denovo¶

Bindings for protocols::rna::denovo namespace

class pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer¶

Bases: pybind11_builtins.pybind11_object

Object used in RNA_FragmentMonteCarlo to handle setup of pose & fold-tree, and: jump changes.

initialize_for_de_novo_protocol(*args, **kwargs)¶

Overloaded function.

initialize_for_de_novo_protocol(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, pose: pyrosetta.rosetta.core.pose.Pose) -> None
initialize_for_de_novo_protocol(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, pose: pyrosetta.rosetta.core.pose.Pose, ignore_secstruct: bool) -> None

“classic” setup, used in denovo protocol. Note: changes pose (virtualizes phosphate).: and requires later call of setup_fold_tree_and_jumps_and_variants

C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_for_de_novo_protocol(class core::pose::Pose &, const bool) –> void

model_with_density(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer) → bool¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::model_with_density() const –> bool

new_fold_tree_initializer(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer) → bool¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::new_fold_tree_initializer() const –> bool

rna_params(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer) → pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::rna_params() const –> const class core::import_pose::RNA_DeNovoParameters &

set_bps_moves(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_bps_moves(const bool &) –> void

set_center_jumps_in_single_stranded(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_center_jumps_in_single_stranded(const bool &) –> void

set_dock_each_chunk(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_dock_each_chunk(const bool &) –> void

set_dock_each_chunk_per_chain(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_dock_each_chunk_per_chain(const bool &) –> void

set_model_with_density(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_model_with_density(const bool &) –> void

set_new_fold_tree_initializer(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_new_fold_tree_initializer(const bool &) –> void

set_root_at_first_rigid_body(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, setting: bool) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_root_at_first_rigid_body(const bool) –> void

setup_chainbreak_variants(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap) → None¶: C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(class core::pose::Pose &, class std::shared_ptr<class core::pose::toolbox::AtomLevelDomainMap>) const –> void

setup_fold_tree_and_jumps_and_variants(*args, **kwargs)¶

Overloaded function.

setup_fold_tree_and_jumps_and_variants(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, pose: pyrosetta.rosetta.core.pose.Pose, rna_jump_mover: pyrosetta.rosetta.core.import_pose.RNA_JumpMover, atom_level_domain_map: pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap, rna_chunk_library: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary) -> None
setup_fold_tree_and_jumps_and_variants(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, pose: pyrosetta.rosetta.core.pose.Pose, rna_jump_mover: pyrosetta.rosetta.core.import_pose.RNA_JumpMover, atom_level_domain_map: pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap, rna_chunk_library: pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary, enumerate: bool) -> None

C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_and_jumps_and_variants(class core::pose::Pose &, const class core::import_pose::RNA_JumpMover &, class std::shared_ptr<class core::pose::toolbox::AtomLevelDomainMap>, const class core::import_pose::libraries::RNA_ChunkLibrary &, const bool &) const –> void

setup_fold_tree_and_jumps_and_variants(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_and_jumps_and_variants(class core::pose::Pose &) const –> void

class pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

The RNA de novo structure modeling protocol

align_and_output_to_silent_file(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, pose: pyrosetta.rosetta.core.pose.Pose, silent_file: str, out_file_tag: str) → None¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::align_and_output_to_silent_file(class core::pose::Pose &, const class std::basic_string<char> &, const class std::basic_string<char> &) const –> void

apply(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the RNA denovo modeling protocol to the input pose

C++: protocols::rna::denovo::RNA_DeNovoProtocol::apply(class core::pose::Pose &) –> void

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

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol) → pyrosetta.rosetta.protocols.moves.Mover¶

Clone this object

C++: protocols::rna::denovo::RNA_DeNovoProtocol::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

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

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

name() → str¶: C++: protocols::moves::Mover::name() –> std::string

options(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol) → pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::options() const –> class std::shared_ptr<const class core::import_pose::options::RNA_DeNovoProtocolOptions>

output_to_silent_file(*args, **kwargs)¶

Overloaded function.

output_to_silent_file(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, pose: pyrosetta.rosetta.core.pose.Pose, silent_file: str, out_file_tag: str) -> None
output_to_silent_file(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, pose: pyrosetta.rosetta.core.pose.Pose, silent_file: str, out_file_tag: str, score_only: bool) -> None

C++: protocols::rna::denovo::RNA_DeNovoProtocol::output_to_silent_file(class core::pose::Pose &, const class std::basic_string<char> &, const class std::basic_string<char> &, const bool) const –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, movers: pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

rna_fragment_monte_carlo(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol) → protocols::rna::denovo::RNA_FragmentMonteCarlo¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::rna_fragment_monte_carlo() const –> class std::shared_ptr<const class protocols::rna::denovo::RNA_FragmentMonteCarlo>

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶

////////////////////////////end Job Distributor interface////////////////////////////////////////

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const class std::basic_string<char> &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_refine_pose_list(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, setting: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) → None¶: C++: protocols::rna::denovo::RNA_DeNovoProtocol::set_refine_pose_list(const class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶: C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol) -> None
show(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::rna::denovo::RNA_DeNovoProtocol::show(class std::basic_ostream<char> &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

