libraries

Bindings for core::import_pose::libraries namespace

class pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary

Bases: pybind11_builtins.pybind11_object

canonical(self: pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary) → bool

C++: core::import_pose::libraries::BasePairStepLibrary::canonical() const –> bool

database_dir(self: pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary) → str

C++: core::import_pose::libraries::BasePairStepLibrary::database_dir() const –> std::string

has_value(self: pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary, base_pair_step_sequence: pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence) → bool

C++: core::import_pose::libraries::BasePairStepLibrary::has_value(const class core::import_pose::libraries::BasePairStepSequence &) const –> bool

mini_pose_list(self: pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary, base_pair_step_sequence: pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_MiniPose_t

C++: core::import_pose::libraries::BasePairStepLibrary::mini_pose_list(const class core::import_pose::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.core.import_pose.libraries.BasePairStepLibrary, base_pair_step_sequence: pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence) → pyrosetta.rosetta.core.pose.Pose

C++: core::import_pose::libraries::BasePairStepLibrary::scratch_pose(const class core::import_pose::libraries::BasePairStepSequence &) const –> const class std::shared_ptr<const class core::pose::Pose> &

class pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence, : pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence) → pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence

C++: core::import_pose::libraries::BasePairStepSequence::operator=(const class core::import_pose::libraries::BasePairStepSequence &) –> class core::import_pose::libraries::BasePairStepSequence &

num_bulge(self: pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence) → int

C++: core::import_pose::libraries::BasePairStepSequence::num_bulge() const –> const int &

subdir(self: pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence) → str

C++: core::import_pose::libraries::BasePairStepSequence::subdir() const –> std::string

tag(self: pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence) → str

C++: core::import_pose::libraries::BasePairStepSequence::tag() const –> std::string

class pyrosetta.rosetta.core.import_pose.libraries.BasePairType

Bases: pybind11_builtins.pybind11_object

tag(self: pyrosetta.rosetta.core.import_pose.libraries.BasePairType) → str

C++: core::import_pose::libraries::BasePairType::tag() const –> std::string

class pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary

Bases: pybind11_builtins.pybind11_object

add_chunk_set(self: pyrosetta.rosetta.core.import_pose.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++: core::import_pose::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.core.import_pose.libraries.RNA_ChunkLibrary, : pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) → pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary

C++: core::import_pose::libraries::RNA_ChunkLibrary::operator=(const class core::import_pose::libraries::RNA_ChunkLibrary &) –> class core::import_pose::libraries::RNA_ChunkLibrary &

atom_level_domain_map(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) → pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap

C++: core::import_pose::libraries::RNA_ChunkLibrary::atom_level_domain_map() const –> class std::shared_ptr<class core::pose::toolbox::AtomLevelDomainMap>

check_fold_tree_OK(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: core::import_pose::libraries::RNA_ChunkLibrary::check_fold_tree_OK(const class core::pose::Pose &) const –> bool

chunk_coverage(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) → float

C++: core::import_pose::libraries::RNA_ChunkLibrary::chunk_coverage() const –> const double &

chunk_set(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary, n: int) → pyrosetta.rosetta.core.import_pose.libraries.ChunkSet

C++: core::import_pose::libraries::RNA_ChunkLibrary::chunk_set(const unsigned long) const –> class std::shared_ptr<class core::import_pose::libraries::ChunkSet>

chunk_sets(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_import_pose_libraries_ChunkSet_t

C++: core::import_pose::libraries::RNA_ChunkLibrary::chunk_sets() const –> class utility::vector1<class std::shared_ptr<class core::import_pose::libraries::ChunkSet>, class std::allocator<class std::shared_ptr<class core::import_pose::libraries::ChunkSet> > >

clone(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) → pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary

clone the ChunkLibrary

C++: core::import_pose::libraries::RNA_ChunkLibrary::clone() const –> class std::shared_ptr<class core::import_pose::libraries::RNA_ChunkLibrary>

get_alignment_domain(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: core::import_pose::libraries::RNA_ChunkLibrary::get_alignment_domain(const class core::pose::Pose &) const –> unsigned long

get_indices_of_moving_chunks(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::import_pose::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.

1. initialize_random_chunks(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose) -> None
2. initialize_random_chunks(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose, dump_pdb: bool) -> None

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

initialize_rna_chunk_library(*args, **kwargs)

Overloaded function.

1. initialize_rna_chunk_library(self: pyrosetta.rosetta.core.import_pose.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
2. initialize_rna_chunk_library(self: pyrosetta.rosetta.core.import_pose.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++: core::import_pose::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.core.import_pose.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose, chunk_list_index: int, chunk_pose_index: int) → None

C++: core::import_pose::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.core.import_pose.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::import_pose::libraries::RNA_ChunkLibrary::insert_random_protein_chunks(class core::pose::Pose &) const –> void

num_chunk_sets(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) → int

C++: core::import_pose::libraries::RNA_ChunkLibrary::num_chunk_sets() const –> unsigned long

num_chunks(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary, n: int) → int

