –> void

insert_random_protein_chunks(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::insert_random_protein_chunks(class core::pose::Pose &) const –> void

num_chunk_sets(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary) → int¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::num_chunk_sets() const –> unsigned long

num_chunks(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, n: int) → int¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::num_chunks(const unsigned long) const –> unsigned long

num_moving_chunks(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary) → int¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::num_moving_chunks() const –> unsigned long

random_chunk_insertion(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::random_chunk_insertion(class core::pose::Pose &) const –> bool

set_atom_level_domain_map(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, atom_level_domain_map: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap) → None¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::set_atom_level_domain_map(class std::shared_ptr<class protocols::toolbox::AtomLevelDomainMap>) –> void

single_user_input_chunk(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary) → int¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::single_user_input_chunk() const –> unsigned long

superimpose_to_single_user_input_chunk(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::superimpose_to_single_user_input_chunk(class core::pose::Pose &) const –> bool

update_to_move_rosetta_library_chunks(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary) → None¶: C++: protocols::rna::denovo::libraries::RNA_ChunkLibrary::update_to_move_rosetta_library_chunks() –> void

class pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary¶

Bases: pybind11_builtins.pybind11_object

__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__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary, filename: str) -> None
__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary, arg0: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary) -> 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.protocols.rna.denovo.libraries.RNA_JumpLibrary, : pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary) → pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary¶: C++: protocols::rna::denovo::libraries::RNA_JumpLibrary::operator=(const class protocols::rna::denovo::libraries::RNA_JumpLibrary &) –> class protocols::rna::denovo::libraries::RNA_JumpLibrary &

check_forward_backward(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary, atom_name: str, forward: bool, j: pyrosetta.rosetta.core.kinematics.Jump, t: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate) → None¶: C++: protocols::rna::denovo::libraries::RNA_JumpLibrary::check_forward_backward(class std::basic_string<char> &, const bool, class core::kinematics::Jump &, const class std::shared_ptr<class protocols::rna::denovo::libraries::RNA_PairingTemplate> &) const –> void

get_random_base_pair_jump(*args, **kwargs)¶

Overloaded function.

get_random_base_pair_jump(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary, rt1: pyrosetta.rosetta.core.chemical.ResidueType, rt2: pyrosetta.rosetta.core.chemical.ResidueType, edge1: pyrosetta.rosetta.core.chemical.rna.BaseEdge, edge2: pyrosetta.rosetta.core.chemical.rna.BaseEdge, orientation: pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation, atom_name1: str, atom_name2: str, success: bool) -> pyrosetta.rosetta.core.kinematics.Jump
get_random_base_pair_jump(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary, rt1: pyrosetta.rosetta.core.chemical.ResidueType, rt2: pyrosetta.rosetta.core.chemical.ResidueType, edge1: pyrosetta.rosetta.core.chemical.rna.BaseEdge, edge2: pyrosetta.rosetta.core.chemical.rna.BaseEdge, orientation: pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation, atom_name1: str, atom_name2: str, success: bool, forward1: bool) -> pyrosetta.rosetta.core.kinematics.Jump
get_random_base_pair_jump(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary, rt1: pyrosetta.rosetta.core.chemical.ResidueType, rt2: pyrosetta.rosetta.core.chemical.ResidueType, edge1: pyrosetta.rosetta.core.chemical.rna.BaseEdge, edge2: pyrosetta.rosetta.core.chemical.rna.BaseEdge, orientation: pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation, atom_name1: str, atom_name2: str, success: bool, forward1: bool, forward2: bool) -> pyrosetta.rosetta.core.kinematics.Jump

C++: protocols::rna::denovo::libraries::RNA_JumpLibrary::get_random_base_pair_jump(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &, const enum core::chemical::rna::BaseEdge, const enum core::chemical::rna::BaseEdge, const enum core::chemical::rna::BaseDoubletOrientation, class std::basic_string<char> &, class std::basic_string<char> &, bool &, const bool, const bool) const –> class core::kinematics::Jump

has_template(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary, base_pair_type: pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType) → bool¶: C++: protocols::rna::denovo::libraries::RNA_JumpLibrary::has_template(const class protocols::rna::denovo::libraries::BasePairType &) const –> bool

class pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager¶

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_rna_denovo_libraries_RNA_LibraryManager_t

Holds all libraries relevant to FARFAR as CONST copies:

JumpLibrary FullAtomRNA_Fragments BasePairStepLibrary, …

However, those const libraries include some mutable data to allow for efficient, lazy loading – need to put mutexes around those functions that update those data.

