rna¶

Bindings for core::pose::rna namespace

class pyrosetta.rosetta.core.pose.rna.RNA_DataInfo¶

Bases: pybind11_builtins.pybind11_object

Keep track of RNA chemical mapping data inside the pose.

__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.core.pose.rna.RNA_DataInfo) -> None
__init__(self: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo, arg0: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo) -> 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_datum(self: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo, rna_datum: pyrosetta.rosetta.core.pose.rna.RNA_Datum) → None¶: C++: core::pose::rna::RNA_DataInfo::add_datum(const class core::pose::rna::RNA_Datum &) –> void

add_reactivity(self: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo, rna_reactivity: pyrosetta.rosetta.core.pose.rna.RNA_Reactivity) → None¶: C++: core::pose::rna::RNA_DataInfo::add_reactivity(const class core::pose::rna::RNA_Reactivity &) –> void

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

backbone_burial(self: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo) → ObjexxFCL::FArray1D<bool>¶: C++: core::pose::rna::RNA_DataInfo::backbone_burial() const –> const class ObjexxFCL::FArray1D<bool> &

backbone_exposed(self: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo) → ObjexxFCL::FArray1D<bool>¶: C++: core::pose::rna::RNA_DataInfo::backbone_exposed() const –> const class ObjexxFCL::FArray1D<bool> &

clone(self: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo) → pyrosetta.rosetta.core.pose.rna.RNA_DataInfo¶: C++: core::pose::rna::RNA_DataInfo::clone() const –> class std::shared_ptr<class core::pose::rna::RNA_DataInfo>

rna_data(self: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo) → pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Datum¶: C++: core::pose::rna::RNA_DataInfo::rna_data() const –> const class utility::vector1<class core::pose::rna::RNA_Datum, class std::allocator<class core::pose::rna::RNA_Datum> > &

rna_reactivities(self: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo) → pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Reactivity¶: C++: core::pose::rna::RNA_DataInfo::rna_reactivities() const –> const class utility::vector1<class core::pose::rna::RNA_Reactivity, class std::allocator<class core::pose::rna::RNA_Reactivity> > &

set_backbone_burial(self: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo, backbone_burial: ObjexxFCL::FArray1D<bool>) → None¶: C++: core::pose::rna::RNA_DataInfo::set_backbone_burial(const class ObjexxFCL::FArray1D<bool> &) –> void

set_backbone_exposed(self: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo, backbone_exposed: ObjexxFCL::FArray1D<bool>) → None¶: C++: core::pose::rna::RNA_DataInfo::set_backbone_exposed(const class ObjexxFCL::FArray1D<bool> &) –> void

size(self: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo) → int¶: C++: core::pose::rna::RNA_DataInfo::size() const –> unsigned long

zero(self: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo) → None¶: C++: core::pose::rna::RNA_DataInfo::zero() –> void

class pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo¶

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

Keep track of RNA centroid information inside the pose.

/ Rhiju move this to its own namespace!

__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.core.pose.rna.RNA_FilteredBaseBaseInfo) -> None
__init__(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo, arg0: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) -> 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.pose.rna.RNA_FilteredBaseBaseInfo, : pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::operator=(const class core::pose::rna::RNA_FilteredBaseBaseInfo &) –> class core::pose::rna::RNA_FilteredBaseBaseInfo &

base_pair_list(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::base_pair_list() const –> class utility::vector1<class core::pose::rna::BasePair, class std::allocator<class core::pose::rna::BasePair> >

base_stack_list(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → pyrosetta.rosetta.utility.vector1_core_pose_rna_BaseStack¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::base_stack_list() const –> class utility::vector1<class core::pose::rna::BaseStack, class std::allocator<class core::pose::rna::BaseStack> >

basepair_axis_stagger_scaling(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → float¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::basepair_axis_stagger_scaling() const –> const double &

basestack_axis_scaling(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → float¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::basestack_axis_scaling() const –> const double &

calculated(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → bool¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::calculated() –> bool &

carry_out_filtering(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo, raw_base_base_info: core::pose::rna::RNA_RawBaseBaseInfo) → None¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::carry_out_filtering(const class core::pose::rna::RNA_RawBaseBaseInfo &) –> void

