rna¶

Bindings for core::fragment::rna namespace

class pyrosetta.rosetta.core.fragment.rna.FragmentLibrary¶

Bases: pybind11_object

add_torsion(*args, **kwargs)¶

Overloaded function.

add_torsion(self: pyrosetta.rosetta.core.fragment.rna.FragmentLibrary, torsion_set: pyrosetta.rosetta.core.fragment.rna.TorsionSet) -> None

C++: core::fragment::rna::FragmentLibrary::add_torsion(const class core::fragment::rna::TorsionSet &) –> void

add_torsion(self: pyrosetta.rosetta.core.fragment.rna.FragmentLibrary, vall: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments, position: int, size: int) -> None

C++: core::fragment::rna::FragmentLibrary::add_torsion(const class core::fragment::rna::FullAtomRNA_Fragments &, const unsigned long, const unsigned long) –> void

assign(self: pyrosetta.rosetta.core.fragment.rna.FragmentLibrary, : pyrosetta.rosetta.core.fragment.rna.FragmentLibrary) → pyrosetta.rosetta.core.fragment.rna.FragmentLibrary¶: C++: core::fragment::rna::FragmentLibrary::operator=(const class core::fragment::rna::FragmentLibrary &) –> class core::fragment::rna::FragmentLibrary &

get_align_depth(self: pyrosetta.rosetta.core.fragment.rna.FragmentLibrary) → int¶: C++: core::fragment::rna::FragmentLibrary::get_align_depth() const –> unsigned long

get_fragment_torsion(self: pyrosetta.rosetta.core.fragment.rna.FragmentLibrary, num_torsion: int, which_frag: int, offset: int) → float¶: C++: core::fragment::rna::FragmentLibrary::get_fragment_torsion(const unsigned long, const unsigned long, const unsigned long) –> double

get_fragment_torsion_set(self: pyrosetta.rosetta.core.fragment.rna.FragmentLibrary, which_frag: int) → pyrosetta.rosetta.core.fragment.rna.TorsionSet¶: C++: core::fragment::rna::FragmentLibrary::get_fragment_torsion_set(const unsigned long) const –> const class core::fragment::rna::TorsionSet &

class pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments¶

Bases: RNA_Fragments

apply_best_fragment(self: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, position: int, size: int, type: int, homology_exclusion: pyrosetta.rosetta.core.fragment.rna.RNA_FragmentHomologyExclusion, atom_level_domain_map: core::pose::toolbox::AtomLevelDomainMap, symm_hack_arity: int, exhaustive: int) → None¶: C++: core::fragment::rna::FullAtomRNA_Fragments::apply_best_fragment(class std::shared_ptr<class core::scoring::ScoreFunction>, class core::pose::Pose &, const unsigned long, const unsigned long, const unsigned long, const class std::shared_ptr<const class core::fragment::rna::RNA_FragmentHomologyExclusion> &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>, const unsigned long, const unsigned long) const –> void

apply_random_fragment(self: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments, pose: pyrosetta.rosetta.core.pose.Pose, position: int, size: int, type: int, homology_exclusion: pyrosetta.rosetta.core.fragment.rna.RNA_FragmentHomologyExclusion, atom_level_domain_map: core::pose::toolbox::AtomLevelDomainMap, symm_hack_arity: int) → None¶: C++: core::fragment::rna::FullAtomRNA_Fragments::apply_random_fragment(class core::pose::Pose &, const unsigned long, const unsigned long, const unsigned long, const class std::shared_ptr<const class core::fragment::rna::RNA_FragmentHomologyExclusion> &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>, const unsigned long) const –> void

assign(self: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments, : pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments) → pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments¶: C++: core::fragment::rna::FullAtomRNA_Fragments::operator=(const class core::fragment::rna::FullAtomRNA_Fragments &) –> class core::fragment::rna::FullAtomRNA_Fragments &

get_fragment_library_pointer(*args, **kwargs)¶

Overloaded function.

