legacy_sewing¶

Bindings for protocols::legacy_sewing namespace

class pyrosetta.rosetta.protocols.legacy_sewing.Assembly¶

Bases: pybind11_object

An Assembly is a collection of SewSegments. Assemblies are created using the geometric “compatibility” data generated by the Hasher.

add_loop_segment(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop, segment: int) → None¶: C++: protocols::legacy_sewing::Assembly::add_loop_segment(const class core::pose::Pose &, class protocols::loops::Loop, unsigned long) –> void

add_model(*args, **kwargs)¶

Overloaded function.

add_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, graph: protocols::legacy_sewing::SewGraph, model: pyrosetta.rosetta.protocols.legacy_sewing.Model) -> None
add_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, graph: protocols::legacy_sewing::SewGraph, model: pyrosetta.rosetta.protocols.legacy_sewing.Model, available: bool) -> None

Add a model to the Assembly. Only used for first node and special cases.

C++: protocols::legacy_sewing::Assembly::add_model(class std::shared_ptr<const class protocols::legacy_sewing::SewGraph>, const struct protocols::legacy_sewing::Model &, bool) –> void

align_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, mobile_model: pyrosetta.rosetta.protocols.legacy_sewing.Model, atom_alignments: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_model_id: int) → None¶: C++: protocols::legacy_sewing::Assembly::align_model(struct protocols::legacy_sewing::Model &, const class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > > &, int) const –> void

all_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_legacy_sewing_SewSegment_std_allocator_protocols_legacy_sewing_SewSegment_t¶: C++: protocols::legacy_sewing::Assembly::all_segments() const –> class utility::vector1<class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> >, class std::allocator<class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> > > >

append_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, model: pyrosetta.rosetta.protocols.legacy_sewing.Model, edge_score: Tuple[Tuple[pyrosetta.rosetta.protocols.legacy_sewing.Basis, pyrosetta.rosetta.protocols.legacy_sewing.Basis], pyrosetta.rosetta.protocols.legacy_sewing.HashResult]) → None¶

append the given model to the end of the assembly

C++: protocols::legacy_sewing::Assembly::append_model(const struct protocols::legacy_sewing::Model &, const struct std::pair<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> &) –> void

append_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, segments: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment) → None¶

append the segments to the given assembly. This should be used very infrequently. The normal way to add segments is to follow an edge

C++: protocols::legacy_sewing::Assembly::append_segments(const class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> > &) –> void

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

atom_map_from_score_result(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, alignment_scores: Tuple[Tuple[pyrosetta.rosetta.protocols.legacy_sewing.Basis, pyrosetta.rosetta.protocols.legacy_sewing.Basis], pyrosetta.rosetta.protocols.legacy_sewing.HashResult]) → pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID¶: C++: protocols::legacy_sewing::Assembly::atom_map_from_score_result(const struct std::pair<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> &) const –> class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > >

property blosum_history_¶

clone(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.protocols.legacy_sewing.Assembly¶: C++: protocols::legacy_sewing::Assembly::clone() –> class std::shared_ptr<class protocols::legacy_sewing::Assembly>

create_chimera_segment(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, reference_segment: pyrosetta.rosetta.protocols.legacy_sewing.SewSegment, mobile_segment: pyrosetta.rosetta.protocols.legacy_sewing.SewSegment, atom_map: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_is_nter: bool) → pyrosetta.rosetta.protocols.legacy_sewing.SewSegment¶: C++: protocols::legacy_sewing::Assembly::create_chimera_segment(const struct protocols::legacy_sewing::SewSegment &, const struct protocols::legacy_sewing::SewSegment &, const class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > > &, bool) const –> struct protocols::legacy_sewing::SewSegment

delete_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, seg_index: int) → None¶

delete segments at the given index. This should be used very infrequently

C++: protocols::legacy_sewing::Assembly::delete_segments(unsigned long) –> void

disconnected_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::legacy_sewing::Assembly::disconnected_segments() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

ending_node(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → protocols::legacy_sewing::ModelNode¶: C++: protocols::legacy_sewing::Assembly::ending_node() const –> const class protocols::legacy_sewing::ModelNode *

find_possible_orders(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, max_loop_distance: float) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t¶: C++: protocols::legacy_sewing::Assembly::find_possible_orders(double) const –> class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >

follow_edge(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, graph: protocols::legacy_sewing::SewGraph, edge: protocols::legacy_sewing::HashEdge, source_index: int) → None¶: C++: protocols::legacy_sewing::Assembly::follow_edge(class std::shared_ptr<const class protocols::legacy_sewing::SewGraph>, const class protocols::legacy_sewing::HashEdge *const, unsigned long) –> void

generate_native_rotamers_map(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t¶: C++: protocols::legacy_sewing::Assembly::generate_native_rotamers_map() const –> class std::map<unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > > > > >

get_model_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, model_id: int) → pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment¶: C++: protocols::legacy_sewing::Assembly::get_model_segments(int) const –> class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> >

get_next_reference_node(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, graph: protocols::legacy_sewing::SewGraph) → int¶

Pick which model to use as the reference model for the next node additon

C++: protocols::legacy_sewing::Assembly::get_next_reference_node(class std::shared_ptr<class protocols::legacy_sewing::SewGraph>) const –> unsigned long

get_partner(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::Assembly::get_partner() const –> class std::shared_ptr<class core::pose::Pose>

get_score_result(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, model_1_node: protocols::legacy_sewing::ModelNode, cur_edge: protocols::legacy_sewing::HashEdge, graph: protocols::legacy_sewing::SewGraph) → Tuple[Tuple[pyrosetta.rosetta.protocols.legacy_sewing.Basis, pyrosetta.rosetta.protocols.legacy_sewing.Basis], pyrosetta.rosetta.protocols.legacy_sewing.HashResult]¶: C++: protocols::legacy_sewing::Assembly::get_score_result(const class protocols::legacy_sewing::ModelNode *, const class protocols::legacy_sewing::HashEdge *const, class std::shared_ptr<const class protocols::legacy_sewing::SewGraph>) const –> struct std::pair<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult>

map_residues(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, reference_model_id: int, mobile_model: pyrosetta.rosetta.protocols.legacy_sewing.Model, atom_alignments: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID) → None¶

create mappings between SewResidues in the Assembly that map to the same pose number

C++: protocols::legacy_sewing::Assembly::map_residues(int, struct protocols::legacy_sewing::Model, const class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > > &) –> void

model_ids(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: protocols::legacy_sewing::Assembly::model_ids() const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

native_positions(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: protocols::legacy_sewing::Assembly::native_positions(const class core::pose::Pose &) const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

natives_select(*args, **kwargs)¶

Overloaded function.

natives_select(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) -> str
natives_select(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, object_name: str) -> str

print pymol selection of “native” positions

C++: protocols::legacy_sewing::Assembly::natives_select(const class core::pose::Pose &, std::string) const –> std::string

path(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t¶: C++: protocols::legacy_sewing::Assembly::path() const –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

percent_native(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

count the amount of ‘native’ residues retained in the pose

C++: protocols::legacy_sewing::Assembly::percent_native(const class core::pose::Pose &) const –> double

pose_loop_anchors(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::legacy_sewing::Assembly::pose_loop_anchors() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pose_num(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, model_id: int, resnum: int) → int¶: C++: protocols::legacy_sewing::Assembly::pose_num(int, unsigned long) const –> unsigned long

prepare_for_packing(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory, base_native_bonus: float, neighbor_cutoff: int) → None¶

Update the task factory such that the ‘native’ rotamers are added to the rotamer set, and the native residues are favored

C++: protocols::legacy_sewing::Assembly::prepare_for_packing(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::TaskFactory>, double, unsigned long) const –> void

regenerate_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, model_id: int) → pyrosetta.rosetta.protocols.legacy_sewing.Model¶: C++: protocols::legacy_sewing::Assembly::regenerate_model(int) const –> struct protocols::legacy_sewing::Model

reorder(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, new_order: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::legacy_sewing::Assembly::reorder(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

reorder_randomly(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, max_loop_distance: float) → bool¶

reorder segments in a random fashion that satisfies the maximum loop distance cutoff If this is not possible then return false, otherwise true

C++: protocols::legacy_sewing::Assembly::reorder_randomly(double) –> bool

segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment¶: C++: protocols::legacy_sewing::Assembly::segments() const –> class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> >

set_partner(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, partner_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::Assembly::set_partner(class std::shared_ptr<class core::pose::Pose>) –> void

starting_node(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → protocols::legacy_sewing::ModelNode¶: C++: protocols::legacy_sewing::Assembly::starting_node() const –> const class protocols::legacy_sewing::ModelNode *

string_blosum(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, blosum_history: pyrosetta.rosetta.utility.vector1_std_pair_double_unsigned_long_t) → str¶: C++: protocols::legacy_sewing::Assembly::string_blosum(class utility::vector1<struct std::pair<double, unsigned long>, class std::allocator<struct std::pair<double, unsigned long> > >) const –> std::string

string_path(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → str¶: C++: protocols::legacy_sewing::Assembly::string_path() const –> std::string

to_multichain_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, residue_type_set: str) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::Assembly::to_multichain_pose(std::string) const –> class core::pose::Pose

to_pose(*args, **kwargs)¶

Overloaded function.

to_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, residue_type_set: str) -> pyrosetta.rosetta.core.pose.Pose
to_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, residue_type_set: str, create_cuts: bool) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::legacy_sewing::Assembly::to_pose(std::string, bool) const –> class core::pose::Pose

total_residue(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → int¶: C++: protocols::legacy_sewing::Assembly::total_residue() const –> unsigned long

update_coords_from_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::Assembly::update_coords_from_pose(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.legacy_sewing.AssemblyFactory¶

Bases: pybind11_object

An Assembly is a collection of SewSegments. Assemblies are created using the geometric “compatibility” data generated by the Hasher.

static create_assembly(assembly_name: str) → pyrosetta.rosetta.protocols.legacy_sewing.Assembly¶: C++: protocols::legacy_sewing::AssemblyFactory::create_assembly(std::string) –> class std::shared_ptr<class protocols::legacy_sewing::Assembly>

class pyrosetta.rosetta.protocols.legacy_sewing.Basis¶

Bases: pybind11_object

//////////////////////// HashMap for score results ///////////////////////////////

assign(self: pyrosetta.rosetta.protocols.legacy_sewing.Basis, : pyrosetta.rosetta.protocols.legacy_sewing.Basis) → pyrosetta.rosetta.protocols.legacy_sewing.Basis¶: C++: protocols::legacy_sewing::Basis::operator=(const struct protocols::legacy_sewing::Basis &) –> struct protocols::legacy_sewing::Basis &

property model_id¶

property resnum¶

class pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly¶

Bases: Assembly

An Assembly is a collection of SewSegments. Assemblies are created using the geometric “compatibility” data generated by the Hasher.

add_loop_segment(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop, segment: int) → None¶: C++: protocols::legacy_sewing::Assembly::add_loop_segment(const class core::pose::Pose &, class protocols::loops::Loop, unsigned long) –> void

add_model(*args, **kwargs)¶

Overloaded function.

add_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, graph: protocols::legacy_sewing::SewGraph, model: pyrosetta.rosetta.protocols.legacy_sewing.Model) -> None
add_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, graph: protocols::legacy_sewing::SewGraph, model: pyrosetta.rosetta.protocols.legacy_sewing.Model, available: bool) -> None

Add a model to the Assembly. Only used for first node and special cases.

