rna¶

secstruct_legacy

Bindings for core::pose::rna namespace

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

Bases: pybind11_object

property x¶

property y¶

property z¶

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

Bases: pybind11_object

LW_orientation(self: pyrosetta.rosetta.core.pose.rna.BasePair) → pyrosetta.rosetta.core.chemical.rna.LW_BaseDoubletOrientation¶: C++: core::pose::rna::BasePair::LW_orientation() const –> enum core::chemical::rna::LW_BaseDoubletOrientation

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

edge1(self: pyrosetta.rosetta.core.pose.rna.BasePair) → pyrosetta.rosetta.core.chemical.rna.BaseEdge¶: C++: core::pose::rna::BasePair::edge1() const –> enum core::chemical::rna::BaseEdge

edge2(self: pyrosetta.rosetta.core.pose.rna.BasePair) → pyrosetta.rosetta.core.chemical.rna.BaseEdge¶: C++: core::pose::rna::BasePair::edge2() const –> enum core::chemical::rna::BaseEdge

flipped(self: pyrosetta.rosetta.core.pose.rna.BasePair) → pyrosetta.rosetta.core.pose.rna.BasePair¶: C++: core::pose::rna::BasePair::flipped() const –> class core::pose::rna::BasePair

orientation(self: pyrosetta.rosetta.core.pose.rna.BasePair) → pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation¶: C++: core::pose::rna::BasePair::orientation() const –> enum core::chemical::rna::BaseDoubletOrientation

print_info(*args, **kwargs)¶

Overloaded function.

print_info(self: pyrosetta.rosetta.core.pose.rna.BasePair) -> None
print_info(self: pyrosetta.rosetta.core.pose.rna.BasePair, out: pyrosetta.rosetta.std.ostream) -> None

C++: core::pose::rna::BasePair::print_info(std::ostream &) const –> void

res1(self: pyrosetta.rosetta.core.pose.rna.BasePair) → int¶: C++: core::pose::rna::BasePair::res1() const –> unsigned long

res2(self: pyrosetta.rosetta.core.pose.rna.BasePair) → int¶: C++: core::pose::rna::BasePair::res2() const –> unsigned long

set_edge1(self: pyrosetta.rosetta.core.pose.rna.BasePair, setting: pyrosetta.rosetta.core.chemical.rna.BaseEdge) → None¶: C++: core::pose::rna::BasePair::set_edge1(const enum core::chemical::rna::BaseEdge &) –> void

set_edge2(self: pyrosetta.rosetta.core.pose.rna.BasePair, setting: pyrosetta.rosetta.core.chemical.rna.BaseEdge) → None¶: C++: core::pose::rna::BasePair::set_edge2(const enum core::chemical::rna::BaseEdge &) –> void

set_orientation(self: pyrosetta.rosetta.core.pose.rna.BasePair, setting: pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation) → None¶: C++: core::pose::rna::BasePair::set_orientation(const enum core::chemical::rna::BaseDoubletOrientation &) –> void

set_res1(self: pyrosetta.rosetta.core.pose.rna.BasePair, setting: int) → None¶: C++: core::pose::rna::BasePair::set_res1(const unsigned long &) –> void

set_res2(self: pyrosetta.rosetta.core.pose.rna.BasePair, setting: int) → None¶: C++: core::pose::rna::BasePair::set_res2(const unsigned long &) –> void

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

Bases: pybind11_object

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

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

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

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

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

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

Bases: pybind11_object

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

flipped(self: pyrosetta.rosetta.core.pose.rna.BaseStack) → pyrosetta.rosetta.core.pose.rna.BaseStack¶: C++: core::pose::rna::BaseStack::flipped() const –> class core::pose::rna::BaseStack

orientation(self: pyrosetta.rosetta.core.pose.rna.BaseStack) → pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation¶: C++: core::pose::rna::BaseStack::orientation() const –> enum core::chemical::rna::BaseDoubletOrientation

res1(self: pyrosetta.rosetta.core.pose.rna.BaseStack) → int¶: C++: core::pose::rna::BaseStack::res1() const –> unsigned long

res2(self: pyrosetta.rosetta.core.pose.rna.BaseStack) → int¶: C++: core::pose::rna::BaseStack::res2() const –> unsigned long

