denovo

• base_pairs
• coarse
• fragments
• libraries
• movers
• options
• output
• secstruct_legacy
• setup

Bindings for protocols::rna::denovo namespace

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

Bases: pyrosetta.rosetta.protocols.moves.Mover

The RNA de novo structure modeling protocol

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, arg0: protocols::rna::denovo::options::RNA_DeNovoProtocolOptions) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, options: protocols::rna::denovo::options::RNA_DeNovoProtocolOptions, params: pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoParameters) -> None
4. __init__(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol, arg0: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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) → protocols::rna::denovo::options::RNA_DeNovoProtocolOptions

C++: protocols::rna::denovo::RNA_DeNovoProtocol::options() const –> class std::shared_ptr<const class protocols::rna::denovo::options::RNA_DeNovoProtocolOptions>

output_to_silent_file(*args, **kwargs)

Overloaded function.

1. 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
2. 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

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.

1. show(self: pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol) -> None
2. 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.

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

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

2. 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.base_pair_moving(base_pair: pyrosetta.rosetta.core.pose.rna.BasePair, atom_level_domain_map: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::rna::denovo::base_pair_moving(const class core::pose::rna::BasePair &, class std::shared_ptr<const class protocols::toolbox::AtomLevelDomainMap>, const class core::pose::Pose &) –> bool

pyrosetta.rosetta.protocols.rna.denovo.base_pair_step_moving(base_pair_step: pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep, atom_level_domain_map: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::rna::denovo::base_pair_step_moving(const class protocols::rna::denovo::base_pairs::BasePairStep &, class std::shared_ptr<const class protocols::toolbox::AtomLevelDomainMap>, const class core::pose::Pose &) –> bool

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.compare_RNA_char(char1: str, char2: str) → bool

C++: protocols::rna::denovo::compare_RNA_char(const char, const char) –> bool

pyrosetta.rosetta.protocols.rna.denovo.compare_RNA_secstruct(char1: str, char2: str) → bool

C++: protocols::rna::denovo::compare_RNA_secstruct(const char, const char) –> bool

pyrosetta.rosetta.protocols.rna.denovo.convert_based_on_match_type(RNA_string: str, type: int) → str

C++: protocols::rna::denovo::convert_based_on_match_type(const class std::basic_string<char> &, const unsigned long) –> const std::string

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

Overloaded function.

1. 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

2. 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.

1. 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
2. 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.

1. figure_out_base_pair_partner(pose: pyrosetta.rosetta.core.pose.Pose, partner: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) -> None
2. 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.figure_out_secstruct(pose: pyrosetta.rosetta.core.pose.Pose) → None

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

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

Overloaded function.

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

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

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

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

pyrosetta.rosetta.protocols.rna.denovo.get_anchor_rsd(pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::rna::denovo::get_anchor_rsd(const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.rna.denovo.get_base_pairing_info(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, secstruct: str, edge_is_base_pairing: ObjexxFCL::FArray1D<bool>) → None

C++: protocols::rna::denovo::get_base_pairing_info(const class core::pose::Pose &, const unsigned long &, char &, class ObjexxFCL::FArray1D<bool> &) –> void

pyrosetta.rosetta.protocols.rna.denovo.get_moving_res(pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: pyrosetta.rosetta.protocols.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 protocols::toolbox::AtomLevelDomainMap>) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.rna.denovo.get_rigid_body_jumps(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

pyrosetta.rosetta.protocols.rna.denovo.get_rna_hires_scorefxn() → pyrosetta.rosetta.core.scoring.ScoreFunction

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

pyrosetta.rosetta.protocols.rna.denovo.get_sugar_centroid(rsd: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::rna::denovo::get_sugar_centroid(const class core::conformation::Residue &) –> class numeric::xyzVector<double>

pyrosetta.rosetta.protocols.rna.denovo.involved_in_phosphate_torsion(atomname: str) → bool

C++: protocols::rna::denovo::involved_in_phosphate_torsion(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.

1. let_rigid_body_jumps_move(movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
2. let_rigid_body_jumps_move(movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, move_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) –> bool

pyrosetta.rosetta.protocols.rna.denovo.make_coarse_pose(pose: pyrosetta.rosetta.core.pose.Pose, coarse_pose: pyrosetta.rosetta.core.pose.Pose) → None

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

pyrosetta.rosetta.protocols.rna.denovo.make_extended_coarse_pose(coarse_pose: pyrosetta.rosetta.core.pose.Pose, full_sequence: str) → None

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

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

Overloaded function.

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

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

2. moveable_jump(jump_pos1: int, jump_pos2: int, atom_level_domain_map: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap) -> bool

C++: protocols::rna::denovo::moveable_jump(const unsigned long, const unsigned long, const class protocols::toolbox::AtomLevelDomainMap &) –> 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.process_input_file(*args, **kwargs)

Overloaded function.

1. process_input_file(silent_file: str, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> None
2. process_input_file(silent_file: str, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, is_pdb: bool) -> None
3. process_input_file(silent_file: str, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, is_pdb: bool, coarse_rna: bool) -> None

C++: protocols::rna::denovo::process_input_file(const 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> > > &, bool, bool) –> void

pyrosetta.rosetta.protocols.rna.denovo.remove_cutpoint_closed(pose: pyrosetta.rosetta.core.pose.Pose, i: int) → None

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

pyrosetta.rosetta.protocols.rna.denovo.remove_cutpoints_closed(pose: pyrosetta.rosetta.core.pose.Pose) → None

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

pyrosetta.rosetta.protocols.rna.denovo.set_output_res_and_chain(extended_pose: pyrosetta.rosetta.core.pose.Pose, output_resnum_and_chain_and_segid: Tuple[pyrosetta.rosetta.utility.vector1_int, pyrosetta.rosetta.utility.vector1_char, pyrosetta.rosetta.utility.vector1_std_string]) → None

C++: protocols::rna::denovo::set_output_res_and_chain(class core::pose::Pose &, const class std::tuple<class utility::vector1<int, class std::allocator<int> >, class utility::vector1<char, class std::allocator<char> >, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > > &) –> 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