C++: protocols::legacy_sewing::Assembly::add_model(class std::shared_ptr<const class protocols::legacy_sewing::SewGraph>, const struct protocols::legacy_sewing::Model &, bool) –> void

align_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, mobile_model: pyrosetta.rosetta.protocols.legacy_sewing.Model, atom_alignments: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_model_id: int) → None¶: C++: protocols::legacy_sewing::Assembly::align_model(struct protocols::legacy_sewing::Model &, const class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > > &, int) const –> void

all_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_legacy_sewing_SewSegment_std_allocator_protocols_legacy_sewing_SewSegment_t¶: C++: protocols::legacy_sewing::Assembly::all_segments() const –> class utility::vector1<class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> >, class std::allocator<class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> > > >

append_model(self: pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly, model: pyrosetta.rosetta.protocols.legacy_sewing.Model, edge_score: Tuple[Tuple[pyrosetta.rosetta.protocols.legacy_sewing.Basis, pyrosetta.rosetta.protocols.legacy_sewing.Basis], pyrosetta.rosetta.protocols.legacy_sewing.HashResult]) → None¶

Needs to be implemented.

C++: protocols::legacy_sewing::ContinuousAssembly::append_model(const struct protocols::legacy_sewing::Model &, const struct std::pair<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> &) –> void

append_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, segments: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment) → None¶

append the segments to the given assembly. This should be used very infrequently. The normal way to add segments is to follow an edge

C++: protocols::legacy_sewing::Assembly::append_segments(const class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> > &) –> void

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

atom_map_from_score_result(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, alignment_scores: Tuple[Tuple[pyrosetta.rosetta.protocols.legacy_sewing.Basis, pyrosetta.rosetta.protocols.legacy_sewing.Basis], pyrosetta.rosetta.protocols.legacy_sewing.HashResult]) → pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID¶: C++: protocols::legacy_sewing::Assembly::atom_map_from_score_result(const struct std::pair<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> &) const –> class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > >

property blosum_history_¶

clone(self: pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly) → pyrosetta.rosetta.protocols.legacy_sewing.Assembly¶: C++: protocols::legacy_sewing::ContinuousAssembly::clone() –> class std::shared_ptr<class protocols::legacy_sewing::Assembly>

create_chimera_segment(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, reference_segment: pyrosetta.rosetta.protocols.legacy_sewing.SewSegment, mobile_segment: pyrosetta.rosetta.protocols.legacy_sewing.SewSegment, atom_map: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_is_nter: bool) → pyrosetta.rosetta.protocols.legacy_sewing.SewSegment¶: C++: protocols::legacy_sewing::Assembly::create_chimera_segment(const struct protocols::legacy_sewing::SewSegment &, const struct protocols::legacy_sewing::SewSegment &, const class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > > &, bool) const –> struct protocols::legacy_sewing::SewSegment

delete_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, seg_index: int) → None¶

delete segments at the given index. This should be used very infrequently

C++: protocols::legacy_sewing::Assembly::delete_segments(unsigned long) –> void

disconnected_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::legacy_sewing::Assembly::disconnected_segments() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

ending_node(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → protocols::legacy_sewing::ModelNode¶: C++: protocols::legacy_sewing::Assembly::ending_node() const –> const class protocols::legacy_sewing::ModelNode *

find_possible_orders(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, max_loop_distance: float) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t¶: C++: protocols::legacy_sewing::Assembly::find_possible_orders(double) const –> class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >

follow_edge(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, graph: protocols::legacy_sewing::SewGraph, edge: protocols::legacy_sewing::HashEdge, source_index: int) → None¶: C++: protocols::legacy_sewing::Assembly::follow_edge(class std::shared_ptr<const class protocols::legacy_sewing::SewGraph>, const class protocols::legacy_sewing::HashEdge *const, unsigned long) –> void

generate_native_rotamers_map(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t¶: C++: protocols::legacy_sewing::Assembly::generate_native_rotamers_map() const –> class std::map<unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > > > > >

get_model_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, model_id: int) → pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment¶: C++: protocols::legacy_sewing::Assembly::get_model_segments(int) const –> class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> >

get_next_reference_node(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, graph: protocols::legacy_sewing::SewGraph) → int¶

Pick which model to use as the reference model for the next node additon

C++: protocols::legacy_sewing::Assembly::get_next_reference_node(class std::shared_ptr<class protocols::legacy_sewing::SewGraph>) const –> unsigned long

get_partner(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::Assembly::get_partner() const –> class std::shared_ptr<class core::pose::Pose>

get_score_result(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, model_1_node: protocols::legacy_sewing::ModelNode, cur_edge: protocols::legacy_sewing::HashEdge, graph: protocols::legacy_sewing::SewGraph) → Tuple[Tuple[pyrosetta.rosetta.protocols.legacy_sewing.Basis, pyrosetta.rosetta.protocols.legacy_sewing.Basis], pyrosetta.rosetta.protocols.legacy_sewing.HashResult]¶: C++: protocols::legacy_sewing::Assembly::get_score_result(const class protocols::legacy_sewing::ModelNode *, const class protocols::legacy_sewing::HashEdge *const, class std::shared_ptr<const class protocols::legacy_sewing::SewGraph>) const –> struct std::pair<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult>

map_residues(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, reference_model_id: int, mobile_model: pyrosetta.rosetta.protocols.legacy_sewing.Model, atom_alignments: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID) → None¶

create mappings between SewResidues in the Assembly that map to the same pose number

C++: protocols::legacy_sewing::Assembly::map_residues(int, struct protocols::legacy_sewing::Model, const class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > > &) –> void

model_ids(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: protocols::legacy_sewing::Assembly::model_ids() const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

native_positions(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: protocols::legacy_sewing::Assembly::native_positions(const class core::pose::Pose &) const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

natives_select(*args, **kwargs)¶

Overloaded function.

natives_select(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) -> str
natives_select(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, object_name: str) -> str

print pymol selection of “native” positions

C++: protocols::legacy_sewing::Assembly::natives_select(const class core::pose::Pose &, std::string) const –> std::string

path(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t¶: C++: protocols::legacy_sewing::Assembly::path() const –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

percent_native(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

count the amount of ‘native’ residues retained in the pose

C++: protocols::legacy_sewing::Assembly::percent_native(const class core::pose::Pose &) const –> double

pose_loop_anchors(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::legacy_sewing::Assembly::pose_loop_anchors() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pose_num(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, model_id: int, resnum: int) → int¶: C++: protocols::legacy_sewing::Assembly::pose_num(int, unsigned long) const –> unsigned long

prepare_for_packing(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory, base_native_bonus: float, neighbor_cutoff: int) → None¶

Update the task factory such that the ‘native’ rotamers are added to the rotamer set, and the native residues are favored

C++: protocols::legacy_sewing::Assembly::prepare_for_packing(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::TaskFactory>, double, unsigned long) const –> void

regenerate_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, model_id: int) → pyrosetta.rosetta.protocols.legacy_sewing.Model¶: C++: protocols::legacy_sewing::Assembly::regenerate_model(int) const –> struct protocols::legacy_sewing::Model

reorder(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, new_order: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::legacy_sewing::Assembly::reorder(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

reorder_randomly(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, max_loop_distance: float) → bool¶

reorder segments in a random fashion that satisfies the maximum loop distance cutoff If this is not possible then return false, otherwise true

C++: protocols::legacy_sewing::Assembly::reorder_randomly(double) –> bool

segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment¶: C++: protocols::legacy_sewing::Assembly::segments() const –> class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> >

set_partner(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, partner_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::Assembly::set_partner(class std::shared_ptr<class core::pose::Pose>) –> void

starting_node(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → protocols::legacy_sewing::ModelNode¶: C++: protocols::legacy_sewing::Assembly::starting_node() const –> const class protocols::legacy_sewing::ModelNode *

string_blosum(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, blosum_history: pyrosetta.rosetta.utility.vector1_std_pair_double_unsigned_long_t) → str¶: C++: protocols::legacy_sewing::Assembly::string_blosum(class utility::vector1<struct std::pair<double, unsigned long>, class std::allocator<struct std::pair<double, unsigned long> > >) const –> std::string

string_path(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → str¶: C++: protocols::legacy_sewing::Assembly::string_path() const –> std::string

to_multichain_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, residue_type_set: str) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::Assembly::to_multichain_pose(std::string) const –> class core::pose::Pose

to_pose(*args, **kwargs)¶

Overloaded function.

to_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, residue_type_set: str) -> pyrosetta.rosetta.core.pose.Pose
to_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, residue_type_set: str, create_cuts: bool) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::legacy_sewing::Assembly::to_pose(std::string, bool) const –> class core::pose::Pose

total_residue(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → int¶: C++: protocols::legacy_sewing::Assembly::total_residue() const –> unsigned long

update_coords_from_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::Assembly::update_coords_from_pose(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly¶

Bases: Assembly

An Assembly is a collection of SewSegments. Assemblies are created using the geometric “compatibility” data generated by the Hasher.

add_loop_segment(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop, segment: int) → None¶: C++: protocols::legacy_sewing::Assembly::add_loop_segment(const class core::pose::Pose &, class protocols::loops::Loop, unsigned long) –> void

add_model(*args, **kwargs)¶

Overloaded function.

add_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, graph: protocols::legacy_sewing::SewGraph, model: pyrosetta.rosetta.protocols.legacy_sewing.Model) -> None
add_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, graph: protocols::legacy_sewing::SewGraph, model: pyrosetta.rosetta.protocols.legacy_sewing.Model, available: bool) -> None

Add a model to the Assembly. Only used for first node and special cases.