set_orientation(self: pyrosetta.rosetta.core.pose.rna.BaseStack, setting: pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation) → None¶: C++: core::pose::rna::BaseStack::set_orientation(const enum core::chemical::rna::BaseDoubletOrientation &) –> void

set_res1(self: pyrosetta.rosetta.core.pose.rna.BaseStack, setting: int) → None¶: C++: core::pose::rna::BaseStack::set_res1(const unsigned long &) –> void

set_res2(self: pyrosetta.rosetta.core.pose.rna.BaseStack, setting: int) → None¶: C++: core::pose::rna::BaseStack::set_res2(const unsigned long &) –> void

set_which_side(self: pyrosetta.rosetta.core.pose.rna.BaseStack, setting: pyrosetta.rosetta.core.chemical.rna.BaseStackWhichSide) → None¶: C++: core::pose::rna::BaseStack::set_which_side(const enum core::chemical::rna::BaseStackWhichSide &) –> void

which_side(self: pyrosetta.rosetta.core.pose.rna.BaseStack) → pyrosetta.rosetta.core.chemical.rna.BaseStackWhichSide¶: C++: core::pose::rna::BaseStack::which_side() const –> enum core::chemical::rna::BaseStackWhichSide

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

Bases: pybind11_object

Keep track of RNA chemical mapping data inside the pose.

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) → pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t¶: C++: core::pose::rna::RNA_DataInfo::backbone_burial() const –> const class ObjexxFCL::FArray1D<bool> &

backbone_exposed(self: pyrosetta.rosetta.core.pose.rna.RNA_DataInfo) → pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t¶: 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: pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t) → 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: pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t) → 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_Datum¶

Bases: pybind11_object

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

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

set_edge(self: pyrosetta.rosetta.core.pose.rna.RNA_Datum, setting: int) → None¶: C++: core::pose::rna::RNA_Datum::set_edge(const unsigned long) –> void

set_position(self: pyrosetta.rosetta.core.pose.rna.RNA_Datum, setting: int) → None¶: C++: core::pose::rna::RNA_Datum::set_position(const unsigned long) –> void

set_weight(self: pyrosetta.rosetta.core.pose.rna.RNA_Datum, setting: float) → None¶: C++: core::pose::rna::RNA_Datum::set_weight(const double) –> void

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

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

Bases: CacheableData

Keep track of RNA centroid information inside the pose.

/ Rhiju move this to its own namespace!

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) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶: 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) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶: 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) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶: 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) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶: 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) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶: 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_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> > >

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

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_IdealCoord¶

Bases: pybind11_object

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.core.pose.rna.RNA_IdealCoord, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, pucker: pyrosetta.rosetta.core.chemical.rna.PuckerState) -> None
apply(self: pyrosetta.rosetta.core.pose.rna.RNA_IdealCoord, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, pucker: pyrosetta.rosetta.core.chemical.rna.PuckerState, keep_backbone_torsion: bool) -> None

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

apply(self: pyrosetta.rosetta.core.pose.rna.RNA_IdealCoord, pose: pyrosetta.rosetta.core.pose.Pose, puckers: pyrosetta.rosetta.utility.vector1_core_chemical_rna_PuckerState) -> None
apply(self: pyrosetta.rosetta.core.pose.rna.RNA_IdealCoord, pose: pyrosetta.rosetta.core.pose.Pose, puckers: pyrosetta.rosetta.utility.vector1_core_chemical_rna_PuckerState, keep_backbone_torsion: bool) -> None

C++: core::pose::rna::RNA_IdealCoord::apply(class core::pose::Pose &, const class utility::vector1<enum core::chemical::rna::PuckerState, class std::allocator<enum core::chemical::rna::PuckerState> > &, const bool) const –> void

apply(self: pyrosetta.rosetta.core.pose.rna.RNA_IdealCoord, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.pose.rna.RNA_IdealCoord, pose: pyrosetta.rosetta.core.pose.Pose, keep_backbone_torsion: bool) -> None

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

apply_pucker(*args, **kwargs)¶

Overloaded function.