get_fragment_library_pointer(self: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments, RNA_string: str, RNA_secstruct_string: str, homology_exclusion: pyrosetta.rosetta.core.fragment.rna.RNA_FragmentHomologyExclusion) -> core::fragment::rna::FragmentLibrary
get_fragment_library_pointer(self: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments, RNA_string: str, RNA_secstruct_string: str, homology_exclusion: pyrosetta.rosetta.core.fragment.rna.RNA_FragmentHomologyExclusion, restriction: pyrosetta.rosetta.utility.vector1_core_fragment_rna_SYN_ANTI_RESTRICTION) -> core::fragment::rna::FragmentLibrary
get_fragment_library_pointer(self: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments, RNA_string: str, RNA_secstruct_string: str, homology_exclusion: pyrosetta.rosetta.core.fragment.rna.RNA_FragmentHomologyExclusion, restriction: pyrosetta.rosetta.utility.vector1_core_fragment_rna_SYN_ANTI_RESTRICTION, type: int) -> core::fragment::rna::FragmentLibrary

C++: core::fragment::rna::FullAtomRNA_Fragments::get_fragment_library_pointer(const std::string &, const std::string &, const class std::shared_ptr<const class core::fragment::rna::RNA_FragmentHomologyExclusion> &, const class utility::vector1<enum core::fragment::rna::SYN_ANTI_RESTRICTION, class std::allocator<enum core::fragment::rna::SYN_ANTI_RESTRICTION> > &, const unsigned long) const –> class std::shared_ptr<class core::fragment::rna::FragmentLibrary>

insert_fragment(self: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments, pose: pyrosetta.rosetta.core.pose.Pose, position: int, torsion_set: core::fragment::rna::TorsionSet, atom_level_domain_map: core::pose::toolbox::AtomLevelDomainMap) → None¶: C++: core::fragment::rna::FullAtomRNA_Fragments::insert_fragment(class core::pose::Pose &, const unsigned long, const class core::fragment::rna::TorsionSet &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>) const –> void

is_fullatom(self: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments) → bool¶: C++: core::fragment::rna::FullAtomRNA_Fragments::is_fullatom() –> bool

name(self: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments, i: int) → str¶: C++: core::fragment::rna::FullAtomRNA_Fragments::name(const unsigned long &) const –> std::string

non_main_chain_sugar_coords(self: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments, i: int, j: int, k: int) → float¶: C++: core::fragment::rna::FullAtomRNA_Fragments::non_main_chain_sugar_coords(const unsigned long &, const unsigned long &, const unsigned long &) const –> double

non_main_chain_sugar_coords_defined(self: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments) → bool¶: C++: core::fragment::rna::FullAtomRNA_Fragments::non_main_chain_sugar_coords_defined() const –> bool

secstruct(self: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments, i: int) → str¶: C++: core::fragment::rna::FullAtomRNA_Fragments::secstruct(const unsigned long &) const –> char

torsions(self: pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments, i: int, j: int) → float¶: C++: core::fragment::rna::FullAtomRNA_Fragments::torsions(const unsigned long &, const unsigned long &) const –> double

class pyrosetta.rosetta.core.fragment.rna.RNA_FragmentHomologyExclusion¶

Bases: pybind11_object

get_fragment_lines(self: pyrosetta.rosetta.core.fragment.rna.RNA_FragmentHomologyExclusion) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: core::fragment::rna::RNA_FragmentHomologyExclusion::get_fragment_lines() const –> const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &

class pyrosetta.rosetta.core.fragment.rna.RNA_Fragments¶

Bases: pybind11_object

apply_best_fragment(self: pyrosetta.rosetta.core.fragment.rna.RNA_Fragments, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, position: int, size: int, type: int, homology_exclusion: core::fragment::rna::RNA_FragmentHomologyExclusion, atom_level_domain_map: core::pose::toolbox::AtomLevelDomainMap, symm_hack_arity: int, exhaustive: int) → None¶: C++: core::fragment::rna::RNA_Fragments::apply_best_fragment(class std::shared_ptr<class core::scoring::ScoreFunction>, class core::pose::Pose &, const unsigned long, const unsigned long, const unsigned long, const class std::shared_ptr<const class core::fragment::rna::RNA_FragmentHomologyExclusion> &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>, const unsigned long, const unsigned long) const –> void