C++: protocols::legacy_sewing::Assembly::add_model(class std::shared_ptr<const class protocols::legacy_sewing::SewGraph>, const struct protocols::legacy_sewing::Model &, bool) –> void

align_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, mobile_model: pyrosetta.rosetta.protocols.legacy_sewing.Model, atom_alignments: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_model_id: int) → None¶: C++: protocols::legacy_sewing::Assembly::align_model(struct protocols::legacy_sewing::Model &, const class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > > &, int) const –> void

all_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_legacy_sewing_SewSegment_std_allocator_protocols_legacy_sewing_SewSegment_t¶: C++: protocols::legacy_sewing::Assembly::all_segments() const –> class utility::vector1<class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> >, class std::allocator<class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> > > >

append_model(self: pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly, model: pyrosetta.rosetta.protocols.legacy_sewing.Model, edge_score: Tuple[Tuple[pyrosetta.rosetta.protocols.legacy_sewing.Basis, pyrosetta.rosetta.protocols.legacy_sewing.Basis], pyrosetta.rosetta.protocols.legacy_sewing.HashResult]) → None¶: C++: protocols::legacy_sewing::DisembodiedAssembly::append_model(const struct protocols::legacy_sewing::Model &, const struct std::pair<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> &) –> void

append_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, segments: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment) → None¶

append the segments to the given assembly. This should be used very infrequently. The normal way to add segments is to follow an edge

C++: protocols::legacy_sewing::Assembly::append_segments(const class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> > &) –> void

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

atom_map_from_score_result(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, alignment_scores: Tuple[Tuple[pyrosetta.rosetta.protocols.legacy_sewing.Basis, pyrosetta.rosetta.protocols.legacy_sewing.Basis], pyrosetta.rosetta.protocols.legacy_sewing.HashResult]) → pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID¶: C++: protocols::legacy_sewing::Assembly::atom_map_from_score_result(const struct std::pair<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> &) const –> class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > >

property blosum_history_¶

clone(self: pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly) → pyrosetta.rosetta.protocols.legacy_sewing.Assembly¶: C++: protocols::legacy_sewing::DisembodiedAssembly::clone() –> class std::shared_ptr<class protocols::legacy_sewing::Assembly>

create_chimera_segment(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, reference_segment: pyrosetta.rosetta.protocols.legacy_sewing.SewSegment, mobile_segment: pyrosetta.rosetta.protocols.legacy_sewing.SewSegment, atom_map: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_is_nter: bool) → pyrosetta.rosetta.protocols.legacy_sewing.SewSegment¶: C++: protocols::legacy_sewing::Assembly::create_chimera_segment(const struct protocols::legacy_sewing::SewSegment &, const struct protocols::legacy_sewing::SewSegment &, const class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > > &, bool) const –> struct protocols::legacy_sewing::SewSegment

delete_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, seg_index: int) → None¶

delete segments at the given index. This should be used very infrequently

C++: protocols::legacy_sewing::Assembly::delete_segments(unsigned long) –> void

disconnected_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::legacy_sewing::Assembly::disconnected_segments() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

ending_node(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → protocols::legacy_sewing::ModelNode¶: C++: protocols::legacy_sewing::Assembly::ending_node() const –> const class protocols::legacy_sewing::ModelNode *

find_possible_orders(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, max_loop_distance: float) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t¶: C++: protocols::legacy_sewing::Assembly::find_possible_orders(double) const –> class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >

follow_edge(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, graph: protocols::legacy_sewing::SewGraph, edge: protocols::legacy_sewing::HashEdge, source_index: int) → None¶: C++: protocols::legacy_sewing::Assembly::follow_edge(class std::shared_ptr<const class protocols::legacy_sewing::SewGraph>, const class protocols::legacy_sewing::HashEdge *const, unsigned long) –> void

generate_native_rotamers_map(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t¶: C++: protocols::legacy_sewing::Assembly::generate_native_rotamers_map() const –> class std::map<unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > > > > >

get_model_segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, model_id: int) → pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment¶: C++: protocols::legacy_sewing::Assembly::get_model_segments(int) const –> class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> >

get_next_reference_node(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, graph: protocols::legacy_sewing::SewGraph) → int¶

Pick which model to use as the reference model for the next node additon

C++: protocols::legacy_sewing::Assembly::get_next_reference_node(class std::shared_ptr<class protocols::legacy_sewing::SewGraph>) const –> unsigned long

get_partner(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::Assembly::get_partner() const –> class std::shared_ptr<class core::pose::Pose>

get_score_result(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, model_1_node: protocols::legacy_sewing::ModelNode, cur_edge: protocols::legacy_sewing::HashEdge, graph: protocols::legacy_sewing::SewGraph) → Tuple[Tuple[pyrosetta.rosetta.protocols.legacy_sewing.Basis, pyrosetta.rosetta.protocols.legacy_sewing.Basis], pyrosetta.rosetta.protocols.legacy_sewing.HashResult]¶: C++: protocols::legacy_sewing::Assembly::get_score_result(const class protocols::legacy_sewing::ModelNode *, const class protocols::legacy_sewing::HashEdge *const, class std::shared_ptr<const class protocols::legacy_sewing::SewGraph>) const –> struct std::pair<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult>

map_residues(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, reference_model_id: int, mobile_model: pyrosetta.rosetta.protocols.legacy_sewing.Model, atom_alignments: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID) → None¶

create mappings between SewResidues in the Assembly that map to the same pose number

C++: protocols::legacy_sewing::Assembly::map_residues(int, struct protocols::legacy_sewing::Model, const class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > > &) –> void

model_ids(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: protocols::legacy_sewing::Assembly::model_ids() const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

native_positions(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: protocols::legacy_sewing::Assembly::native_positions(const class core::pose::Pose &) const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

natives_select(*args, **kwargs)¶

Overloaded function.

natives_select(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) -> str
natives_select(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, object_name: str) -> str

print pymol selection of “native” positions

C++: protocols::legacy_sewing::Assembly::natives_select(const class core::pose::Pose &, std::string) const –> std::string

path(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t¶: C++: protocols::legacy_sewing::Assembly::path() const –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

percent_native(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

count the amount of ‘native’ residues retained in the pose

C++: protocols::legacy_sewing::Assembly::percent_native(const class core::pose::Pose &) const –> double

pose_loop_anchors(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::legacy_sewing::Assembly::pose_loop_anchors() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pose_num(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, model_id: int, resnum: int) → int¶: C++: protocols::legacy_sewing::Assembly::pose_num(int, unsigned long) const –> unsigned long

prepare_for_packing(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory, base_native_bonus: float, neighbor_cutoff: int) → None¶

Update the task factory such that the ‘native’ rotamers are added to the rotamer set, and the native residues are favored

C++: protocols::legacy_sewing::Assembly::prepare_for_packing(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::TaskFactory>, double, unsigned long) const –> void

regenerate_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, model_id: int) → pyrosetta.rosetta.protocols.legacy_sewing.Model¶: C++: protocols::legacy_sewing::Assembly::regenerate_model(int) const –> struct protocols::legacy_sewing::Model

reorder(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, new_order: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::legacy_sewing::Assembly::reorder(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

reorder_randomly(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, max_loop_distance: float) → bool¶

reorder segments in a random fashion that satisfies the maximum loop distance cutoff If this is not possible then return false, otherwise true

C++: protocols::legacy_sewing::Assembly::reorder_randomly(double) –> bool

segments(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment¶: C++: protocols::legacy_sewing::Assembly::segments() const –> class utility::vector1<struct protocols::legacy_sewing::SewSegment, class std::allocator<struct protocols::legacy_sewing::SewSegment> >

set_partner(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, partner_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::Assembly::set_partner(class std::shared_ptr<class core::pose::Pose>) –> void

starting_node(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → protocols::legacy_sewing::ModelNode¶: C++: protocols::legacy_sewing::Assembly::starting_node() const –> const class protocols::legacy_sewing::ModelNode *

string_blosum(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, blosum_history: pyrosetta.rosetta.utility.vector1_std_pair_double_unsigned_long_t) → str¶: C++: protocols::legacy_sewing::Assembly::string_blosum(class utility::vector1<struct std::pair<double, unsigned long>, class std::allocator<struct std::pair<double, unsigned long> > >) const –> std::string

string_path(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → str¶: C++: protocols::legacy_sewing::Assembly::string_path() const –> std::string

to_multichain_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, residue_type_set: str) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::Assembly::to_multichain_pose(std::string) const –> class core::pose::Pose

to_pose(*args, **kwargs)¶

Overloaded function.

to_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, residue_type_set: str) -> pyrosetta.rosetta.core.pose.Pose
to_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, residue_type_set: str, create_cuts: bool) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::legacy_sewing::Assembly::to_pose(std::string, bool) const –> class core::pose::Pose

total_residue(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → int¶: C++: protocols::legacy_sewing::Assembly::total_residue() const –> unsigned long

update_coords_from_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::Assembly::update_coords_from_pose(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.legacy_sewing.HashEdge¶

Bases: Edge

basis_pair(*args, **kwargs)¶

Overloaded function.

basis_pair(self: pyrosetta.rosetta.protocols.legacy_sewing.HashEdge, basis_pair: Tuple[pyrosetta.rosetta.protocols.legacy_sewing.Basis, pyrosetta.rosetta.protocols.legacy_sewing.Basis]) -> None

C++: protocols::legacy_sewing::HashEdge::basis_pair(struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>) –> void

basis_pair(self: pyrosetta.rosetta.protocols.legacy_sewing.HashEdge) -> Tuple[pyrosetta.rosetta.protocols.legacy_sewing.Basis, pyrosetta.rosetta.protocols.legacy_sewing.Basis]

C++: protocols::legacy_sewing::HashEdge::basis_pair() const –> const struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis> &

copy_from(self: pyrosetta.rosetta.utility.graph.Edge, source: pyrosetta.rosetta.utility.graph.Edge) → None¶

copy-from for use in Graph::operator= and copy ctors

C++: utility::graph::Edge::copy_from(const class utility::graph::Edge *) –> void

count_dynamic_memory(self: pyrosetta.rosetta.utility.graph.Edge) → int¶

how much memory is dynamically allocated by this edge – must be recursively invoked: by a derived class.

C++: utility::graph::Edge::count_dynamic_memory() const –> unsigned long

count_static_memory(self: pyrosetta.rosetta.utility.graph.Edge) → int¶

how much memory is statically allocated by this edge

C++: utility::graph::Edge::count_static_memory() const –> unsigned long

get_first_node_ind(self: pyrosetta.rosetta.utility.graph.Edge) → int¶

returns the index of the lower node

C++: utility::graph::Edge::get_first_node_ind() const –> unsigned long

get_other_ind(self: pyrosetta.rosetta.utility.graph.Edge, node_index: int) → int¶

returns the index of the one node given the index of the other.: node_index must be one of the two nodes that this edge is incident upon.

C++: utility::graph::Edge::get_other_ind(unsigned long) const –> unsigned long

get_other_node(self: pyrosetta.rosetta.utility.graph.Edge, node_index: int) → pyrosetta.rosetta.utility.graph.Node¶

returns a non-const pointer to one node given the index of the other.: node_index must be one of the two nodes that this edge is incident upon.

C++: utility::graph::Edge::get_other_node(unsigned long) –> class utility::graph::Node *

get_second_node_ind(self: pyrosetta.rosetta.utility.graph.Edge) → int¶

returns the index of the upper node

C++: utility::graph::Edge::get_second_node_ind() const –> unsigned long

is_loop(self: pyrosetta.rosetta.utility.graph.Edge) → bool¶

Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex.

C++: utility::graph::Edge::is_loop() const –> bool

model_resnum(self: pyrosetta.rosetta.protocols.legacy_sewing.HashEdge, model_id: int) → int¶: C++: protocols::legacy_sewing::HashEdge::model_resnum(int) const –> unsigned long

same_edge(self: pyrosetta.rosetta.utility.graph.Edge, node1: int, node2: int) → bool¶

Is this the same edge as another edge (node1,node2)? Note:: this graph does not work for multi-graphs. Edges must be unique.

C++: utility::graph::Edge::same_edge(unsigned long, unsigned long) const –> bool

set_pos_in_owners_list(self: pyrosetta.rosetta.utility.graph.Edge, edge_iterator: pyrosetta.rosetta.utility.graph.EdgeListIterator) → None¶

called only by class Graph, this function gives the Edge the data it needs: to later delete itself from its owner’s edge list in constant time.