apply_pucker(self: pyrosetta.rosetta.core.pose.rna.RNA_IdealCoord, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, pucker: pyrosetta.rosetta.core.chemical.rna.PuckerState) -> None
apply_pucker(self: pyrosetta.rosetta.core.pose.rna.RNA_IdealCoord, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, pucker: pyrosetta.rosetta.core.chemical.rna.PuckerState, keep_backbone_torsion: bool) -> None

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

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

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

Bases: 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 (!) /

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) → pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t¶: 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) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶: 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) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶: 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) → pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t¶: C++: core::pose::rna::RNA_RawBaseBaseInfo::base_pair_array() –> class ObjexxFCL::FArray3D<double> &

base_stack_array(self: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶: 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) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶: 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) → pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t¶: 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_Reactivity¶

Bases: pybind11_object

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

set_position(self: pyrosetta.rosetta.core.pose.rna.RNA_Reactivity, setting: int) → None¶: C++: core::pose::rna::RNA_Reactivity::set_position(const unsigned long) –> void

set_type(self: pyrosetta.rosetta.core.pose.rna.RNA_Reactivity, setting: pyrosetta.rosetta.core.pose.rna.RNA_ReactivityType) → None¶: C++: core::pose::rna::RNA_Reactivity::set_type(const enum core::pose::rna::RNA_ReactivityType) –> void

set_value(self: pyrosetta.rosetta.core.pose.rna.RNA_Reactivity, setting: float) → None¶: C++: core::pose::rna::RNA_Reactivity::set_value(const double) –> void

type(self: pyrosetta.rosetta.core.pose.rna.RNA_Reactivity) → pyrosetta.rosetta.core.pose.rna.RNA_ReactivityType¶: C++: core::pose::rna::RNA_Reactivity::type() const –> enum core::pose::rna::RNA_ReactivityType

value(self: pyrosetta.rosetta.core.pose.rna.RNA_Reactivity) → float¶: C++: core::pose::rna::RNA_Reactivity::value() const –> double

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

Bases: pybind11_object

Members:

NO_REACTIVITY

DMS

CMCT

SHAPE_1M7

HRF

CMCT = <RNA_ReactivityType.CMCT: 2>¶

DMS = <RNA_ReactivityType.DMS: 1>¶

HRF = <RNA_ReactivityType.HRF: 4>¶

NO_REACTIVITY = <RNA_ReactivityType.NO_REACTIVITY: 0>¶

SHAPE_1M7 = <RNA_ReactivityType.SHAPE_1M7: 3>¶

property name¶

property value¶

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

Bases: pybind11_object

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

base_pairs(self: pyrosetta.rosetta.core.pose.rna.RNA_SecStruct) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t¶: C++: core::pose::rna::RNA_SecStruct::base_pairs() const –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

blank(self: pyrosetta.rosetta.core.pose.rna.RNA_SecStruct) → bool¶: C++: core::pose::rna::RNA_SecStruct::blank() const –> bool

check_compatible_with_sequence(*args, **kwargs)¶

Overloaded function.

check_compatible_with_sequence(self: pyrosetta.rosetta.core.pose.rna.RNA_SecStruct, sequence_in: str) -> None
check_compatible_with_sequence(self: pyrosetta.rosetta.core.pose.rna.RNA_SecStruct, sequence_in: str, check_complementarity: bool) -> None

C++: core::pose::rna::RNA_SecStruct::check_compatible_with_sequence(const std::string &, const bool) const –> void

in_helix(self: pyrosetta.rosetta.core.pose.rna.RNA_SecStruct, i: int) → bool¶: C++: core::pose::rna::RNA_SecStruct::in_helix(const unsigned long &) const –> bool

in_same_helix(self: pyrosetta.rosetta.core.pose.rna.RNA_SecStruct, i: int, j: int) → bool¶: C++: core::pose::rna::RNA_SecStruct::in_same_helix(const unsigned long &, const unsigned long &) const –> bool

remove_pair(self: pyrosetta.rosetta.core.pose.rna.RNA_SecStruct, pair: Tuple[int, int]) → None¶: C++: core::pose::rna::RNA_SecStruct::remove_pair(struct std::pair<unsigned long, unsigned long>) –> void

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

secstruct(self: pyrosetta.rosetta.core.pose.rna.RNA_SecStruct) → str¶: C++: core::pose::rna::RNA_SecStruct::secstruct() const –> std::string