C++: protocols::moves::Mover::type() const –> const std::string &

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.rna.denovo.check_base_pair(pose: pyrosetta.rosetta.core.pose.Pose, struct_type: ObjexxFCL::FArray1D<int>) → None¶: C++: protocols::rna::denovo::check_base_pair(class core::pose::Pose &, class ObjexxFCL::FArray1D<int> &) –> void

pyrosetta.rosetta.protocols.rna.denovo.classify_base_pairs_lores(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair¶: C++: protocols::rna::denovo::classify_base_pairs_lores(const class core::pose::Pose &) –> class utility::vector1<class core::pose::rna::BasePair, class std::allocator<class core::pose::rna::BasePair> >

pyrosetta.rosetta.protocols.rna.denovo.create_rna_vall_torsions(*args, **kwargs)¶

Overloaded function.

create_rna_vall_torsions(pose: pyrosetta.rosetta.core.pose.Pose, torsions_out: pyrosetta.rosetta.utility.io.ozstream, exclude_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::rna::denovo::create_rna_vall_torsions(class core::pose::Pose &, class utility::io::ozstream &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

create_rna_vall_torsions(pose: pyrosetta.rosetta.core.pose.Pose, outfile: str, exclude_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

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

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

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

pyrosetta.rosetta.protocols.rna.denovo.export_packer_results(*args, **kwargs)¶

Overloaded function.

export_packer_results(results: pyrosetta.rosetta.utility.vector1_std_pair_double_std_string_t, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, outfile: str) -> None
export_packer_results(results: pyrosetta.rosetta.utility.vector1_std_pair_double_std_string_t, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, outfile: str, dumo: bool) -> None

C++: protocols::rna::denovo::export_packer_results(class utility::vector1<struct std::pair<double, class std::basic_string<char> >, class std::allocator<struct std::pair<double, class std::basic_string<char> > > > &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >, class std::shared_ptr<class core::scoring::ScoreFunction> &, const class std::basic_string<char> &, const bool) –> void

pyrosetta.rosetta.protocols.rna.denovo.figure_out_base_pair_partner(*args, **kwargs)¶

Overloaded function.

figure_out_base_pair_partner(pose: pyrosetta.rosetta.core.pose.Pose, partner: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) -> None
figure_out_base_pair_partner(pose: pyrosetta.rosetta.core.pose.Pose, partner: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, strict: bool) -> None

C++: protocols::rna::denovo::figure_out_base_pair_partner(class core::pose::Pose &, class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const bool) –> void

pyrosetta.rosetta.protocols.rna.denovo.get_moving_res(pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::rna::denovo::get_moving_res(const class core::pose::Pose &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.rna.denovo.get_residues_within_dist_of_RNA(pose: pyrosetta.rosetta.core.pose.Pose, dist_cutoff: float) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::rna::denovo::get_residues_within_dist_of_RNA(const class core::pose::Pose &, const double &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.rna.denovo.get_rna_hires_scorefxn(*args, **kwargs)¶

Overloaded function.

get_rna_hires_scorefxn() -> pyrosetta.rosetta.core.scoring.ScoreFunction
get_rna_hires_scorefxn(include_protein_terms: bool) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::rna::denovo::get_rna_hires_scorefxn(const bool &) –> class std::shared_ptr<class core::scoring::ScoreFunction>

pyrosetta.rosetta.protocols.rna.denovo.get_rnp_docking_fold_tree(*args, **kwargs)¶

Overloaded function.

get_rnp_docking_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.FoldTree
get_rnp_docking_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, with_density: bool) -> pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::rna::denovo::get_rnp_docking_fold_tree(const class core::pose::Pose &, const bool &) –> class core::kinematics::FoldTree

pyrosetta.rosetta.protocols.rna.denovo.involved_in_phosphate_torsion(atomname: str) → bool¶: C++: protocols::rna::denovo::involved_in_phosphate_torsion(const class std::basic_string<char> &) –> bool

pyrosetta.rosetta.protocols.rna.denovo.is_num_in_list(i: int, list: pyrosetta.rosetta.utility.vector1_unsigned_long) → bool¶: C++: protocols::rna::denovo::is_num_in_list(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool

pyrosetta.rosetta.protocols.rna.denovo.let_rigid_body_jumps_move(*args, **kwargs)¶

Overloaded function.

let_rigid_body_jumps_move(movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
let_rigid_body_jumps_move(movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, move_first_rigid_body: bool) -> bool
let_rigid_body_jumps_move(movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, move_first_rigid_body: bool, allow_first_rigid_body: bool) -> bool

C++: protocols::rna::denovo::let_rigid_body_jumps_move(class core::kinematics::MoveMap &, const class core::pose::Pose &, const bool &, const bool &) –> bool

pyrosetta.rosetta.protocols.rna.denovo.possible_root(f: pyrosetta.rosetta.core.kinematics.FoldTree, n: int) → bool¶: C++: protocols::rna::denovo::possible_root(const class core::kinematics::FoldTree &, const unsigned long &) –> bool

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

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

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

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

pyrosetta.rosetta.protocols.rna.denovo.virtualize_bulges(input_pose: pyrosetta.rosetta.core.pose.Pose, in_allow_bulge_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, tag: str, allow_pre_virtualize: bool, allow_consecutive_bulges: bool, verbose: bool) → int¶: C++: protocols::rna::denovo::virtualize_bulges(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class std::shared_ptr<const class core::scoring::ScoreFunction> &, const class std::basic_string<char> &, const bool, const bool, const bool) –> unsigned long