__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__¶: Initialize self. See help(type(self)) for accurate signature.

__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).

canonical_base_pair_step_library(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager) → pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary¶: C++: protocols::rna::denovo::libraries::RNA_LibraryManager::canonical_base_pair_step_library() –> const class protocols::rna::denovo::libraries::BasePairStepLibrary &

general_base_pair_step_library(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager) → pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary¶: C++: protocols::rna::denovo::libraries::RNA_LibraryManager::general_base_pair_step_library() –> const class protocols::rna::denovo::libraries::BasePairStepLibrary &

get_instance() → protocols::rna::denovo::libraries::RNA_LibraryManager¶: C++: utility::SingletonBase<protocols::rna::denovo::libraries::RNA_LibraryManager>::get_instance() –> class protocols::rna::denovo::libraries::RNA_LibraryManager *

rna_fragment_library(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager, tag: str) → pyrosetta.rosetta.protocols.rna.denovo.fragments.RNA_Fragments¶: C++: protocols::rna::denovo::libraries::RNA_LibraryManager::rna_fragment_library(const class std::basic_string<char> &) –> const class protocols::rna::denovo::fragments::RNA_Fragments &

rna_jump_library(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager, tag: str) → pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary¶: C++: protocols::rna::denovo::libraries::RNA_LibraryManager::rna_jump_library(const class std::basic_string<char> &) –> const class protocols::rna::denovo::libraries::RNA_JumpLibrary &

rna_jump_library_cop(*args, **kwargs)¶

Overloaded function.

rna_jump_library_cop(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager, tag: str) -> pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary

C++: protocols::rna::denovo::libraries::RNA_LibraryManager::rna_jump_library_cop(const class std::basic_string<char> &) –> const class std::shared_ptr<const class protocols::rna::denovo::libraries::RNA_JumpLibrary> &

rna_jump_library_cop(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager) -> pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary

C++: protocols::rna::denovo::libraries::RNA_LibraryManager::rna_jump_library_cop() –> const class std::shared_ptr<const class protocols::rna::denovo::libraries::RNA_JumpLibrary> &

class pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate¶

Bases: pybind11_builtins.pybind11_object

__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__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate, j: pyrosetta.rosetta.core.kinematics.Jump, atom_name1: str, atom_name2: str) -> None
__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate, j1: pyrosetta.rosetta.core.kinematics.Jump, j2: pyrosetta.rosetta.core.kinematics.Jump, atom_name1: str, atom_name2: str) -> None
__init__(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate, arg0: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate) -> 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).

atom_name1(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate) → str¶: C++: protocols::rna::denovo::libraries::RNA_PairingTemplate::atom_name1() const –> const std::string &

atom_name2(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate) → str¶: C++: protocols::rna::denovo::libraries::RNA_PairingTemplate::atom_name2() const –> const std::string &

jump(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate) → pyrosetta.rosetta.core.kinematics.Jump¶: C++: protocols::rna::denovo::libraries::RNA_PairingTemplate::jump() const –> const class core::kinematics::Jump &

jump_backward(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate) → pyrosetta.rosetta.core.kinematics.Jump¶: C++: protocols::rna::denovo::libraries::RNA_PairingTemplate::jump_backward() const –> const class core::kinematics::Jump &

jump_forward(self: pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate) → pyrosetta.rosetta.core.kinematics.Jump¶: C++: protocols::rna::denovo::libraries::RNA_PairingTemplate::jump_forward() const –> const class core::kinematics::Jump &