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

stems(self: pyrosetta.rosetta.core.pose.rna.RNA_SecStruct) → pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t¶: C++: core::pose::rna::RNA_SecStruct::stems() const –> class utility::vector1<class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >, class std::allocator<class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > > >

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

Bases: pybind11_object

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 &

property dist¶

property name¶

property suiteness¶

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

Bases: pybind11_object

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 &

property classifier¶

property name¶

property torsion¶

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

Bases: pybind11_object

property alphamax¶

property alphamin¶

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

property betamax¶

property betamin¶

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

property delta2max¶

property delta2min¶

property delta3max¶

property delta3min¶

property delta_cutoff¶

property epsilonmax¶

property epsilonmin¶

property gamma_cutoff1¶

property gamma_cutoff2¶

property gammammax¶

property gammammin¶

property gammapmax¶

property gammapmin¶

property gammatmax¶

property gammatmin¶

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 std::string &) const –> class core::pose::rna::RNA_SuiteInfo

property zetamax¶

property zetamin¶

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

Bases: 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 ]

Members:

NONE

BASE_CENTROID

O3P_TO_O5P

CHAINBREAK

BASE_CENTROID = <StubStubType.BASE_CENTROID: 1>¶

CHAINBREAK = <StubStubType.CHAINBREAK: 3>¶

NONE = <StubStubType.NONE: 0>¶

O3P_TO_O5P = <StubStubType.O3P_TO_O5P: 2>¶

property name¶

property value¶

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

Bases: pybind11_object

Members:

FIVE_PRIME

THREE_PRIME

FIVE_PRIME = <Terminus.FIVE_PRIME: 0>¶

THREE_PRIME = <Terminus.THREE_PRIME: 1>¶

property name¶

property value¶

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

Bases: pybind11_object

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

get_atom_bin_size(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid) → float¶: C++: core::pose::rna::VDW_Grid::get_atom_bin_size() const –> double

get_bin(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid, x: int, y: int, z: int) → bool¶: C++: core::pose::rna::VDW_Grid::get_bin(const int, const int, const int) const –> bool

get_bin_max(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid) → int¶: C++: core::pose::rna::VDW_Grid::get_bin_max() const –> int

get_bin_offset(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid) → int¶: C++: core::pose::rna::VDW_Grid::get_bin_offset() const –> int

get_ref_xyz(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: core::pose::rna::VDW_Grid::get_ref_xyz() const –> class numeric::xyzVector<double>

get_xyz_bin(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid, xyz_bin: pyrosetta.rosetta.core.pose.rna.Atom_Bin) → bool¶: C++: core::pose::rna::VDW_Grid::get_xyz_bin(const struct core::pose::rna::Atom_Bin &) const –> bool

is_occupied(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid) → bool¶: C++: core::pose::rna::VDW_Grid::is_occupied() const –> bool

reset(*args, **kwargs)¶

Overloaded function.

reset(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid) -> None

C++: core::pose::rna::VDW_Grid::reset() const –> void

reset(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid, occupied_xyz_bins_: pyrosetta.rosetta.utility.vector1_core_pose_rna_Atom_Bin) -> None

C++: core::pose::rna::VDW_Grid::reset(const class utility::vector1<struct core::pose::rna::Atom_Bin, class std::allocator<struct core::pose::rna::Atom_Bin> > &) const –> void

set_atom_bin_size(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid, value: float) → None¶: C++: core::pose::rna::VDW_Grid::set_atom_bin_size(const double) const –> void

set_bin(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid, x: int, y: int, z: int, value: bool) → None¶: C++: core::pose::rna::VDW_Grid::set_bin(const int, const int, const int, const bool) const –> void

set_bin_max(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid, value: int) → None¶: C++: core::pose::rna::VDW_Grid::set_bin_max(const int) const –> void

set_bin_offset(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid, value: int) → None¶: C++: core::pose::rna::VDW_Grid::set_bin_offset(const int) const –> void

set_ref_xyz(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid, value: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::pose::rna::VDW_Grid::set_ref_xyz(const class numeric::xyzVector<double> &) const –> void

set_xyz_bin(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid, xyz_bin: pyrosetta.rosetta.core.pose.rna.Atom_Bin, value: bool) → None¶: C++: core::pose::rna::VDW_Grid::set_xyz_bin(const struct core::pose::rna::Atom_Bin &, const bool) const –> void

setup(self: pyrosetta.rosetta.core.pose.rna.VDW_Grid, bin_max: int) → None¶: C++: core::pose::rna::VDW_Grid::setup(const int) const –> void