C++: utility::graph::Edge::set_pos_in_owners_list(class utility::graph::EdgeListIterator) –> void

class pyrosetta.rosetta.protocols.legacy_sewing.HashResult¶

Bases: pybind11_object

property clash_count¶

property segment_match_counts¶

property segment_matches¶

class pyrosetta.rosetta.protocols.legacy_sewing.HashValue¶

Bases: pybind11_object

property atomno¶

property basis_resnum¶

property model_id¶

property resnum¶

property segment_id¶

class pyrosetta.rosetta.protocols.legacy_sewing.Hasher¶

Bases: pybind11_object

//////////////////////// End HashMap for score results ///////////////////////////////

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

generate_key(self: pyrosetta.rosetta.protocols.legacy_sewing.Hasher, atom: pyrosetta.rosetta.protocols.legacy_sewing.SewAtom) → pyrosetta.rosetta.utility.fixedsizearray1_int_3_t¶

Create the HashKey from a SewAtom

C++: protocols::legacy_sewing::Hasher::generate_key(const struct protocols::legacy_sewing::SewAtom &) const –> class utility::fixedsizearray1<int, 3>

hash_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Hasher, transformed_model: pyrosetta.rosetta.protocols.legacy_sewing.Model, basis_residue: pyrosetta.rosetta.protocols.legacy_sewing.SewResidue) → None¶

Hash the transformed residues into the HashMap

C++: protocols::legacy_sewing::Hasher::hash_model(const struct protocols::legacy_sewing::Model &, const struct protocols::legacy_sewing::SewResidue &) –> void

insert(self: pyrosetta.rosetta.protocols.legacy_sewing.Hasher, model: pyrosetta.rosetta.protocols.legacy_sewing.Model) → None¶

Insert this model into the hash table

C++: protocols::legacy_sewing::Hasher::insert(const struct protocols::legacy_sewing::Model &) –> void

read_from_disk(self: pyrosetta.rosetta.protocols.legacy_sewing.Hasher, filename: str) → None¶

Populate the hash table from one on disk.

C++: protocols::legacy_sewing::Hasher::read_from_disk(std::string) –> void

remove edges between segments that both have ‘next’ or ‘previous’ segments

C++: protocols::legacy_sewing::Hasher::remove_connection_inconsistencies(const class std::map<int, struct protocols::legacy_sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::legacy_sewing::Model> > > &, class std::map<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult, struct std::less<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> > > &) const –> void

keep only best scoring alignment between two models

C++: protocols::legacy_sewing::Hasher::remove_duplicates(const class std::map<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult, struct std::less<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> > > &) const –> class std::map<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult, struct std::less<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> > >

score(*args, **kwargs)¶

Overloaded function.

score(self: pyrosetta.rosetta.protocols.legacy_sewing.Hasher, model: pyrosetta.rosetta.protocols.legacy_sewing.Model, num_segment_matches: int, min_segment_score: int, max_clash_score: int, score_segments: pyrosetta.rosetta.std.set_unsigned_long_t, store_atoms: bool, box_length: int) -> pyrosetta.rosetta.std.map_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_protocols_legacy_sewing_HashResult_std_less_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_std_allocator_std_pair_const_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_protocols_legacy_sewing_HashResult_t

C++: protocols::legacy_sewing::Hasher::score(const struct protocols::legacy_sewing::Model &, unsigned long, unsigned long, unsigned long, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, bool, unsigned long) const –> class std::map<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult, struct std::less<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> > >

score(self: pyrosetta.rosetta.protocols.legacy_sewing.Hasher, model: pyrosetta.rosetta.protocols.legacy_sewing.Model, num_segment_matches: int, min_segment_score: int, max_clash_score: int, store_atoms: bool, box_length: int) -> pyrosetta.rosetta.std.map_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_protocols_legacy_sewing_HashResult_std_less_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_std_allocator_std_pair_const_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_protocols_legacy_sewing_HashResult_t

Score the given model against the models in the hash table

C++: protocols::legacy_sewing::Hasher::score(const struct protocols::legacy_sewing::Model &, unsigned long, unsigned long, unsigned long, bool, unsigned long) const –> class std::map<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult, struct std::less<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> > >

score_basis(self: pyrosetta.rosetta.protocols.legacy_sewing.Hasher, alignment_scores: pyrosetta.rosetta.std.map_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_protocols_legacy_sewing_HashResult_std_less_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_std_allocator_std_pair_const_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_protocols_legacy_sewing_HashResult_t, transformed_model: pyrosetta.rosetta.protocols.legacy_sewing.Model, basis_residue: pyrosetta.rosetta.protocols.legacy_sewing.SewResidue, store_atoms: bool) → None¶: C++: protocols::legacy_sewing::Hasher::score_basis(class std::map<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult, struct std::less<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> > > &, const struct protocols::legacy_sewing::Model &, const struct protocols::legacy_sewing::SewResidue &, bool) const –> void

score_basis_125(self: pyrosetta.rosetta.protocols.legacy_sewing.Hasher, alignment_scores: pyrosetta.rosetta.std.map_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_protocols_legacy_sewing_HashResult_std_less_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_std_allocator_std_pair_const_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_protocols_legacy_sewing_HashResult_t, transformed_model: pyrosetta.rosetta.protocols.legacy_sewing.Model, basis_residue: pyrosetta.rosetta.protocols.legacy_sewing.SewResidue, store_atoms: bool) → None¶: C++: protocols::legacy_sewing::Hasher::score_basis_125(class std::map<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult, struct std::less<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> > > &, const struct protocols::legacy_sewing::Model &, const struct protocols::legacy_sewing::SewResidue &, bool) const –> void

score_one(self: pyrosetta.rosetta.protocols.legacy_sewing.Hasher, m1: pyrosetta.rosetta.protocols.legacy_sewing.Model, m1_basis: pyrosetta.rosetta.protocols.legacy_sewing.SewResidue, m2: pyrosetta.rosetta.protocols.legacy_sewing.Model, m2_basis: pyrosetta.rosetta.protocols.legacy_sewing.SewResidue, box_length: int) → Tuple[Tuple[pyrosetta.rosetta.protocols.legacy_sewing.Basis, pyrosetta.rosetta.protocols.legacy_sewing.Basis], pyrosetta.rosetta.protocols.legacy_sewing.HashResult]¶: C++: protocols::legacy_sewing::Hasher::score_one(const struct protocols::legacy_sewing::Model &, const struct protocols::legacy_sewing::SewResidue &, const struct protocols::legacy_sewing::Model &, const struct protocols::legacy_sewing::SewResidue &, unsigned long) –> struct std::pair<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult>

transform_model(self: pyrosetta.rosetta.protocols.legacy_sewing.Hasher, model: pyrosetta.rosetta.protocols.legacy_sewing.Model, basis_residue: pyrosetta.rosetta.protocols.legacy_sewing.SewResidue) → pyrosetta.rosetta.protocols.legacy_sewing.Model¶

Transform all features to the local coordinate frame of the basis set

C++: protocols::legacy_sewing::Hasher::transform_model(const struct protocols::legacy_sewing::Model &, const struct protocols::legacy_sewing::SewResidue &) const –> struct protocols::legacy_sewing::Model

Trim the ScoreResults to remove weak hits

C++: protocols::legacy_sewing::Hasher::trim_scores(class std::map<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult, struct std::less<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> > > &, unsigned long, unsigned long, unsigned long) const –> void

write_to_disk(self: pyrosetta.rosetta.protocols.legacy_sewing.Hasher, filename: str) → None¶

Serialize hash table to disk

C++: protocols::legacy_sewing::Hasher::write_to_disk(std::string) const –> void

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::LegacyAddStartnodeFragments::apply(class core::pose::Pose &) –> void

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

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.legacy_sewing.LegacyAddStartnodeFragments) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::legacy_sewing::LegacyAddStartnodeFragments::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.legacy_sewing.LegacyAddStartnodeFragments) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::legacy_sewing::LegacyAddStartnodeFragments::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.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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.legacy_sewing.LegacyAddStartnodeFragments) → str¶: C++: protocols::legacy_sewing::LegacyAddStartnodeFragments::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_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

static mover_name() → str¶: C++: protocols::legacy_sewing::LegacyAddStartnodeFragments::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAddStartnodeFragments::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyAddStartnodeFragments::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static 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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: 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 std::string &) –> 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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) 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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragmentsCreator¶

Bases: MoverCreator

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

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

keyname(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragmentsCreator) → str¶: C++: protocols::legacy_sewing::LegacyAddStartnodeFragmentsCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragmentsCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyAddStartnodeFragmentsCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover¶

Bases: LegacyMonteCarloAssemblyMover

add_starting_model(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → None¶

The starting node for the Assembly from the append mover will always be the input PDB

C++: protocols::legacy_sewing::LegacyAppendAssemblyMover::add_starting_model(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> void

append_movie_frame(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, cycle: int) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::append_movie_frame(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, unsigned long) const –> void

apply(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::LegacyAppendAssemblyMover::apply(class core::pose::Pose &) –> void

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

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.legacy_sewing.LegacyAppendAssemblyMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::legacy_sewing::LegacyAppendAssemblyMover::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>

static define_assembly_mover_ct_gen(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::define_assembly_mover_ct_gen(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

static define_mc_assembly_mover_ct_gen(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::define_mc_assembly_mover_ct_gen(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

follow_random_edge_from_node(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, reference_node: protocols::legacy_sewing::ModelNode) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::follow_random_edge_from_node(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, const class protocols::legacy_sewing::ModelNode *) const –> bool

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

generate_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover) → pyrosetta.rosetta.protocols.legacy_sewing.Assembly¶: C++: protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::generate_assembly() –> class std::shared_ptr<class protocols::legacy_sewing::Assembly>

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.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_centroid_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_centroid_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> 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_fullatom_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_fullatom_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> class core::pose::Pose

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.legacy_sewing.LegacyAppendAssemblyMover) → str¶: C++: protocols::legacy_sewing::LegacyAppendAssemblyMover::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

hash_pdb_model(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover, pdb_model: pyrosetta.rosetta.protocols.legacy_sewing.Model) → None¶: C++: protocols::legacy_sewing::LegacyAppendAssemblyMover::hash_pdb_model(const struct protocols::legacy_sewing::Model &) –> void

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

static legacy_assembly_mover_ct_namer(: str) → str¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::legacy_assembly_mover_ct_namer(const std::string &) –> std::string

static mover_name() → str¶: C++: protocols::legacy_sewing::LegacyAppendAssemblyMover::mover_name() –> std::string

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

output_stats(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, indicator_whether_from_LegacyMonteCarloAssemblyMover_or_LegacyExhaustiveAssemblyMover: str) → None¶

add several outputs to the score file Pose can’t be const due to scoring.

