utils

Bindings for protocols::fold_from_loops::utils namespace

class pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub

Bases: pybind11_object

apply(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, pose: pyrosetta.rosetta.core.pose.Pose, template_selection: pyrosetta.rosetta.utility.vector1_bool, template_pieces: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, disulfides: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → None

Produces the unfolded pose

C++: protocols::fold_from_loops::utils::Nub::apply(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<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> > > &) –> void

apply_binder_selector(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: protocols::fold_from_loops::utils::Nub::apply_binder_selector(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

apply_binder_selector_as_ranges(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.select.residue_selector.ResidueRanges

C++: protocols::fold_from_loops::utils::Nub::apply_binder_selector_as_ranges(const class core::pose::Pose &) const –> class core::select::residue_selector::ResidueRanges

apply_selector(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: protocols::fold_from_loops::utils::Nub::apply_selector(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

apply_selector_as_ranges(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.select.residue_selector.ResidueRanges

C++: protocols::fold_from_loops::utils::Nub::apply_selector_as_ranges(const class core::pose::Pose &) const –> class core::select::residue_selector::ResidueRanges

assign(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, : pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) → pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub

C++: protocols::fold_from_loops::utils::Nub::operator=(const class protocols::fold_from_loops::utils::Nub &) –> class protocols::fold_from_loops::utils::Nub &

binder_selector(*args, **kwargs)

Overloaded function.

1. binder_selector(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::fold_from_loops::utils::Nub::binder_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

2. binder_selector(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::fold_from_loops::utils::Nub::binder_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

static coldspot_label() → str

C++: protocols::fold_from_loops::utils::Nub::coldspot_label() –> std::string

static complex_object_name(tag_name: str) → str

C++: protocols::fold_from_loops::utils::Nub::complex_object_name(std::string) –> std::string

static contact_label() → str

C++: protocols::fold_from_loops::utils::Nub::contact_label() –> std::string

static context_label() → str

C++: protocols::fold_from_loops::utils::Nub::context_label() –> std::string

default_flexibility(*args, **kwargs)

Overloaded function.

1. default_flexibility(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) -> int

C++: protocols::fold_from_loops::utils::Nub::default_flexibility() const –> unsigned long

2. default_flexibility(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, pick: int) -> None

C++: protocols::fold_from_loops::utils::Nub::default_flexibility(unsigned long) –> void

static default_selector() → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::fold_from_loops::utils::Nub::default_selector() –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

design_chain(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) → str

C++: protocols::fold_from_loops::utils::Nub::design_chain() const –> std::string

design_size(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) → int

C++: protocols::fold_from_loops::utils::Nub::design_size() const –> unsigned long

static disulfide_label() → str

C++: protocols::fold_from_loops::utils::Nub::disulfide_label() –> std::string

disulfides(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

C++: protocols::fold_from_loops::utils::Nub::disulfides() const –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

static flexible_label() → str

C++: protocols::fold_from_loops::utils::Nub::flexible_label() –> std::string

has_binder(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) → bool

C++: protocols::fold_from_loops::utils::Nub::has_binder() const –> bool

static hotspot_label() → str

C++: protocols::fold_from_loops::utils::Nub::hotspot_label() –> std::string

is_multisegment(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) → bool

C++: protocols::fold_from_loops::utils::Nub::is_multisegment() const –> bool

large_fragments(*args, **kwargs)

Overloaded function.

1. large_fragments(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) -> pyrosetta.rosetta.core.fragment.FragSet

C++: protocols::fold_from_loops::utils::Nub::large_fragments() const –> class std::shared_ptr<class core::fragment::FragSet>

2. large_fragments(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, fragset: pyrosetta.rosetta.core.fragment.FragSet) -> None

C++: protocols::fold_from_loops::utils::Nub::large_fragments(class std::shared_ptr<class core::fragment::FragSet>) –> void

static motif_label() → str

C++: protocols::fold_from_loops::utils::Nub::motif_label() –> std::string

movemap(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) → pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::fold_from_loops::utils::Nub::movemap() const –> class std::shared_ptr<class core::kinematics::MoveMap>

movemapfactory(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) → pyrosetta.rosetta.core.select.movemap.MoveMapFactory

C++: protocols::fold_from_loops::utils::Nub::movemapfactory() const –> class std::shared_ptr<class core::select::movemap::MoveMapFactory>

static object_name() → str

C++: protocols::fold_from_loops::utils::Nub::object_name() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::fold_from_loops::utils::Nub::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pieces(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t

C++: protocols::fold_from_loops::utils::Nub::pieces() const –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

static provide_xml_definition(xsd: utility::tag::XMLSchemaDefinition, elements: utility::tag::XMLSchemaSimpleSubelementList) → None

C++: protocols::fold_from_loops::utils::Nub::provide_xml_definition(class utility::tag::XMLSchemaDefinition &, class utility::tag::XMLSchemaSimpleSubelementList &) –> void

reference_pose(*args, **kwargs)

Overloaded function.

1. reference_pose(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::fold_from_loops::utils::Nub::reference_pose() const –> class std::shared_ptr<class core::pose::Pose>

2. reference_pose(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::fold_from_loops::utils::Nub::reference_pose(const class std::shared_ptr<class core::pose::Pose> &) –> void

refit_motif_sidechains(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::fold_from_loops::utils::Nub::refit_motif_sidechains(class core::pose::Pose &) –> void

static segment_object_name() → str

C++: protocols::fold_from_loops::utils::Nub::segment_object_name() –> std::string

selector(*args, **kwargs)

Overloaded function.

1. selector(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::fold_from_loops::utils::Nub::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

2. selector(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::fold_from_loops::utils::Nub::selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

small_fragments(*args, **kwargs)

Overloaded function.