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

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

Bases: pybind11_object

property VDW_align_res¶

property VDW_ignore_res¶

property VDW_pose¶

property align_working_to_vdw_atom_id_map¶

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

property full_align_res¶

property import_ID¶

property in_root_partition¶

property input_string¶

property pose_name¶

property working_align_res¶

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: pyrosetta.rosetta.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: pyrosetta.rosetta.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.assert_phosphate_nomenclature_matches_mini(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::pose::rna::assert_phosphate_nomenclature_matches_mini(const class core::pose::Pose &) –> 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.base_pair_moving(base_pair: pyrosetta.rosetta.core.pose.rna.BasePair, atom_level_domain_map: core::pose::toolbox::AtomLevelDomainMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: core::pose::rna::base_pair_moving(const class core::pose::rna::BasePair &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>, const class core::pose::Pose &) –> bool

pyrosetta.rosetta.core.pose.rna.base_pair_step_moving(base_pair_step: pyrosetta.rosetta.core.pose.rna.BasePairStep, atom_level_domain_map: core::pose::toolbox::AtomLevelDomainMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: core::pose::rna::base_pair_step_moving(const class core::pose::rna::BasePairStep &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>, const class core::pose::Pose &) –> bool

pyrosetta.rosetta.core.pose.rna.check_in_base_pair_list(base_pair: pyrosetta.rosetta.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.check_phosphate_contacts_donor(*args, **kwargs)¶

Overloaded function.

check_phosphate_contacts_donor(op_xyz_list: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, donor_atom_xyz_list: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, donor_base_atom_xyz_list: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) -> bool

C++: core::pose::rna::check_phosphate_contacts_donor(const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> bool

check_phosphate_contacts_donor(pose: pyrosetta.rosetta.core.pose.Pose, n: int) -> bool

C++: core::pose::rna::check_phosphate_contacts_donor(const class core::pose::Pose &, const unsigned long) –> 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.detect_base_contacts(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::pose::rna::detect_base_contacts(const class core::pose::Pose &) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.core.pose.rna.detect_phosphate_contacts(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::pose::rna::detect_phosphate_contacts(const class core::pose::Pose &) –> class utility::vector1<bool, class std::allocator<bool> >

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

Overloaded function.

detect_sugar_contacts(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_bool

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

detect_sugar_contacts(pose: pyrosetta.rosetta.core.pose.Pose, moving_res: int) -> bool
detect_sugar_contacts(pose: pyrosetta.rosetta.core.pose.Pose, moving_res: int, o2prime_contact_distance_cutoff_: float) -> bool

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

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

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

Overloaded function.

fill_in_default_jump_atoms(f: pyrosetta.rosetta.core.kinematics.FoldTree, pose: pyrosetta.rosetta.core.pose.Pose) -> None

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

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

C++: core::pose::rna::fill_in_default_jump_atoms(class core::pose::Pose &) –> 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<std::string, class std::allocator<std::string > >, 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_base_pairing_info(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, secstruct: str, edge_is_base_pairing: pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t) → None¶: C++: core::pose::rna::get_base_pairing_info(const class core::pose::Pose &, const unsigned long &, char &, class ObjexxFCL::FArray1D<bool> &) –> void

pyrosetta.rosetta.core.pose.rna.get_base_pairing_list(pose: pyrosetta.rosetta.core.pose.Pose, base_pairing_list: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → None¶: C++: core::pose::rna::get_base_pairing_list(class core::pose::Pose &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> void

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_phosphate_atom_and_neighbor_list(pose: pyrosetta.rosetta.core.pose.Pose, n: int, t: pyrosetta.rosetta.core.pose.rna.Terminus, donor_atom_xyz_list: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, donor_base_atom_xyz_list: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, neighbor_copy_dofs: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::pose::rna::get_phosphate_atom_and_neighbor_list(const class core::pose::Pose &, const unsigned long, const enum core::pose::rna::Terminus, class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