C++: protocols::legacy_sewing::LegacyAssemblyMover::output_stats(const class std::shared_ptr<class protocols::legacy_sewing::Assembly> &, class core::pose::Pose &, std::string) –> void

parse_global_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_global_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_intra_segment_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_intra_segment_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAppendAssemblyMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyAppendAssemblyMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refine_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAppendAssemblyMover::refine_assembly(class std::shared_ptr<class protocols::legacy_sewing::Assembly> &) –> class core::pose::Pose

static 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.legacy_sewing.LegacyAssemblyMover) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: 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 std::string &) –> 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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) 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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMoverCreator¶

Bases: MoverCreator

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

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

keyname(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMoverCreator) → str¶: C++: protocols::legacy_sewing::LegacyAppendAssemblyMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyAppendAssemblyMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover¶

Bases: Mover

///////////LegacyAssemblyConstraintsMover/////////////////

apply(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyConstraintsMover::apply(class core::pose::Pose &) –> void

apply_repeat(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyConstraintsMover::apply_repeat(class core::pose::Pose &) –> void

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

base_native_bonus(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover, base_native_bonus: float) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyConstraintsMover::base_native_bonus(double) –> void

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.legacy_sewing.LegacyAssemblyConstraintsMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::legacy_sewing::LegacyAssemblyConstraintsMover::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.legacy_sewing.LegacyAssemblyConstraintsMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::legacy_sewing::LegacyAssemblyConstraintsMover::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.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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.legacy_sewing.LegacyAssemblyConstraintsMover) → str¶: C++: protocols::legacy_sewing::LegacyAssemblyConstraintsMover::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_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

static mover_name() → str¶: C++: protocols::legacy_sewing::LegacyAssemblyConstraintsMover::mover_name() –> std::string

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

nat_ro_map(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover, nat_ro_map: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyConstraintsMover::nat_ro_map(const class std::map<unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > > > > > &) –> void

neighbor_cutoff(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover, neighbor_cutoff: float) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyConstraintsMover::neighbor_cutoff(double) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyConstraintsMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyConstraintsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static 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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: 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 std::string &) –> 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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) 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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMoverCreator¶

Bases: MoverCreator

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

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

keyname(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMoverCreator) → str¶: C++: protocols::legacy_sewing::LegacyAssemblyConstraintsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyConstraintsMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover¶

Bases: Mover

add_starting_model(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::add_starting_model(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> void

append_movie_frame(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, cycle: int) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::append_movie_frame(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, unsigned long) const –> void

apply(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::apply(class core::pose::Pose &) –> void

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

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.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::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>

static define_assembly_mover_ct_gen(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::define_assembly_mover_ct_gen(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

follow_random_edge_from_node(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, reference_node: protocols::legacy_sewing::ModelNode) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::follow_random_edge_from_node(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, const class protocols::legacy_sewing::ModelNode *) const –> bool

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>

generate_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover) → pyrosetta.rosetta.protocols.legacy_sewing.Assembly¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::generate_assembly() –> class std::shared_ptr<class protocols::legacy_sewing::Assembly>

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.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_centroid_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_centroid_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> 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_fullatom_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_fullatom_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> class core::pose::Pose

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.legacy_sewing.LegacyAssemblyMover) → str¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::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_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

static legacy_assembly_mover_ct_namer(: str) → str¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::legacy_assembly_mover_ct_namer(const std::string &) –> std::string

static mover_name() → str¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::mover_name() –> std::string

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

output_stats(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, indicator_whether_from_LegacyMonteCarloAssemblyMover_or_LegacyExhaustiveAssemblyMover: str) → None¶

add several outputs to the score file Pose can’t be const due to scoring.

C++: protocols::legacy_sewing::LegacyAssemblyMover::output_stats(const class std::shared_ptr<class protocols::legacy_sewing::Assembly> &, class core::pose::Pose &, std::string) –> void

parse_global_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_global_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_intra_segment_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_intra_segment_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refine_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::refine_assembly(class std::shared_ptr<class protocols::legacy_sewing::Assembly> &) –> class core::pose::Pose

static 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.legacy_sewing.LegacyAssemblyMover) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: 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 std::string &) –> 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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) 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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover¶

Bases: LegacyAssemblyMover

add_starting_model(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::add_starting_model(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> void

append_movie_frame(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, cycle: int) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::append_movie_frame(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, unsigned long) const –> void

apply(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::apply(class core::pose::Pose &) –> void

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

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.legacy_sewing.LegacyEnumerateAssemblyMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::legacy_sewing::LegacyEnumerateAssemblyMover::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>

static define_assembly_mover_ct_gen(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::define_assembly_mover_ct_gen(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

follow_random_edge_from_node(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, reference_node: protocols::legacy_sewing::ModelNode) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::follow_random_edge_from_node(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, const class protocols::legacy_sewing::ModelNode *) const –> bool

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

generate_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover) → pyrosetta.rosetta.protocols.legacy_sewing.Assembly¶: C++: protocols::legacy_sewing::LegacyEnumerateAssemblyMover::generate_assembly() –> class std::shared_ptr<class protocols::legacy_sewing::Assembly>

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.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_centroid_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_centroid_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> 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_fullatom_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_fullatom_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> class core::pose::Pose

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.legacy_sewing.LegacyEnumerateAssemblyMover) → str¶: C++: protocols::legacy_sewing::LegacyEnumerateAssemblyMover::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_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

static legacy_assembly_mover_ct_namer(: str) → str¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::legacy_assembly_mover_ct_namer(const std::string &) –> std::string

static mover_name() → str¶: C++: protocols::legacy_sewing::LegacyEnumerateAssemblyMover::mover_name() –> std::string

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

output_stats(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, indicator_whether_from_LegacyMonteCarloAssemblyMover_or_LegacyExhaustiveAssemblyMover: str) → None¶

add several outputs to the score file Pose can’t be const due to scoring.

C++: protocols::legacy_sewing::LegacyAssemblyMover::output_stats(const class std::shared_ptr<class protocols::legacy_sewing::Assembly> &, class core::pose::Pose &, std::string) –> void

parse_global_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_global_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_intra_segment_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_intra_segment_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyEnumerateAssemblyMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyEnumerateAssemblyMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refine_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::refine_assembly(class std::shared_ptr<class protocols::legacy_sewing::Assembly> &) –> class core::pose::Pose

static 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.legacy_sewing.LegacyAssemblyMover) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: 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 std::string &) –> 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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) 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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMoverCreator¶

Bases: MoverCreator

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

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

keyname(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMoverCreator) → str¶: C++: protocols::legacy_sewing::LegacyEnumerateAssemblyMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyEnumerateAssemblyMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover¶

Bases: LegacyAssemblyMover

add_starting_model(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::add_starting_model(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> void

append_movie_frame(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, cycle: int) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::append_movie_frame(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, unsigned long) const –> void

apply(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::apply(class core::pose::Pose &) –> void

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

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.legacy_sewing.LegacyGivenPathAssemblyMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::legacy_sewing::LegacyGivenPathAssemblyMover::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>

static define_assembly_mover_ct_gen(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::define_assembly_mover_ct_gen(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

follow_random_edge_from_node(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, reference_node: protocols::legacy_sewing::ModelNode) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::follow_random_edge_from_node(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, const class protocols::legacy_sewing::ModelNode *) const –> bool

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

generate_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover) → pyrosetta.rosetta.protocols.legacy_sewing.Assembly¶: C++: protocols::legacy_sewing::LegacyGivenPathAssemblyMover::generate_assembly() –> class std::shared_ptr<class protocols::legacy_sewing::Assembly>

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.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_centroid_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_centroid_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> 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_fullatom_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_fullatom_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> class core::pose::Pose

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.legacy_sewing.LegacyGivenPathAssemblyMover) → str¶: C++: protocols::legacy_sewing::LegacyGivenPathAssemblyMover::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_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

static legacy_assembly_mover_ct_namer(: str) → str¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::legacy_assembly_mover_ct_namer(const std::string &) –> std::string

static mover_name() → str¶: C++: protocols::legacy_sewing::LegacyGivenPathAssemblyMover::mover_name() –> std::string

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

output_stats(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, indicator_whether_from_LegacyMonteCarloAssemblyMover_or_LegacyExhaustiveAssemblyMover: str) → None¶

add several outputs to the score file Pose can’t be const due to scoring.

C++: protocols::legacy_sewing::LegacyAssemblyMover::output_stats(const class std::shared_ptr<class protocols::legacy_sewing::Assembly> &, class core::pose::Pose &, std::string) –> void

parse_global_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_global_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_intra_segment_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_intra_segment_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyGivenPathAssemblyMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyGivenPathAssemblyMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refine_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::refine_assembly(class std::shared_ptr<class protocols::legacy_sewing::Assembly> &) –> class core::pose::Pose

static 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.legacy_sewing.LegacyAssemblyMover) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: 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 std::string &) –> 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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) 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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMoverCreator¶

Bases: MoverCreator

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

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

keyname(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMoverCreator) → str¶: C++: protocols::legacy_sewing::LegacyGivenPathAssemblyMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyGivenPathAssemblyMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover¶

Bases: LegacyAssemblyMover

add_starting_model(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::add_starting_model(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> void

append_movie_frame(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, cycle: int) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::append_movie_frame(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, unsigned long) const –> void

apply(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::apply(class core::pose::Pose &) –> void

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

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.legacy_sewing.LegacyGreedyAssemblyMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::legacy_sewing::LegacyGreedyAssemblyMover::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>

static define_assembly_mover_ct_gen(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::define_assembly_mover_ct_gen(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

follow_random_edge_from_node(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, reference_node: protocols::legacy_sewing::ModelNode) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::follow_random_edge_from_node(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, const class protocols::legacy_sewing::ModelNode *) const –> bool

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

generate_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover) → pyrosetta.rosetta.protocols.legacy_sewing.Assembly¶: C++: protocols::legacy_sewing::LegacyGreedyAssemblyMover::generate_assembly() –> class std::shared_ptr<class protocols::legacy_sewing::Assembly>

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.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_centroid_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_centroid_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> 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_fullatom_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_fullatom_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> class core::pose::Pose

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.legacy_sewing.LegacyGreedyAssemblyMover) → str¶: C++: protocols::legacy_sewing::LegacyGreedyAssemblyMover::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_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

static legacy_assembly_mover_ct_namer(: str) → str¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::legacy_assembly_mover_ct_namer(const std::string &) –> std::string

static mover_name() → str¶: C++: protocols::legacy_sewing::LegacyGreedyAssemblyMover::mover_name() –> std::string

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

output_stats(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, indicator_whether_from_LegacyMonteCarloAssemblyMover_or_LegacyExhaustiveAssemblyMover: str) → None¶

add several outputs to the score file Pose can’t be const due to scoring.

C++: protocols::legacy_sewing::LegacyAssemblyMover::output_stats(const class std::shared_ptr<class protocols::legacy_sewing::Assembly> &, class core::pose::Pose &, std::string) –> void

parse_global_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_global_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_intra_segment_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_intra_segment_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyGreedyAssemblyMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyGreedyAssemblyMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refine_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::refine_assembly(class std::shared_ptr<class protocols::legacy_sewing::Assembly> &) –> class core::pose::Pose

static 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.legacy_sewing.LegacyAssemblyMover) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: 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 std::string &) –> 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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) 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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMoverCreator¶

Bases: MoverCreator

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

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

keyname(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMoverCreator) → str¶: C++: protocols::legacy_sewing::LegacyGreedyAssemblyMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyGreedyAssemblyMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover¶

Bases: LegacyAssemblyMover

add_starting_model(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::add_starting_model(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> void

append_movie_frame(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, cycle: int) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::append_movie_frame(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, unsigned long) const –> void

apply(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::apply(class core::pose::Pose &) –> void

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

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.legacy_sewing.LegacyMonteCarloAssemblyMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::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>

static define_assembly_mover_ct_gen(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::define_assembly_mover_ct_gen(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

static define_mc_assembly_mover_ct_gen(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::define_mc_assembly_mover_ct_gen(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

follow_random_edge_from_node(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, reference_node: protocols::legacy_sewing::ModelNode) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::follow_random_edge_from_node(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, const class protocols::legacy_sewing::ModelNode *) const –> bool

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

generate_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover) → pyrosetta.rosetta.protocols.legacy_sewing.Assembly¶: C++: protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::generate_assembly() –> class std::shared_ptr<class protocols::legacy_sewing::Assembly>

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.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_centroid_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_centroid_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> 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_fullatom_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_fullatom_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> class core::pose::Pose

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.legacy_sewing.LegacyMonteCarloAssemblyMover) → str¶: C++: protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::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_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

static legacy_assembly_mover_ct_namer(: str) → str¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::legacy_assembly_mover_ct_namer(const std::string &) –> std::string

static mover_name() → str¶: C++: protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::mover_name() –> std::string

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

output_stats(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, indicator_whether_from_LegacyMonteCarloAssemblyMover_or_LegacyExhaustiveAssemblyMover: str) → None¶

add several outputs to the score file Pose can’t be const due to scoring.