1. small_fragments(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) -> pyrosetta.rosetta.core.fragment.FragSet

C++: protocols::fold_from_loops::utils::Nub::small_fragments() const –> class std::shared_ptr<class core::fragment::FragSet>

2. small_fragments(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, fragset: pyrosetta.rosetta.core.fragment.FragSet) -> None

C++: protocols::fold_from_loops::utils::Nub::small_fragments(class std::shared_ptr<class core::fragment::FragSet>) –> void

static template_label() → str

C++: protocols::fold_from_loops::utils::Nub::template_label() –> std::string

template_to_unfolded_mapping(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) → pyrosetta.rosetta.core.id.SequenceMapping

C++: protocols::fold_from_loops::utils::Nub::template_to_unfolded_mapping() const –> class core::id::SequenceMapping

transfer_unfolded_conformation(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::fold_from_loops::utils::Nub::transfer_unfolded_conformation(class core::pose::Pose &) –> void

unfolded_jump(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) → int

C++: protocols::fold_from_loops::utils::Nub::unfolded_jump() const –> unsigned long

unfolded_pose(self: pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::fold_from_loops::utils::Nub::unfolded_pose() const –> class std::shared_ptr<class core::pose::Pose>

class pyrosetta.rosetta.protocols.fold_from_loops.utils.NubSegment

Bases: pybind11_object

property c_flex

property coldspots

property n_flex

property order

pyrosetta.rosetta.protocols.fold_from_loops.utils.append_pose_to_pose_keep_fold_tree(scaffold: pyrosetta.rosetta.core.pose.Pose, insert: pyrosetta.rosetta.core.pose.Pose, new_chain: bool) → None

Basically works as ‘core::pose::append_pose_to_pose’ but the FoldTree is build by joining by jump the

root of ‘insert’ FoldTree to that of ‘scaffold’ FoldTree. PDBInfo is lost.

C++: protocols::fold_from_loops::utils::append_pose_to_pose_keep_fold_tree(class core::pose::Pose &, const class core::pose::Pose &, bool) –> void

pyrosetta.rosetta.protocols.fold_from_loops.utils.attach_n_and_c_unfolded_poses_to_pose(n_insert: pyrosetta.rosetta.core.pose.Pose, scaffold: pyrosetta.rosetta.core.pose.Pose, c_insert: pyrosetta.rosetta.core.pose.Pose) → None

To a given scaffold it attaches a unfolded version of a pose to the N-terminal and another to the C-terminal

Generates a FoldTree that goes from the middle of ‘scaffold’ towards both directions

C++: protocols::fold_from_loops::utils::attach_n_and_c_unfolded_poses_to_pose(const class core::pose::Pose &, class core::pose::Pose &, const class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.fold_from_loops.utils.attach_unfolded_pose_to_pose_c_term(insert: pyrosetta.rosetta.core.pose.Pose, scaffold: pyrosetta.rosetta.core.pose.Pose, rsd_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → None

adds the ‘insert’ unfolded pose to the C-terminal of the provided pose

C++: protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_c_term(const class core::pose::Pose &, class core::pose::Pose &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> void

pyrosetta.rosetta.protocols.fold_from_loops.utils.attach_unfolded_pose_to_pose_n_term(insert: pyrosetta.rosetta.core.pose.Pose, scaffold: pyrosetta.rosetta.core.pose.Pose, rsd_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → None

adds the ‘insert’ unfolded pose to the N-terminal of the provided pose

C++: protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_n_term(const class core::pose::Pose &, class core::pose::Pose &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> void

pyrosetta.rosetta.protocols.fold_from_loops.utils.find_cutpoint_from_secondary_structure(structure: str) → int

Given a Secondary Structure definition as a string, it finds what

it considers the optimal cutpoint. This means that, if there is no loop ‘L’ segment it will return the middle point as a residue; otherwise it will try to split the larger loop ‘L’ region.

C++: protocols::fold_from_loops::utils::find_cutpoint_from_secondary_structure(std::string) –> unsigned long

pyrosetta.rosetta.protocols.fold_from_loops.utils.map_by_residue_subsets(p1: pyrosetta.rosetta.core.pose.Pose, r1: pyrosetta.rosetta.utility.vector1_bool, p2: pyrosetta.rosetta.core.pose.Pose, r2: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.core.id.SequenceMapping

Creates a sequence mapping betwee two proteins assuming that the False selections on a ResidueSubset

marks the residues that are the same for both of them. Assumes the same number of non-selected patches for each pose.

C++: protocols::fold_from_loops::utils::map_by_residue_subsets(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) –> class core::id::SequenceMapping

pyrosetta.rosetta.protocols.fold_from_loops.utils.report_unfolded(pose: pyrosetta.rosetta.core.pose.Pose, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None

@ brief reports the conditions of the pose

C++: protocols::fold_from_loops::utils::report_unfolded(const class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> void

pyrosetta.rosetta.protocols.fold_from_loops.utils.split_mid_ranges(structure: str, ranges: pyrosetta.rosetta.core.select.residue_selector.ResidueRanges) → pyrosetta.rosetta.core.select.residue_selector.ResidueRanges

It will take each range that is not the first or the last one

and split it into two, following the logic of `find_cutpoint_from_secondary_structure` Input Ranges are not modified, a new ResidueRanges is returned. WARNING1: When splitting a range of 1 residue, it splits into 1 range of 1 and another from 0 to 0, so that it is easy to filter afterwards ( for the purpose of NubInitio, this means adding and empty pose to the vector, for example ). WARNING2: If the first ResidueRange does not start with 1, an empty_range (0,0) is set at the begining too.

C++: protocols::fold_from_loops::utils::split_mid_ranges(std::string, const class core::select::residue_selector::ResidueRanges &) –> class core::select::residue_selector::ResidueRanges