clone(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

filtered_base_axis_array(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → ObjexxFCL::FArray2D<double>¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_axis_array() –> class ObjexxFCL::FArray2D<double> &

filtered_base_pair_array(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → ObjexxFCL::FArray2D<double>¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_pair_array() –> class ObjexxFCL::FArray2D<double> &

filtered_base_stack_array(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → ObjexxFCL::FArray2D<double>¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_array() –> class ObjexxFCL::FArray2D<double> &

filtered_base_stack_axis_array(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → ObjexxFCL::FArray2D<double>¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_axis_array() –> class ObjexxFCL::FArray2D<double> &

filtered_base_stagger_array(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → ObjexxFCL::FArray2D<double>¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stagger_array() –> class ObjexxFCL::FArray2D<double> &

get_data_score(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo, rna_data_info: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo) → float¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::get_data_score(const class core::pose::rna::RNA_DataInfo &) const –> double

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t¶: C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

get_total_base_axis_score(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → float¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_axis_score() const –> const double &

get_total_base_pair_score(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → float¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_pair_score() const –> const double &

get_total_base_stack_axis_score(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → float¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_stack_axis_score() const –> const double &

get_total_base_stack_score(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → float¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_stack_score() const –> const double &

get_total_base_stagger_score(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → float¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_stagger_score() const –> const double &

resize(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo, total_residue: int) → None¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::resize(const unsigned long &) –> void

scale_axis_stagger(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → bool¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::scale_axis_stagger() const –> const bool &

scored_base_pair_list(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BasePair_std_allocator_std_pair_double_core_pose_rna_BasePair_t¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_pair_list() const –> const class std::list<struct std::pair<double, class core::pose::rna::BasePair>, class std::allocator<struct std::pair<double, class core::pose::rna::BasePair> > >

set_calculated(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo, setting: bool) → None¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::set_calculated(const bool &) –> void

size(self: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → int¶: C++: core::pose::rna::RNA_FilteredBaseBaseInfo::size() const –> unsigned long

class pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo¶

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

Keep track of RNA centroid information inside the pose.

/ Rhiju move this to its own namespace! / Also, should probably use EnergyGraph instead of FArrays – much smaller memory footprint (!) /

__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.core.pose.rna.RNA_RawBaseBaseInfo) -> None
__init__(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo, arg0: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) -> 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.pose.rna.RNA_RawBaseBaseInfo, : pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) → pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::operator=(const class core::pose::rna::RNA_RawBaseBaseInfo &) –> class core::pose::rna::RNA_RawBaseBaseInfo &

base_axis_array(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) → ObjexxFCL::FArray3D<double>¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::base_axis_array() –> class ObjexxFCL::FArray3D<double> &

base_geometry_height_array(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) → ObjexxFCL::FArray2D<double>¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::base_geometry_height_array() –> class ObjexxFCL::FArray2D<double> &

base_geometry_orientation_array(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) → ObjexxFCL::FArray2D<double>¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::base_geometry_orientation_array() –> class ObjexxFCL::FArray2D<double> &

base_pair_array(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) → ObjexxFCL::FArray3D<double>¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::base_pair_array() –> class ObjexxFCL::FArray3D<double> &

base_stack_array(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) → ObjexxFCL::FArray2D<double>¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::base_stack_array() –> class ObjexxFCL::FArray2D<double> &

base_stack_axis_array(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) → ObjexxFCL::FArray2D<double>¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::base_stack_axis_array() –> class ObjexxFCL::FArray2D<double> &

base_stagger_array(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) → ObjexxFCL::FArray3D<double>¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::base_stagger_array() –> class ObjexxFCL::FArray3D<double> &

calculated(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) → bool¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::calculated() –> bool &

clone(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

copy_values(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo, src: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo, i: int, j: int) → None¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::copy_values(const class core::pose::rna::RNA_RawBaseBaseInfo &, const unsigned long &, const unsigned long &) –> void