C++: protocols::legacy_sewing::LegacyAssemblyMover::output_stats(const class std::shared_ptr<class protocols::legacy_sewing::Assembly> &, class core::pose::Pose &, std::string) –> void

parse_global_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_global_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_intra_segment_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_intra_segment_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refine_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::refine_assembly(class std::shared_ptr<class protocols::legacy_sewing::Assembly> &) –> class core::pose::Pose

static 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.legacy_sewing.LegacyAssemblyMover) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: 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 std::string &) –> 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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) 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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMoverCreator¶

Bases: MoverCreator

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

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

keyname(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMoverCreator) → str¶: C++: protocols::legacy_sewing::LegacyMonteCarloAssemblyMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyMonteCarloAssemblyMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile¶

Bases: TaskOperation

///////////LegacyReadNativeRotamersFile/////////////////

apply(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::legacy_sewing::LegacyReadNativeRotamersFile::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

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

clone(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::legacy_sewing::LegacyReadNativeRotamersFile::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::legacy_sewing::LegacyReadNativeRotamersFile::keyname() –> std::string

native_rotamers_map(*args, **kwargs)¶

Overloaded function.

native_rotamers_map(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile, nat_ro_map: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t) -> None

C++: protocols::legacy_sewing::LegacyReadNativeRotamersFile::native_rotamers_map(const class std::map<unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > > > > > &) –> void

native_rotamers_map(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile) -> pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t

C++: protocols::legacy_sewing::LegacyReadNativeRotamersFile::native_rotamers_map() const –> const class std::map<unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > > > > > &

parse_tag(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyReadNativeRotamersFile::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyReadNativeRotamersFile::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFileCreator¶

Bases: TaskOperationCreator

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

create_task_operation(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFileCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::legacy_sewing::LegacyReadNativeRotamersFileCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFileCreator) → str¶: C++: protocols::legacy_sewing::LegacyReadNativeRotamersFileCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFileCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyReadNativeRotamersFileCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool¶

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile¶

Bases: LegacyReadNativeRotamersFile

///////////LegacyReadRepeatNativeRotamersFile/////////////////

apply(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

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

clone(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile::keyname() –> std::string

native_rotamers_map(*args, **kwargs)¶

Overloaded function.

native_rotamers_map(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile, nat_ro_map: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t) -> None

C++: protocols::legacy_sewing::LegacyReadNativeRotamersFile::native_rotamers_map(const class std::map<unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > > > > > &) –> void

native_rotamers_map(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile) -> pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t

C++: protocols::legacy_sewing::LegacyReadNativeRotamersFile::native_rotamers_map() const –> const class std::map<unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > > > > > &

property parent¶

parse_tag(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyReadNativeRotamersFile::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFileCreator¶

Bases: TaskOperationCreator

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

create_task_operation(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFileCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFileCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFileCreator) → str¶: C++: protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFileCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFileCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFileCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool¶

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover¶

Bases: LegacyAssemblyMover

add_repeats(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → None¶: C++: protocols::legacy_sewing::LegacyRepeatAssemblyMover::add_repeats(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> void

add_starting_model(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::add_starting_model(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> void

append_movie_frame(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, cycle: int) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::append_movie_frame(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, unsigned long) const –> void

apply(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::apply(class core::pose::Pose &) –> void

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

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.legacy_sewing.LegacyRepeatAssemblyMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::legacy_sewing::LegacyRepeatAssemblyMover::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>

static define_assembly_mover_ct_gen(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::define_assembly_mover_ct_gen(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

dfs_cycle_finder(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover, reference_node: protocols::legacy_sewing::ModelNode, visited_nodes: pyrosetta.rosetta.utility.vector1_const_protocols_legacy_sewing_ModelNode_*, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → Tuple[bool, pyrosetta.rosetta.protocols.legacy_sewing.Assembly]¶: C++: protocols::legacy_sewing::LegacyRepeatAssemblyMover::dfs_cycle_finder(const class protocols::legacy_sewing::ModelNode *, class utility::vector1<const class protocols::legacy_sewing::ModelNode *, class std::allocator<const class protocols::legacy_sewing::ModelNode *> >, class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> struct std::pair<bool, class std::shared_ptr<class protocols::legacy_sewing::Assembly> >

follow_random_edge_from_node(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, reference_node: protocols::legacy_sewing::ModelNode) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::follow_random_edge_from_node(class std::shared_ptr<class protocols::legacy_sewing::Assembly>, const class protocols::legacy_sewing::ModelNode *) const –> bool

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

generate_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover) → pyrosetta.rosetta.protocols.legacy_sewing.Assembly¶: C++: protocols::legacy_sewing::LegacyRepeatAssemblyMover::generate_assembly() –> class std::shared_ptr<class protocols::legacy_sewing::Assembly>

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.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_centroid_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_centroid_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> 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_fullatom_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::get_fullatom_pose(class std::shared_ptr<class protocols::legacy_sewing::Assembly>) const –> class core::pose::Pose

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.legacy_sewing.LegacyRepeatAssemblyMover) → str¶: C++: protocols::legacy_sewing::LegacyRepeatAssemblyMover::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_segment_coords(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover, segment: pyrosetta.rosetta.protocols.legacy_sewing.SewSegment) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t¶: C++: protocols::legacy_sewing::LegacyRepeatAssemblyMover::get_segment_coords(const struct protocols::legacy_sewing::SewSegment &) const –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

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_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

static legacy_assembly_mover_ct_namer(: str) → str¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::legacy_assembly_mover_ct_namer(const std::string &) –> std::string

static mover_name() → str¶: C++: protocols::legacy_sewing::LegacyRepeatAssemblyMover::mover_name() –> std::string

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

output_base_stats(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → None¶

adds single repeat unit data to score file

C++: protocols::legacy_sewing::LegacyRepeatAssemblyMover::output_base_stats(const class std::shared_ptr<class protocols::legacy_sewing::Assembly> &) –> void

output_stats(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, indicator_whether_from_LegacyMonteCarloAssemblyMover_or_LegacyExhaustiveAssemblyMover: str) → None¶

add several outputs to the score file Pose can’t be const due to scoring.

C++: protocols::legacy_sewing::LegacyAssemblyMover::output_stats(const class std::shared_ptr<class protocols::legacy_sewing::Assembly> &, class core::pose::Pose &, std::string) –> void

parse_global_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_global_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_intra_segment_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_intra_segment_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyRepeatAssemblyMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_requirements(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::parse_requirements(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyRepeatAssemblyMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refine_assembly(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover, assembly: pyrosetta.rosetta.protocols.legacy_sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::legacy_sewing::LegacyRepeatAssemblyMover::refine_assembly(class std::shared_ptr<class protocols::legacy_sewing::Assembly> &) –> class core::pose::Pose

static 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.legacy_sewing.LegacyAssemblyMover) → bool¶: C++: protocols::legacy_sewing::LegacyAssemblyMover::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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: 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 std::string &) –> 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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) 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

transform_segment_coords(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover, segment: pyrosetta.rosetta.protocols.legacy_sewing.SewSegment, transformer: pyrosetta.rosetta.numeric.xyzTransform_double_t, com: pyrosetta.rosetta.numeric.xyzVector_float_t, n_transformations: int) → None¶: C++: protocols::legacy_sewing::LegacyRepeatAssemblyMover::transform_segment_coords(struct protocols::legacy_sewing::SewSegment &, class numeric::xyzTransform<double>, class numeric::xyzVector<float>, unsigned long) const –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMoverCreator¶

Bases: MoverCreator

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

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

keyname(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMoverCreator) → str¶: C++: protocols::legacy_sewing::LegacyRepeatAssemblyMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::legacy_sewing::LegacyRepeatAssemblyMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.legacy_sewing.Model¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.legacy_sewing.Model, : pyrosetta.rosetta.protocols.legacy_sewing.Model) → pyrosetta.rosetta.protocols.legacy_sewing.Model¶: C++: protocols::legacy_sewing::Model::operator=(const struct protocols::legacy_sewing::Model &) –> struct protocols::legacy_sewing::Model &

property distance_¶

get_residue(self: pyrosetta.rosetta.protocols.legacy_sewing.Model, resnum: int) → pyrosetta.rosetta.protocols.legacy_sewing.SewResidue¶: C++: protocols::legacy_sewing::Model::get_residue(unsigned long) const –> struct protocols::legacy_sewing::SewResidue

property hoist_angle_degrees_¶

property meridian_angle_degrees_¶

property model_id_¶

property packing_angle_degrees_¶

property pdb_code_¶

pose_number(self: pyrosetta.rosetta.protocols.legacy_sewing.Model, resnum: int) → int¶

get the corresponding pose resnum from the

C++: protocols::legacy_sewing::Model::pose_number(unsigned long) const –> unsigned long

segment_ids(self: pyrosetta.rosetta.protocols.legacy_sewing.Model) → pyrosetta.rosetta.std.set_unsigned_long_t¶

return the set of segment ids for this model

C++: protocols::legacy_sewing::Model::segment_ids() const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

property segments_¶

property structure_id_¶

to_pose_from_db(self: pyrosetta.rosetta.protocols.legacy_sewing.Model) → pyrosetta.rosetta.core.pose.Pose¶

create a pose for this model from the database

C++: protocols::legacy_sewing::Model::to_pose_from_db() const –> class core::pose::Pose

trim_db_pose(self: pyrosetta.rosetta.protocols.legacy_sewing.Model, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

trim the given pose to include only model residues

C++: protocols::legacy_sewing::Model::trim_db_pose(class core::pose::Pose &) const –> void

class pyrosetta.rosetta.protocols.legacy_sewing.ModelNode¶

Bases: Node

add_edge(self: pyrosetta.rosetta.utility.graph.Node, edge_ptr: utility::graph::Edge, : pyrosetta.rosetta.utility.graph.EdgeListIterator) → None¶

adds edge pointer to edge list; returns an iterator to the new: list element

C++: utility::graph::Node::add_edge(class utility::graph::Edge *, class utility::graph::EdgeListIterator &) –> void

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the beginning of its edge list

C++: utility::graph::Node::const_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the end of its edge list

C++: utility::graph::Node::const_edge_list_end() const –> class utility::graph::EdgeListConstIterator

const_lower_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the beginning of its lower-edge list

C++: utility::graph::Node::const_lower_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_lower_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the end of its lower-edge list

C++: utility::graph::Node::const_lower_edge_list_end() const –> class utility::graph::EdgeListConstIterator

const_upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the beginning of its upper-edge list

C++: utility::graph::Node::const_upper_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the end of its upper-edge list

C++: utility::graph::Node::const_upper_edge_list_end() const –> class utility::graph::EdgeListConstIterator

copy_from(self: pyrosetta.rosetta.protocols.legacy_sewing.ModelNode, source: pyrosetta.rosetta.utility.graph.Node) → None¶: C++: protocols::legacy_sewing::ModelNode::copy_from(const class utility::graph::Node *) –> void

count_dynamic_memory(self: pyrosetta.rosetta.utility.graph.Node) → int¶

memory accounting scheme

C++: utility::graph::Node::count_dynamic_memory() const –> unsigned long

count_static_memory(self: pyrosetta.rosetta.utility.graph.Node) → int¶

memory accounting scheme

C++: utility::graph::Node::count_static_memory() const –> unsigned long

drop_all_edges(self: pyrosetta.rosetta.utility.graph.Node) → None¶

deletes all edges incident upon this node

C++: utility::graph::Node::drop_all_edges() –> void

drop_edge(self: pyrosetta.rosetta.utility.graph.Node, edge_iterator: pyrosetta.rosetta.utility.graph.EdgeListIterator) → None¶

removes an edge iterator from the node’s edge list. Only called by Edge class.