apply_random_fragment(self: pyrosetta.rosetta.core.fragment.rna.RNA_Fragments, pose: pyrosetta.rosetta.core.pose.Pose, position: int, size: int, type: int, homology_exclusion: core::fragment::rna::RNA_FragmentHomologyExclusion, atom_level_domain_map: core::pose::toolbox::AtomLevelDomainMap, symm_hack_arity: int) → None¶: C++: core::fragment::rna::RNA_Fragments::apply_random_fragment(class core::pose::Pose &, const unsigned long, const unsigned long, const unsigned long, const class std::shared_ptr<const class core::fragment::rna::RNA_FragmentHomologyExclusion> &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>, const unsigned long) const –> void

assign(self: pyrosetta.rosetta.core.fragment.rna.RNA_Fragments, : pyrosetta.rosetta.core.fragment.rna.RNA_Fragments) → pyrosetta.rosetta.core.fragment.rna.RNA_Fragments¶: C++: core::fragment::rna::RNA_Fragments::operator=(const class core::fragment::rna::RNA_Fragments &) –> class core::fragment::rna::RNA_Fragments &

get_fragment_library_pointer(self: pyrosetta.rosetta.core.fragment.rna.RNA_Fragments, : str, : str, : core::fragment::rna::RNA_FragmentHomologyExclusion, : pyrosetta.rosetta.utility.vector1_core_fragment_rna_SYN_ANTI_RESTRICTION, : int) → core::fragment::rna::FragmentLibrary¶: C++: core::fragment::rna::RNA_Fragments::get_fragment_library_pointer(const std::string &, const std::string &, const class std::shared_ptr<const class core::fragment::rna::RNA_FragmentHomologyExclusion> &, const class utility::vector1<enum core::fragment::rna::SYN_ANTI_RESTRICTION, class std::allocator<enum core::fragment::rna::SYN_ANTI_RESTRICTION> > &, const unsigned long) const –> class std::shared_ptr<class core::fragment::rna::FragmentLibrary>

insert_fragment(self: pyrosetta.rosetta.core.fragment.rna.RNA_Fragments, : pyrosetta.rosetta.core.pose.Pose, : int, : core::fragment::rna::TorsionSet, : core::pose::toolbox::AtomLevelDomainMap) → None¶: C++: core::fragment::rna::RNA_Fragments::insert_fragment(class core::pose::Pose &, const unsigned long, const class core::fragment::rna::TorsionSet &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>) const –> void

is_fullatom(self: pyrosetta.rosetta.core.fragment.rna.RNA_Fragments) → bool¶: C++: core::fragment::rna::RNA_Fragments::is_fullatom() –> bool

class pyrosetta.rosetta.core.fragment.rna.SYN_ANTI_RESTRICTION¶

Bases: pybind11_object

Members:

SYN

ANTI

ANY

ANTI = <SYN_ANTI_RESTRICTION.ANTI: 1>¶

ANY = <SYN_ANTI_RESTRICTION.ANY: 2>¶

SYN = <SYN_ANTI_RESTRICTION.SYN: 0>¶

property name¶

property value¶

class pyrosetta.rosetta.core.fragment.rna.TorsionSet¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.fragment.rna.TorsionSet, : pyrosetta.rosetta.core.fragment.rna.TorsionSet) → pyrosetta.rosetta.core.fragment.rna.TorsionSet¶: C++: core::fragment::rna::TorsionSet::operator=(const class core::fragment::rna::TorsionSet &) –> class core::fragment::rna::TorsionSet &

get_index_in_vall(self: pyrosetta.rosetta.core.fragment.rna.TorsionSet) → int¶: C++: core::fragment::rna::TorsionSet::get_index_in_vall() const –> unsigned long

get_size(self: pyrosetta.rosetta.core.fragment.rna.TorsionSet) → int¶: C++: core::fragment::rna::TorsionSet::get_size() const –> unsigned long

property non_main_chain_sugar_coords¶

property non_main_chain_sugar_coords_defined¶

property secstruct¶

property torsion_source_name¶

property torsions¶

class pyrosetta.rosetta.core.fragment.rna._RNA_MatchType_¶

Bases: pybind11_object

Members:

MATCH_ALL

MATCH_YR

MATCH_EXACT

MATCH_ALL = <_RNA_MatchType_.MATCH_ALL: 0>¶

MATCH_EXACT = <_RNA_MatchType_.MATCH_EXACT: 2>¶

MATCH_YR = <_RNA_MatchType_.MATCH_YR: 1>¶

property name¶

property value¶