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t¶: C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

resize(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo, total_residue: int) → None¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::resize(const unsigned long &) –> void

set_calculated(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo, setting: bool) → None¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::set_calculated(const bool &) –> void

size(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) → int¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::size() const –> unsigned long

zero(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) → None¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::zero() –> void

class pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment¶

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.core.pose.rna.RNA_SuiteAssignment, name_in: str, suiteness_in: float, dist_in: float) -> None
__init__(self: pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment) -> None
__init__(self: pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment, arg0: pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment) -> 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.pose.rna.RNA_SuiteAssignment, : pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment) → pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment¶: C++: core::pose::rna::RNA_SuiteAssignment::operator=(const class core::pose::rna::RNA_SuiteAssignment &) –> class core::pose::rna::RNA_SuiteAssignment &

class pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo¶

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.core.pose.rna.RNA_SuiteInfo, name_in: str, classifier_in: int, torsion_in: pyrosetta.rosetta.utility.fixedsizearray1_double_7_t) -> None
__init__(self: pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo) -> None
__init__(self: pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo, arg0: pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo) -> 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.pose.rna.RNA_SuiteInfo, : pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo) → pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo¶: C++: core::pose::rna::RNA_SuiteInfo::operator=(const class core::pose::rna::RNA_SuiteInfo &) –> class core::pose::rna::RNA_SuiteInfo &

class pyrosetta.rosetta.core.pose.rna.RNA_SuiteName¶

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.core.pose.rna.RNA_SuiteName) → 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(*args, **kwargs)¶

Overloaded function.

assign(self: pyrosetta.rosetta.core.pose.rna.RNA_SuiteName, torsions_in: pyrosetta.rosetta.utility.fixedsizearray1_double_7_t) -> pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment

C++: core::pose::rna::RNA_SuiteName::assign(const class utility::fixedsizearray1<double, 7> &) const –> class core::pose::rna::RNA_SuiteAssignment

assign(self: pyrosetta.rosetta.core.pose.rna.RNA_SuiteName, torsions_in: pyrosetta.rosetta.utility.fixedsizearray1_double_7_t, deriv: pyrosetta.rosetta.utility.fixedsizearray1_double_7_t) -> pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment

C++: core::pose::rna::RNA_SuiteName::assign(const class utility::fixedsizearray1<double, 7> &, class utility::fixedsizearray1<double, 7> &) const –> class core::pose::rna::RNA_SuiteAssignment

assign(self: pyrosetta.rosetta.core.pose.rna.RNA_SuiteName, pose: pyrosetta.rosetta.core.pose.Pose, res: int) -> pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment

C++: core::pose::rna::RNA_SuiteName::assign(const class core::pose::Pose &, const unsigned long) const –> class core::pose::rna::RNA_SuiteAssignment

closest_by_dist4(*args, **kwargs)¶

Overloaded function.

closest_by_dist4(self: pyrosetta.rosetta.core.pose.rna.RNA_SuiteName, suite_dihedrals: pyrosetta.rosetta.utility.fixedsizearray1_double_7_t) -> pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo

C++: core::pose::rna::RNA_SuiteName::closest_by_dist4(const class utility::fixedsizearray1<double, 7> &) const –> class core::pose::rna::RNA_SuiteInfo

closest_by_dist4(self: pyrosetta.rosetta.core.pose.rna.RNA_SuiteName, pose: pyrosetta.rosetta.core.pose.Pose, res: int) -> pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo

C++: core::pose::rna::RNA_SuiteName::closest_by_dist4(const class core::pose::Pose &, const unsigned long) const –> class core::pose::rna::RNA_SuiteInfo

closest_suite(*args, **kwargs)¶

Overloaded function.

closest_suite(self: pyrosetta.rosetta.core.pose.rna.RNA_SuiteName, suite_dihedrals: pyrosetta.rosetta.utility.fixedsizearray1_double_7_t) -> pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo

C++: core::pose::rna::RNA_SuiteName::closest_suite(const class utility::fixedsizearray1<double, 7> &) const –> class core::pose::rna::RNA_SuiteInfo

closest_suite(self: pyrosetta.rosetta.core.pose.rna.RNA_SuiteName, pose: pyrosetta.rosetta.core.pose.Pose, res: int) -> pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo

C++: core::pose::rna::RNA_SuiteName::closest_suite(const class core::pose::Pose &, const unsigned long) const –> class core::pose::rna::RNA_SuiteInfo

name2suite(self: pyrosetta.rosetta.core.pose.rna.RNA_SuiteName, name: str) → pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo¶: C++: core::pose::rna::RNA_SuiteName::name2suite(const class std::basic_string<char> &) const –> class core::pose::rna::RNA_SuiteInfo

class pyrosetta.rosetta.core.pose.rna.StubStubType¶

Bases: pybind11_builtins.pybind11_object

O3P_TO_O5P …-C4’-C3’-O3’ to O5’-C5’-C4’-… Centers are O3’ and O5’. CHAINBREAK O3’-OVL1-OVL2 to OVU-P-O5’, centered on OVL1 and P [overlap means transl = 0, rotation = I ]

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(*args, **kwargs)¶

Overloaded function.

__eq__(self: pyrosetta.rosetta.core.pose.rna.StubStubType, arg0: pyrosetta.rosetta.core.pose.rna.StubStubType) -> bool
__eq__(self: pyrosetta.rosetta.core.pose.rna.StubStubType, arg0: int) -> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.core.pose.rna.StubStubType) → tuple¶

__gt__¶: Return self>value.

__hash__(self: pyrosetta.rosetta.core.pose.rna.StubStubType) → int¶

__init__(self: pyrosetta.rosetta.core.pose.rna.StubStubType, arg0: int) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

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

__int__(self: pyrosetta.rosetta.core.pose.rna.StubStubType) → int¶

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(*args, **kwargs)¶

Overloaded function.

__ne__(self: pyrosetta.rosetta.core.pose.rna.StubStubType, arg0: pyrosetta.rosetta.core.pose.rna.StubStubType) -> bool
__ne__(self: pyrosetta.rosetta.core.pose.rna.StubStubType, arg0: int) -> bool

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__(self: pyrosetta.rosetta.core.pose.rna.StubStubType) → str¶

__setattr__¶: Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.core.pose.rna.StubStubType, arg0: tuple) → None¶

__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).

pyrosetta.rosetta.core.pose.rna.add_anti_chi_constraints(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::pose::rna::add_anti_chi_constraints(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.pose.rna.add_chi_constraints(pose: pyrosetta.rosetta.core.pose.Pose, chi_potential_restraint: core::scoring::func::Func, rna_chi_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::pose::rna::add_chi_constraints(class core::pose::Pose &, class std::shared_ptr<class core::scoring::func::Func>, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.pose.rna.add_number_base_pairs(*args, **kwargs)¶

Overloaded function.

add_number_base_pairs(pose: pyrosetta.rosetta.core.pose.Pose, s: core::io::silent::SilentStruct) -> None

C++: core::pose::rna::add_number_base_pairs(const class core::pose::Pose &, class core::io::silent::SilentStruct &) –> void

add_number_base_pairs(pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: core::pose::rna::add_number_base_pairs(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.pose.rna.add_number_native_base_pairs(*args, **kwargs)¶

Overloaded function.

add_number_native_base_pairs(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, s: core::io::silent::SilentStruct) -> None

C++: core::pose::rna::add_number_native_base_pairs(class core::pose::Pose &, const class core::pose::Pose &, class core::io::silent::SilentStruct &) –> void

add_number_native_base_pairs(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: core::pose::rna::add_number_native_base_pairs(class core::pose::Pose &, const class core::pose::Pose &) –> void

pyrosetta.rosetta.core.pose.rna.add_syn_anti_chi_constraints(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::pose::rna::add_syn_anti_chi_constraints(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.pose.rna.add_syn_chi_constraints(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::pose::rna::add_syn_chi_constraints(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.pose.rna.add_virtual_O2Prime_hydrogen(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::pose::rna::add_virtual_O2Prime_hydrogen(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.pose.rna.apply_Aform_torsions(pose: pyrosetta.rosetta.core.pose.Pose, n: int) → None¶: C++: core::pose::rna::apply_Aform_torsions(class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.core.pose.rna.apply_ideal_c2endo_sugar_coords(pose: pyrosetta.rosetta.core.pose.Pose, i: int) → None¶: C++: core::pose::rna::apply_ideal_c2endo_sugar_coords(class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.core.pose.rna.apply_non_main_chain_sugar_coords(non_main_chain_sugar_coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose, reference_pose: pyrosetta.rosetta.core.pose.Pose, i: int) → None¶: C++: core::pose::rna::apply_non_main_chain_sugar_coords(const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, class core::pose::Pose &, const class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.core.pose.rna.apply_pucker(*args, **kwargs)¶