C++: core::import_pose::libraries::RNA_ChunkLibrary::num_chunks(const unsigned long) const –> unsigned long

num_moving_chunks(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) → int

C++: core::import_pose::libraries::RNA_ChunkLibrary::num_moving_chunks() const –> unsigned long

random_chunk_insertion(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: core::import_pose::libraries::RNA_ChunkLibrary::random_chunk_insertion(class core::pose::Pose &) const –> bool

set_atom_level_domain_map(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary, atom_level_domain_map: pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap) → None

C++: core::import_pose::libraries::RNA_ChunkLibrary::set_atom_level_domain_map(class std::shared_ptr<class core::pose::toolbox::AtomLevelDomainMap>) –> void

single_user_input_chunk(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) → int

C++: core::import_pose::libraries::RNA_ChunkLibrary::single_user_input_chunk() const –> unsigned long

superimpose_to_single_user_input_chunk(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: core::import_pose::libraries::RNA_ChunkLibrary::superimpose_to_single_user_input_chunk(class core::pose::Pose &) const –> bool

update_to_move_rosetta_library_chunks(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) → None

C++: core::import_pose::libraries::RNA_ChunkLibrary::update_to_move_rosetta_library_chunks() –> void

class pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary, : pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary) → pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary

C++: core::import_pose::libraries::RNA_JumpLibrary::operator=(const class core::import_pose::libraries::RNA_JumpLibrary &) –> class core::import_pose::libraries::RNA_JumpLibrary &

check_forward_backward(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary, atom_name: str, forward: bool, j: pyrosetta.rosetta.core.kinematics.Jump, t: pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate) → None

C++: core::import_pose::libraries::RNA_JumpLibrary::check_forward_backward(class std::basic_string<char> &, const bool, class core::kinematics::Jump &, const class std::shared_ptr<class core::import_pose::libraries::RNA_PairingTemplate> &) const –> void

get_random_base_pair_jump(*args, **kwargs)

Overloaded function.

1. get_random_base_pair_jump(self: pyrosetta.rosetta.core.import_pose.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
2. get_random_base_pair_jump(self: pyrosetta.rosetta.core.import_pose.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
3. get_random_base_pair_jump(self: pyrosetta.rosetta.core.import_pose.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++: core::import_pose::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.core.import_pose.libraries.RNA_JumpLibrary, base_pair_type: pyrosetta.rosetta.core.import_pose.libraries.BasePairType) → bool

C++: core::import_pose::libraries::RNA_JumpLibrary::has_template(const class core::import_pose::libraries::BasePairType &) const –> bool

class pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager

Bases: pyrosetta.rosetta.utility.SingletonBase_core_import_pose_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.

canonical_base_pair_step_library(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager) → pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary

C++: core::import_pose::libraries::RNA_LibraryManager::canonical_base_pair_step_library() –> const class core::import_pose::libraries::BasePairStepLibrary &

general_base_pair_step_library(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager) → pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary

C++: core::import_pose::libraries::RNA_LibraryManager::general_base_pair_step_library() –> const class core::import_pose::libraries::BasePairStepLibrary &

get_instance() → core::import_pose::libraries::RNA_LibraryManager

C++: utility::SingletonBase<core::import_pose::libraries::RNA_LibraryManager>::get_instance() –> class core::import_pose::libraries::RNA_LibraryManager *

rna_fragment_library(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager, tag: str) → pyrosetta.rosetta.core.fragment.rna.RNA_Fragments

C++: core::import_pose::libraries::RNA_LibraryManager::rna_fragment_library(const class std::basic_string<char> &) –> const class core::fragment::rna::RNA_Fragments &

rna_jump_library(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager, tag: str) → pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary

C++: core::import_pose::libraries::RNA_LibraryManager::rna_jump_library(const class std::basic_string<char> &) –> const class core::import_pose::libraries::RNA_JumpLibrary &

rna_jump_library_cop(*args, **kwargs)

Overloaded function.

1. rna_jump_library_cop(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager, tag: str) -> pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary

C++: core::import_pose::libraries::RNA_LibraryManager::rna_jump_library_cop(const class std::basic_string<char> &) –> const class std::shared_ptr<const class core::import_pose::libraries::RNA_JumpLibrary> &

2. rna_jump_library_cop(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager) -> pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary

C++: core::import_pose::libraries::RNA_LibraryManager::rna_jump_library_cop() –> const class std::shared_ptr<const class core::import_pose::libraries::RNA_JumpLibrary> &

class pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate

Bases: pybind11_builtins.pybind11_object

atom_name1(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate) → str

C++: core::import_pose::libraries::RNA_PairingTemplate::atom_name1() const –> const std::string &

atom_name2(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate) → str

C++: core::import_pose::libraries::RNA_PairingTemplate::atom_name2() const –> const std::string &

jump(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate) → pyrosetta.rosetta.core.kinematics.Jump

C++: core::import_pose::libraries::RNA_PairingTemplate::jump() const –> const class core::kinematics::Jump &

jump_backward(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate) → pyrosetta.rosetta.core.kinematics.Jump

C++: core::import_pose::libraries::RNA_PairingTemplate::jump_backward() const –> const class core::kinematics::Jump &

jump_forward(self: pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate) → pyrosetta.rosetta.core.kinematics.Jump

C++: core::import_pose::libraries::RNA_PairingTemplate::jump_forward() const –> const class core::kinematics::Jump &