C++: utility::graph::Node::drop_edge(class utility::graph::EdgeListIterator) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the beginning of its edge list

C++: utility::graph::Node::edge_list_begin() –> class utility::graph::EdgeListIterator

edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the end of its edge list

C++: utility::graph::Node::edge_list_end() –> class utility::graph::EdgeListIterator

find_edge(self: pyrosetta.rosetta.utility.graph.Node, other_node_index: int) → utility::graph::Edge¶: C++: utility::graph::Node::find_edge(unsigned long) –> class utility::graph::Edge *

get_node_index(self: pyrosetta.rosetta.utility.graph.Node) → int¶

the index for this node

C++: utility::graph::Node::get_node_index() const –> unsigned long

get_num_edges_to_larger_indexed_nodes(self: pyrosetta.rosetta.utility.graph.Node) → int¶

the number of upper neighbors – which “self” neighborness is counted if a loop edge: is present

C++: utility::graph::Node::get_num_edges_to_larger_indexed_nodes() const –> unsigned long

get_num_edges_to_smaller_indexed_nodes(self: pyrosetta.rosetta.utility.graph.Node) → int¶

the number of lower neighbors

C++: utility::graph::Node::get_num_edges_to_smaller_indexed_nodes() const –> unsigned long

loop_incident(self: pyrosetta.rosetta.utility.graph.Node) → bool¶

NOTE TO SELF: remove loop support

C++: utility::graph::Node::loop_incident() const –> bool

lower_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the beginning of its lower-edge list

C++: utility::graph::Node::lower_edge_list_begin() –> class utility::graph::EdgeListIterator

lower_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the end of its lower-edge list

C++: utility::graph::Node::lower_edge_list_end() –> class utility::graph::EdgeListIterator

model(*args, **kwargs)¶

Overloaded function.

model(self: pyrosetta.rosetta.protocols.legacy_sewing.ModelNode) -> pyrosetta.rosetta.protocols.legacy_sewing.Model

C++: protocols::legacy_sewing::ModelNode::model() const –> const struct protocols::legacy_sewing::Model &

model(self: pyrosetta.rosetta.protocols.legacy_sewing.ModelNode, model: pyrosetta.rosetta.protocols.legacy_sewing.Model) -> None

C++: protocols::legacy_sewing::ModelNode::model(const struct protocols::legacy_sewing::Model &) –> void

num_edges(self: pyrosetta.rosetta.utility.graph.Node) → int¶

the number of edges incident on this node, which may include a loop edge

C++: utility::graph::Node::num_edges() const –> unsigned long

num_neighbors_counting_self(self: pyrosetta.rosetta.utility.graph.Node) → int¶

the number of neighbors counting “self” as a neighbor.

C++: utility::graph::Node::num_neighbors_counting_self() const –> unsigned long

num_neighbors_counting_self_static(self: pyrosetta.rosetta.utility.graph.Node) → int¶

the number of neighbors counting “self” as neighbor. Defaults to: num_neighbors_counting_self() but can be set to other values as well. Useful in calculation of symmetrical structures.

C++: utility::graph::Node::num_neighbors_counting_self_static() const –> unsigned long

print(self: pyrosetta.rosetta.utility.graph.Node) → None¶

send summaray data about this node to the screen

C++: utility::graph::Node::print() const –> void

segment_ids(*args, **kwargs)¶

Overloaded function.

segment_ids(self: pyrosetta.rosetta.protocols.legacy_sewing.ModelNode) -> pyrosetta.rosetta.std.set_unsigned_long_t

C++: protocols::legacy_sewing::ModelNode::segment_ids() const –> const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &

segment_ids(self: pyrosetta.rosetta.protocols.legacy_sewing.ModelNode, segment_ids: pyrosetta.rosetta.std.set_unsigned_long_t) -> None

C++: protocols::legacy_sewing::ModelNode::segment_ids(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> void

set_num_neighbors_counting_self_static(self: pyrosetta.rosetta.utility.graph.Node, neighbor: int) → None¶

manually change the number of neighbors for a Node. Used: for symmetry scoring

C++: utility::graph::Node::set_num_neighbors_counting_self_static(unsigned long) –> void

upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the beginning of its upper-edge list

C++: utility::graph::Node::upper_edge_list_begin() –> class utility::graph::EdgeListIterator

upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the end of its upper-edge list

C++: utility::graph::Node::upper_edge_list_end() –> class utility::graph::EdgeListIterator

class pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph¶

Bases: vector1_protocols_legacy_sewing_SewSegment

Simple wrapper around a vector1 of SewSegments, which maintains connection information.

add_connection(self: pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph, i: int, j: int) → None¶: C++: protocols::legacy_sewing::SegmentGraph::add_connection(unsigned long, unsigned long) –> void

append(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment, arg0: protocols::legacy_sewing::SewSegment) → None¶: adds an element to the end

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

back(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment) → protocols::legacy_sewing::SewSegment¶: access the last element

c_segment(self: pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph, ind: int) → int¶: C++: protocols::legacy_sewing::SegmentGraph::c_segment(unsigned long) const –> unsigned long

capacity(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment) → int¶: returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment) → None¶: clears the contents

clear_connections(self: pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph) → None¶: C++: protocols::legacy_sewing::SegmentGraph::clear_connections() –> void

erase(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment, arg0: int) → None¶: erases element at index

extend(othervec)¶

forward_connections(self: pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph) → pyrosetta.rosetta.std.map_unsigned_long_unsigned_long¶: C++: protocols::legacy_sewing::SegmentGraph::forward_connections() const –> class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > >

front(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment) → protocols::legacy_sewing::SewSegment¶: access the first element

has_next(self: pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph, ind: int) → bool¶: C++: protocols::legacy_sewing::SegmentGraph::has_next(unsigned long) const –> bool

has_previous(self: pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph, ind: int) → bool¶: C++: protocols::legacy_sewing::SegmentGraph::has_previous(unsigned long) const –> bool

insert_connected_segment(self: pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph, segment: pyrosetta.rosetta.protocols.legacy_sewing.SewSegment, ind: int) → None¶: C++: protocols::legacy_sewing::SegmentGraph::insert_connected_segment(struct protocols::legacy_sewing::SewSegment, unsigned long) –> void

l(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment) → int¶: lower index

max_size(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment) → int¶: returns the maximum possible number of elements

n_segment(self: pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph, ind: int) → int¶: C++: protocols::legacy_sewing::SegmentGraph::n_segment(unsigned long) const –> unsigned long

next(self: pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph, ind: int) → int¶: C++: protocols::legacy_sewing::SegmentGraph::next(unsigned long) const –> unsigned long

pop(*args, **kwargs)¶

Overloaded function.

pop(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment) -> protocols::legacy_sewing::SewSegment

remove and return last item

pop(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment, arg0: int) -> protocols::legacy_sewing::SewSegment

remove and return item at index

previous(self: pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph, ind: int) → int¶: C++: protocols::legacy_sewing::SegmentGraph::previous(unsigned long) const –> unsigned long

reorder(self: pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph, new_order: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::legacy_sewing::SegmentGraph::reorder(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

reserve(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment, arg0: int) → None¶: reserves storage

resize(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment, arg0: int) → None¶: changes the number of elements stored

reverse_connections(self: pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph) → pyrosetta.rosetta.std.map_unsigned_long_unsigned_long¶: C++: protocols::legacy_sewing::SegmentGraph::reverse_connections() const –> class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > >

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment) → None¶: reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment) → int¶: upper index

class pyrosetta.rosetta.protocols.legacy_sewing.SewAtom¶

Bases: pybind11_object

property atomno_¶

property coords_¶

class pyrosetta.rosetta.protocols.legacy_sewing.SewGraph¶

Bases: Graph

add_all_model_edges_from_binary(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph, filename: str, model_id: int) → None¶: C++: protocols::legacy_sewing::SewGraph::add_all_model_edges_from_binary(std::string, int) –> void

add_edge(*args, **kwargs)¶

Overloaded function.

add_edge(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) -> pyrosetta.rosetta.utility.graph.Edge

add an edge between two vertices. Invokes “create_edge” from the derived class.: Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

C++: utility::graph::Graph::add_edge(unsigned long, unsigned long) –> class utility::graph::Edge *

add_edge(self: pyrosetta.rosetta.utility.graph.Graph, example_edge: pyrosetta.rosetta.utility.graph.Edge) -> pyrosetta.rosetta.utility.graph.Edge

add an edge to this graph copying the data from an edge in another graph.: Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

C++: utility::graph::Graph::add_edge(const class utility::graph::Edge *) –> class utility::graph::Edge *

add_edges_from_binary(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph, filename: str, node_id: int) → None¶: C++: protocols::legacy_sewing::SewGraph::add_edges_from_binary(std::string, unsigned long) –> void

add_special_edges(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph) → None¶: C++: protocols::legacy_sewing::SewGraph::add_special_edges() –> void

all_pairs_shortest_paths(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t¶

O(V^3). Computes all pairs shortest paths using Warshall’s algorithm: and writes all the path distances to the two-dimensional table.

C++: utility::graph::Graph::all_pairs_shortest_paths() const –> class ObjexxFCL::FArray2D<int>

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

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the beginning of the (unordered) edge list for the graph.: this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::const_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the end of the (unordered) edge list for the graph.: this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::const_edge_list_end() const –> class utility::graph::EdgeListConstIterator

copy_connectivity(self: pyrosetta.rosetta.utility.graph.Graph, source: pyrosetta.rosetta.utility.graph.Graph) → None¶

copy the edge connectivity from a source graph with a potentially: unknown type.