Overloaded function.

apply_pucker(pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> None
apply_pucker(pose: pyrosetta.rosetta.core.pose.Pose, i: int, pucker_state: pyrosetta.rosetta.core.chemical.rna.PuckerState) -> None
apply_pucker(pose: pyrosetta.rosetta.core.pose.Pose, i: int, pucker_state: pyrosetta.rosetta.core.chemical.rna.PuckerState, skip_same_state: bool) -> None
apply_pucker(pose: pyrosetta.rosetta.core.pose.Pose, i: int, pucker_state: pyrosetta.rosetta.core.chemical.rna.PuckerState, skip_same_state: bool, idealize_coord: bool) -> None

C++: core::pose::rna::apply_pucker(class core::pose::Pose &, const unsigned long, const enum core::chemical::rna::PuckerState, const bool, const bool) –> void

pyrosetta.rosetta.core.pose.rna.apply_virtual_rna_residue_variant_type(*args, **kwargs)¶

Overloaded function.

apply_virtual_rna_residue_variant_type(pose: pyrosetta.rosetta.core.pose.Pose, seq_num: int) -> None
apply_virtual_rna_residue_variant_type(pose: pyrosetta.rosetta.core.pose.Pose, seq_num: int, apply_check: bool) -> None

C++: core::pose::rna::apply_virtual_rna_residue_variant_type(class core::pose::Pose &, const unsigned long &, const bool) –> void

apply_virtual_rna_residue_variant_type(pose: pyrosetta.rosetta.core.pose.Pose, seq_num: int, working_cutpoint_closed_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
apply_virtual_rna_residue_variant_type(pose: pyrosetta.rosetta.core.pose.Pose, seq_num: int, working_cutpoint_closed_list: pyrosetta.rosetta.utility.vector1_unsigned_long, apply_check: bool) -> None

C++: core::pose::rna::apply_virtual_rna_residue_variant_type(class core::pose::Pose &, const unsigned long &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

pyrosetta.rosetta.core.pose.rna.assign_pucker(pose: pyrosetta.rosetta.core.pose.Pose, rsd_id: int) → pyrosetta.rosetta.core.chemical.rna.PuckerState¶: C++: core::pose::rna::assign_pucker(const class core::pose::Pose &, const unsigned long) –> enum core::chemical::rna::PuckerState

pyrosetta.rosetta.core.pose.rna.check_in_base_pair_list(base_pair: core::pose::rna::BasePair, base_pair_list: pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair) → bool¶: C++: core::pose::rna::check_in_base_pair_list(const class core::pose::rna::BasePair &, const class utility::vector1<class core::pose::rna::BasePair, class std::allocator<class core::pose::rna::BasePair> > &) –> bool

pyrosetta.rosetta.core.pose.rna.classify_base_pairs(*args, **kwargs)¶

Overloaded function.

classify_base_pairs(pose: pyrosetta.rosetta.core.pose.Pose, base_pair_list: pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair, is_bulged: pyrosetta.rosetta.utility.vector1_bool) -> None

C++: core::pose::rna::classify_base_pairs(const class core::pose::Pose &, class utility::vector1<class core::pose::rna::BasePair, class std::allocator<class core::pose::rna::BasePair> > &, class utility::vector1<bool, class std::allocator<bool> > &) –> void

classify_base_pairs(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair

C++: core::pose::rna::classify_base_pairs(const class core::pose::Pose &) –> class utility::vector1<class core::pose::rna::BasePair, class std::allocator<class core::pose::rna::BasePair> >

pyrosetta.rosetta.core.pose.rna.figure_out_reasonable_rna_fold_tree(*args, **kwargs)¶

Overloaded function.

figure_out_reasonable_rna_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose) -> None
figure_out_reasonable_rna_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, force_cut_at_rna_chainbreak: bool) -> None