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_rigid_body_jumps(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::pose::rna::get_rigid_body_jumps(const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.pose.rna.get_scored_base_stack_list(pose_input: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BaseStack_t¶: C++: core::pose::rna::get_scored_base_stack_list(const class core::pose::Pose &) –> class std::list<struct std::pair<double, class core::pose::rna::BaseStack>, class std::allocator<struct std::pair<double, class core::pose::rna::BaseStack> > >

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_sugar_centroid(rsd: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: core::pose::rna::get_sugar_centroid(const class core::conformation::Residue &) –> class numeric::xyzVector<double>

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<std::string, class std::allocator<std::string > > &, 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_tna_chainbreak(pose: pyrosetta.rosetta.core.pose.Pose, i: int) → bool¶: C++: core::pose::rna::is_tna_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.moveable_jump(*args, **kwargs)¶

Overloaded function.

moveable_jump(jump_atom_id1: pyrosetta.rosetta.core.id.AtomID, jump_atom_id2: pyrosetta.rosetta.core.id.AtomID, atom_level_domain_map: core::pose::toolbox::AtomLevelDomainMap) -> bool

C++: core::pose::rna::moveable_jump(const class core::id::AtomID &, const class core::id::AtomID &, const class core::pose::toolbox::AtomLevelDomainMap &) –> bool

moveable_jump(jump_pos1: int, jump_pos2: int, atom_level_domain_map: core::pose::toolbox::AtomLevelDomainMap) -> bool

C++: core::pose::rna::moveable_jump(const unsigned long, const unsigned long, const class core::pose::toolbox::AtomLevelDomainMap &) –> bool

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 std::string &) –> 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_base_pairs(out: pyrosetta.rosetta.std.ostream, base_pair_list: pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Output base pairs detected for RNA, including noncanonicals. Must previously score pose with RNA_LORES.

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

pyrosetta.rosetta.core.pose.rna.output_base_stacks(out: pyrosetta.rosetta.std.ostream, base_stack_list: pyrosetta.rosetta.utility.vector1_core_pose_rna_BaseStack, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Output base stacks detected for RNA. Must previously score pose with RNA_LORES.

C++: core::pose::rna::output_base_stacks(std::ostream &, const class utility::vector1<class core::pose::rna::BaseStack, class std::allocator<class core::pose::rna::BaseStack> > &, const class core::pose::Pose &) –> void

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

pyrosetta.rosetta.core.pose.rna.output_other_contacts(out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Output residue-residue interactions that are not base pairs or base stacks;

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

pyrosetta.rosetta.core.pose.rna.output_stems(out: pyrosetta.rosetta.std.ostream, rna_motifs: core::scoring::rna::RNA_Motifs, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Output stems (>=2 base-pair helices) detected for RNA, including noncanonicals. Must previously score pose with RNA_LORES.

C++: core::pose::rna::output_stems(std::ostream &, const class core::scoring::rna::RNA_Motifs &, const class core::pose::Pose &) –> 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 std::string &, std::string &, class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &) –> void

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

pyrosetta.rosetta.core.pose.rna.remove_upper_lower_variants_from_RNA(pose: pyrosetta.rosetta.core.pose.Pose) → None¶

get rid of Upper and Lower from RNA; useful for cleaner output of annotated_sequence.

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

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.setup_base_pair_constraints(*args, **kwargs)¶

Overloaded function.

setup_base_pair_constraints(pose: pyrosetta.rosetta.core.pose.Pose, pairings: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> None
setup_base_pair_constraints(pose: pyrosetta.rosetta.core.pose.Pose, pairings: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, scale_factor: float) -> None
setup_base_pair_constraints(pose: pyrosetta.rosetta.core.pose.Pose, pairings: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, scale_factor: float, use_flat_harmonic: bool) -> None

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

pyrosetta.rosetta.core.pose.rna.setup_three_prime_phosphate_based_on_next_residue(pose: pyrosetta.rosetta.core.pose.Pose, n: int) → None¶: C++: core::pose::rna::setup_three_prime_phosphate_based_on_next_residue(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 std::string &) –> unsigned long

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

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