C++: core::pose::rna::figure_out_reasonable_rna_fold_tree(class core::pose::Pose &, const bool) –> void

pyrosetta.rosetta.core.pose.rna.fix_sugar_coords(atoms_for_which_we_need_new_dofs: pyrosetta.rosetta.utility.vector1_std_string, non_main_chain_sugar_coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose, reference_pose: pyrosetta.rosetta.core.pose.Pose, i: int) → None¶: C++: core::pose::rna::fix_sugar_coords(class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > >, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, class core::pose::Pose &, const class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.core.pose.rna.get_LW_orientation(edge1: pyrosetta.rosetta.core.chemical.rna.BaseEdge, edge2: pyrosetta.rosetta.core.chemical.rna.BaseEdge, orientation: pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation) → pyrosetta.rosetta.core.chemical.rna.LW_BaseDoubletOrientation¶: C++: core::pose::rna::get_LW_orientation(const enum core::chemical::rna::BaseEdge &, const enum core::chemical::rna::BaseEdge &, const enum core::chemical::rna::BaseDoubletOrientation &) –> enum core::chemical::rna::LW_BaseDoubletOrientation

pyrosetta.rosetta.core.pose.rna.get_atom_bin(atom_pos: pyrosetta.rosetta.numeric.xyzVector_double_t, ref_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, atom_bin_size: float, bin_offset: int) → pyrosetta.rosetta.core.pose.rna.Atom_Bin¶: C++: core::pose::rna::get_atom_bin(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const double, const int) –> struct core::pose::rna::Atom_Bin

pyrosetta.rosetta.core.pose.rna.get_base_doublet_orientation_from_LW(edge1: pyrosetta.rosetta.core.chemical.rna.BaseEdge, edge2: pyrosetta.rosetta.core.chemical.rna.BaseEdge, lw_orientation: pyrosetta.rosetta.core.chemical.rna.LW_BaseDoubletOrientation) → pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation¶: C++: core::pose::rna::get_base_doublet_orientation_from_LW(const enum core::chemical::rna::BaseEdge &, const enum core::chemical::rna::BaseEdge &, const enum core::chemical::rna::LW_BaseDoubletOrientation &) –> enum core::chemical::rna::BaseDoubletOrientation

pyrosetta.rosetta.core.pose.rna.get_number_base_pairs(pose: pyrosetta.rosetta.core.pose.Pose, N_WC: int, N_NWC: int, N_BP: int) → None¶: C++: core::pose::rna::get_number_base_pairs(const class core::pose::Pose &, unsigned long &, unsigned long &, unsigned long &) –> void

pyrosetta.rosetta.core.pose.rna.get_number_base_stacks(pose_input: pyrosetta.rosetta.core.pose.Pose) → int¶: C++: core::pose::rna::get_number_base_stacks(const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.core.pose.rna.get_number_native_base_pairs(pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, pN_WC: int, pN_NWC: int, pN_BP: int, pnatWC: int, pnatNWC: int, pnatBP: int, pf_natWC: float, pf_natNWC: float, pf_natBP: float) → None¶: C++: core::pose::rna::get_number_native_base_pairs(class core::pose::Pose &, const class core::pose::Pose &, unsigned long &, unsigned long &, unsigned long &, unsigned long &, unsigned long &, unsigned long &, double &, double &, double &) –> void

pyrosetta.rosetta.core.pose.rna.get_op2_op1_sign(*args, **kwargs)¶

Overloaded function.

get_op2_op1_sign(pose: pyrosetta.rosetta.core.pose.Pose) -> float

C++: core::pose::rna::get_op2_op1_sign(const class core::pose::Pose &) –> double

get_op2_op1_sign(pose: pyrosetta.rosetta.core.pose.Pose, res_num: int) -> float

C++: core::pose::rna::get_op2_op1_sign(const class core::pose::Pose &, unsigned long) –> double

pyrosetta.rosetta.core.pose.rna.get_residue_base_state(pose: pyrosetta.rosetta.core.pose.Pose, seq_num: int) → pyrosetta.rosetta.core.chemical.rna.ChiState¶: C++: core::pose::rna::get_residue_base_state(const class core::pose::Pose &, const unsigned long) –> enum core::chemical::rna::ChiState

pyrosetta.rosetta.core.pose.rna.get_residue_pucker_state(pose: pyrosetta.rosetta.core.pose.Pose, seq_num: int) → pyrosetta.rosetta.core.chemical.rna.PuckerState¶: C++: core::pose::rna::get_residue_pucker_state(const class core::pose::Pose &, const unsigned long) –> enum core::chemical::rna::PuckerState

pyrosetta.rosetta.core.pose.rna.get_stub_stub(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, stub1: pyrosetta.rosetta.core.kinematics.Stub, stub2: pyrosetta.rosetta.core.kinematics.Stub, stub_stub_type: pyrosetta.rosetta.core.pose.rna.StubStubType) → None¶: C++: core::pose::rna::get_stub_stub(const class core::conformation::Residue &, const class core::conformation::Residue &, class core::kinematics::Stub &, class core::kinematics::Stub &, const enum core::pose::rna::StubStubType &) –> void

pyrosetta.rosetta.core.pose.rna.get_suite_torsion_ids(i: int) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID¶: C++: core::pose::rna::get_suite_torsion_ids(const unsigned long) –> class utility::vector1<class core::id::TorsionID, class std::allocator<class core::id::TorsionID> >

pyrosetta.rosetta.core.pose.rna.has_virtual_rna_residue_variant_type(pose: pyrosetta.rosetta.core.pose.Pose, seq_num: int) → bool¶: C++: core::pose::rna::has_virtual_rna_residue_variant_type(class core::pose::Pose &, const unsigned long &) –> bool

pyrosetta.rosetta.core.pose.rna.initialize_atoms_for_which_we_need_new_dofs(atoms_for_which_we_need_new_dofs: pyrosetta.rosetta.utility.vector1_std_string, pose: pyrosetta.rosetta.core.pose.Pose, i: int) → None¶: C++: core::pose::rna::initialize_atoms_for_which_we_need_new_dofs(class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.core.pose.rna.is_atom_bin_in_range(atom_pos_bin: pyrosetta.rosetta.core.pose.rna.Atom_Bin, bin_max: int) → bool¶: C++: core::pose::rna::is_atom_bin_in_range(const struct core::pose::rna::Atom_Bin &, const int) –> bool

pyrosetta.rosetta.core.pose.rna.is_cutpoint_closed_atom(rsd: pyrosetta.rosetta.core.chemical.ResidueType, id: pyrosetta.rosetta.core.id.AtomID) → bool¶: C++: core::pose::rna::is_cutpoint_closed_atom(const class core::chemical::ResidueType &, const class core::id::AtomID &) –> bool

pyrosetta.rosetta.core.pose.rna.is_cutpoint_closed_torsion(pose: pyrosetta.rosetta.core.pose.Pose, torsion_id: pyrosetta.rosetta.core.id.TorsionID) → bool¶: C++: core::pose::rna::is_cutpoint_closed_torsion(const class core::pose::Pose &, const class core::id::TorsionID &) –> bool

pyrosetta.rosetta.core.pose.rna.is_cutpoint_open(pose: pyrosetta.rosetta.core.pose.Pose, i: int) → bool¶: C++: core::pose::rna::is_cutpoint_open(const class core::pose::Pose &, const unsigned long) –> bool

pyrosetta.rosetta.core.pose.rna.is_rna_chainbreak(pose: pyrosetta.rosetta.core.pose.Pose, i: int) → bool¶: C++: core::pose::rna::is_rna_chainbreak(const class core::pose::Pose &, const unsigned long) –> bool

pyrosetta.rosetta.core.pose.rna.is_torsion_valid(*args, **kwargs)¶

Overloaded function.

is_torsion_valid(pose: pyrosetta.rosetta.core.pose.Pose, torsion_id: pyrosetta.rosetta.core.id.TorsionID) -> bool
is_torsion_valid(pose: pyrosetta.rosetta.core.pose.Pose, torsion_id: pyrosetta.rosetta.core.id.TorsionID, verbose: bool) -> bool
is_torsion_valid(pose: pyrosetta.rosetta.core.pose.Pose, torsion_id: pyrosetta.rosetta.core.id.TorsionID, verbose: bool, skip_chainbreak_torsions: bool) -> bool

C++: core::pose::rna::is_torsion_valid(const class core::pose::Pose &, const class core::id::TorsionID &, bool, bool) –> bool

pyrosetta.rosetta.core.pose.rna.make_phosphate_nomenclature_matches_mini(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::pose::rna::make_phosphate_nomenclature_matches_mini(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.pose.rna.mutate_position(*args, **kwargs)¶

Overloaded function.

mutate_position(pose: pyrosetta.rosetta.core.pose.Pose, i: int, new_seq: str) -> bool

C++: core::pose::rna::mutate_position(class core::pose::Pose &, const unsigned long, const char) –> bool

mutate_position(pose: pyrosetta.rosetta.core.pose.Pose, i: int, name3: str) -> bool

C++: core::pose::rna::mutate_position(class core::pose::Pose &, const unsigned long, const class std::basic_string<char> &) –> bool

mutate_position(pose: pyrosetta.rosetta.core.pose.Pose, i: int, rt: pyrosetta.rosetta.core.chemical.ResidueType) -> bool

C++: core::pose::rna::mutate_position(class core::pose::Pose &, const unsigned long, const class core::chemical::ResidueType &) –> bool

pyrosetta.rosetta.core.pose.rna.output_boolean(tag: str, boolean: bool) → None¶: C++: core::pose::rna::output_boolean(const class std::basic_string<char> &, bool) –> void

pyrosetta.rosetta.core.pose.rna.position_cutpoint_phosphate_torsions(*args, **kwargs)¶

Overloaded function.

position_cutpoint_phosphate_torsions(current_pose: pyrosetta.rosetta.core.pose.Pose, five_prime_chainbreak: int) -> None
position_cutpoint_phosphate_torsions(current_pose: pyrosetta.rosetta.core.pose.Pose, five_prime_chainbreak: int, three_prime_chainbreak: int) -> None

C++: core::pose::rna::position_cutpoint_phosphate_torsions(class core::pose::Pose &, const unsigned long, unsigned long) –> void

pyrosetta.rosetta.core.pose.rna.prepare_scratch_residue(scratch_rsd: pyrosetta.rosetta.core.conformation.Residue, start_rsd: pyrosetta.rosetta.core.conformation.Residue, non_main_chain_sugar_coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::pose::rna::prepare_scratch_residue(class std::shared_ptr<class core::conformation::Residue> &, const class core::conformation::Residue &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class core::pose::Pose &) –> void

pyrosetta.rosetta.core.pose.rna.print_torsion_info(pose: pyrosetta.rosetta.core.pose.Pose, torsion_id: pyrosetta.rosetta.core.id.TorsionID) → None¶: C++: core::pose::rna::print_torsion_info(const class core::pose::Pose &, const class core::id::TorsionID &) –> void

pyrosetta.rosetta.core.pose.rna.remove_and_store_bracketed(working_sequence: str, working_sequence_clean: str, special_res: pyrosetta.rosetta.std.map_unsigned_long_std_string) → None¶: C++: core::pose::rna::remove_and_store_bracketed(const class std::basic_string<char> &, class std::basic_string<char> &, class std::map<unsigned long, class std::basic_string<char>, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::basic_string<char> > > > &) –> void

pyrosetta.rosetta.core.pose.rna.remove_bracketed(sequence: str) → str¶: C++: core::pose::rna::remove_bracketed(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.core.pose.rna.remove_virtual_rna_residue_variant_type(pose: pyrosetta.rosetta.core.pose.Pose, seq_num: int) → None¶: C++: core::pose::rna::remove_virtual_rna_residue_variant_type(class core::pose::Pose &, const unsigned long &) –> void

pyrosetta.rosetta.core.pose.rna.string_to_int(input_string: str) → int¶: C++: core::pose::rna::string_to_int(const class std::basic_string<char> &) –> unsigned long

pyrosetta.rosetta.core.pose.rna.tokenize(str: str, delimiters: str) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: core::pose::rna::tokenize(const class std::basic_string<char> &, const class std::basic_string<char> &) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.core.pose.rna.virtualize_5prime_phosphates(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::pose::rna::virtualize_5prime_phosphates(class core::pose::Pose &) –> void