C++: utility::graph::Graph::copy_connectivity(const class utility::graph::Graph &) –> void

create_new_edge(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph, index1: int, index2: int) → pyrosetta.rosetta.utility.graph.Edge¶

Factory method for edge creation

C++: protocols::legacy_sewing::SewGraph::create_new_edge(unsigned long, unsigned long) –> class utility::graph::Edge *

create_new_node(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph, index: int) → pyrosetta.rosetta.utility.graph.Node¶

Factory method for node creation

C++: protocols::legacy_sewing::SewGraph::create_new_node(unsigned long) –> class utility::graph::Node *

delete_edge(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph, edge: pyrosetta.rosetta.utility.graph.Edge) → None¶: C++: protocols::legacy_sewing::SewGraph::delete_edge(class utility::graph::Edge *) –> void

drop_all_edges(self: pyrosetta.rosetta.utility.graph.Graph) → None¶

delete all the edges present in the graph

C++: utility::graph::Graph::drop_all_edges() –> void

drop_all_edges_for_node(self: pyrosetta.rosetta.utility.graph.Graph, node: int) → None¶

delete all the edges for a single vertex in the graph

C++: utility::graph::Graph::drop_all_edges_for_node(unsigned long) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the beginning of the (unordered) edge list for the graph.: this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::edge_list_begin() –> class utility::graph::EdgeListIterator

edge_list_end(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the end of the (unordered) edge list for the graph.: this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::edge_list_end() –> class utility::graph::EdgeListIterator

find_edge(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) → pyrosetta.rosetta.utility.graph.Edge¶

returns a pointer to the edge connecting nodes node1 and node2, if that edge exists: in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval.

C++: utility::graph::Graph::find_edge(unsigned long, unsigned long) –> class utility::graph::Edge *

find_hash_edge(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph, n1: int, n2: int) → pyrosetta.rosetta.protocols.legacy_sewing.HashEdge¶: C++: protocols::legacy_sewing::SewGraph::find_hash_edge(unsigned long, unsigned long) –> class protocols::legacy_sewing::HashEdge *

focused_edge(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.Edge¶

returns a pointer to the focused edge

C++: utility::graph::Graph::focused_edge() –> class utility::graph::Edge *

generate_binary_score_file(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph, score_filename: str, binary_filename: str) → None¶: C++: protocols::legacy_sewing::SewGraph::generate_binary_score_file(std::string, std::string) –> void

getTotalMemoryUsage(self: pyrosetta.rosetta.utility.graph.Graph) → int¶

returns a count of all the memory used by every vertex and edge in a graph: by invoking the polymorphic count_static_memory and count_dynamic_memory of each (possibly derived) node and edge object as well as for the (possibly derived) graph class.

C++: utility::graph::Graph::getTotalMemoryUsage() const –> unsigned long

get_edge_exists(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) → bool¶

is an edge already present in the graph? O(V) worst case. O(1) iff all vertices have O(1) edges

C++: utility::graph::Graph::get_edge_exists(unsigned long, unsigned long) const –> bool

get_model_node(*args, **kwargs)¶

Overloaded function.

get_model_node(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph, n: int) -> pyrosetta.rosetta.protocols.legacy_sewing.ModelNode

C++: protocols::legacy_sewing::SewGraph::get_model_node(unsigned long) const –> const class protocols::legacy_sewing::ModelNode *

get_model_node(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph, model_id: int, segment_ids: pyrosetta.rosetta.std.set_unsigned_long_t) -> pyrosetta.rosetta.protocols.legacy_sewing.ModelNode

C++: protocols::legacy_sewing::SewGraph::get_model_node(int, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >) const –> const class protocols::legacy_sewing::ModelNode *

get_node(self: pyrosetta.rosetta.utility.graph.Graph, index: int) → pyrosetta.rosetta.utility.graph.Node¶: C++: utility::graph::Graph::get_node(unsigned long) –> class utility::graph::Node *

get_node_indices_from_model_id(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph, model_id: int) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: protocols::legacy_sewing::SewGraph::get_node_indices_from_model_id(int) const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

get_random_node(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph) → pyrosetta.rosetta.protocols.legacy_sewing.ModelNode¶

get a random node from the graph

C++: protocols::legacy_sewing::SewGraph::get_random_node() const –> const class protocols::legacy_sewing::ModelNode *

get_random_node_with_edges(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph) → pyrosetta.rosetta.protocols.legacy_sewing.ModelNode¶

get a random node involved in at least one edge from the graph

C++: protocols::legacy_sewing::SewGraph::get_random_node_with_edges() const –> const class protocols::legacy_sewing::ModelNode *

get_self_ptr(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.Graph¶: C++: utility::graph::Graph::get_self_ptr() –> class std::shared_ptr<class utility::graph::Graph>

num_edges(self: pyrosetta.rosetta.utility.graph.Graph) → int¶: C++: utility::graph::Graph::num_edges() const –> unsigned long

num_nodes(self: pyrosetta.rosetta.utility.graph.Graph) → int¶

the number of nodes in the graph

C++: utility::graph::Graph::num_nodes() const –> unsigned long

output_connectivity(self: pyrosetta.rosetta.utility.graph.Graph, os: pyrosetta.rosetta.std.ostream) → None¶

send an edge list to the stream os.

C++: utility::graph::Graph::output_connectivity(std::ostream &) const –> void

output_dimacs(self: pyrosetta.rosetta.utility.graph.Graph, os: pyrosetta.rosetta.std.ostream) → None¶

describe this graph in dimacs form to the stream os.

C++: utility::graph::Graph::output_dimacs(std::ostream &) const –> void

print_vertices(self: pyrosetta.rosetta.utility.graph.Graph) → None¶

send summary information to the screen for all vertices in the graph

C++: utility::graph::Graph::print_vertices() const –> void

report_binary_stats(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph, models: pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model, filename: str) → None¶: C++: protocols::legacy_sewing::SewGraph::report_binary_stats(const class std::map<int, struct protocols::legacy_sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::legacy_sewing::Model> > > &, std::string) –> void

set_num_nodes(self: pyrosetta.rosetta.utility.graph.Graph, num_nodes: int) → None¶

set the number of nodes in the graph – deletes any existing edges in the graph

C++: utility::graph::Graph::set_num_nodes(unsigned long) –> void

set_special_edges(self: pyrosetta.rosetta.protocols.legacy_sewing.SewGraph, scores: pyrosetta.rosetta.std.map_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_protocols_legacy_sewing_HashResult_std_less_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_std_allocator_std_pair_const_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_protocols_legacy_sewing_HashResult_t) → None¶: C++: protocols::legacy_sewing::SewGraph::set_special_edges(const class std::map<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult, struct std::less<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> > > &) –> void

class pyrosetta.rosetta.protocols.legacy_sewing.SewResidue¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.legacy_sewing.SewResidue, : pyrosetta.rosetta.protocols.legacy_sewing.SewResidue) → pyrosetta.rosetta.protocols.legacy_sewing.SewResidue¶: C++: protocols::legacy_sewing::SewResidue::operator=(const struct protocols::legacy_sewing::SewResidue &) –> struct protocols::legacy_sewing::SewResidue &

property basis_atoms_¶

property chi_angles_¶

property matched_residues_¶

property num_neighbors_¶

property residue_type_¶

property resnum_¶

class pyrosetta.rosetta.protocols.legacy_sewing.SewSegment¶

Bases: pybind11_object

property chimera_¶

property dssp_¶

property hash_¶

property model_id_¶

property parent_segments_¶

property residues_¶

property segment_id_¶

pyrosetta.rosetta.protocols.legacy_sewing.add_linker_segments(models: pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model) → None¶: C++: protocols::legacy_sewing::add_linker_segments(class std::map<int, struct protocols::legacy_sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::legacy_sewing::Model> > > &) –> void

pyrosetta.rosetta.protocols.legacy_sewing.add_num_neighbors(models: pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model) → None¶: C++: protocols::legacy_sewing::add_num_neighbors(class std::map<int, struct protocols::legacy_sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::legacy_sewing::Model> > > &) –> void

class pyrosetta.rosetta.protocols.legacy_sewing.basis_pair_equal_to¶: Bases: pybind11_object

class pyrosetta.rosetta.protocols.legacy_sewing.basis_pair_hash¶: Bases: pybind11_object

class pyrosetta.rosetta.protocols.legacy_sewing.coord_equal_to¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.legacy_sewing.coord_equal_to, : pyrosetta.rosetta.protocols.legacy_sewing.coord_equal_to) → pyrosetta.rosetta.protocols.legacy_sewing.coord_equal_to¶: C++: protocols::legacy_sewing::coord_equal_to::operator=(const struct protocols::legacy_sewing::coord_equal_to &) –> struct protocols::legacy_sewing::coord_equal_to &

class pyrosetta.rosetta.protocols.legacy_sewing.coord_hash¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.legacy_sewing.coord_hash, : pyrosetta.rosetta.protocols.legacy_sewing.coord_hash) → pyrosetta.rosetta.protocols.legacy_sewing.coord_hash¶: C++: protocols::legacy_sewing::coord_hash::operator=(const struct protocols::legacy_sewing::coord_hash &) –> struct protocols::legacy_sewing::coord_hash &

pyrosetta.rosetta.protocols.legacy_sewing.create_alpha_beta_models_table() → None¶: C++: protocols::legacy_sewing::create_alpha_beta_models_table() –> void

pyrosetta.rosetta.protocols.legacy_sewing.create_model_from_pose(pose: pyrosetta.rosetta.core.pose.Pose, segments: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, model_id: int) → pyrosetta.rosetta.protocols.legacy_sewing.Model¶

create a Model from the pose

C++: protocols::legacy_sewing::create_model_from_pose(const 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> > > &, int) –> struct protocols::legacy_sewing::Model

pyrosetta.rosetta.protocols.legacy_sewing.get_5_ss_models_from_db(hash_between: str) → pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model¶: C++: protocols::legacy_sewing::get_5_ss_models_from_db(const std::string &) –> class std::map<int, struct protocols::legacy_sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::legacy_sewing::Model> > >

pyrosetta.rosetta.protocols.legacy_sewing.get_alpha_beta_models_from_db() → pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model¶: C++: protocols::legacy_sewing::get_alpha_beta_models_from_db() –> class std::map<int, struct protocols::legacy_sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::legacy_sewing::Model> > >

pyrosetta.rosetta.protocols.legacy_sewing.get_continuous_models_from_db(hash_between: str) → pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model¶: C++: protocols::legacy_sewing::get_continuous_models_from_db(const std::string &) –> class std::map<int, struct protocols::legacy_sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::legacy_sewing::Model> > >

pyrosetta.rosetta.protocols.legacy_sewing.get_discontinuous_models_from_db() → pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model¶: C++: protocols::legacy_sewing::get_discontinuous_models_from_db() –> class std::map<int, struct protocols::legacy_sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::legacy_sewing::Model> > >

pyrosetta.rosetta.protocols.legacy_sewing.get_strand_sew_models_from_db() → pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model¶: C++: protocols::legacy_sewing::get_strand_sew_models_from_db() –> class std::map<int, struct protocols::legacy_sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::legacy_sewing::Model> > >

pyrosetta.rosetta.protocols.legacy_sewing.largest_continuous_atom_map(atom_map: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID) → pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID¶: C++: protocols::legacy_sewing::largest_continuous_atom_map(const class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > > &) –> class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > >

class pyrosetta.rosetta.protocols.legacy_sewing.move_type¶

Bases: pybind11_object

Members:

ADD_EDGE

DELETE_EDGE

SWITCH_EDGE

ADD_EDGE = <move_type.ADD_EDGE: 1>¶

DELETE_EDGE = <move_type.DELETE_EDGE: 2>¶

SWITCH_EDGE = <move_type.SWITCH_EDGE: 3>¶

property name¶

property value¶

pyrosetta.rosetta.protocols.legacy_sewing.read_model_file(filename: str) → pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model¶: C++: protocols::legacy_sewing::read_model_file(std::string) –> class std::map<int, struct protocols::legacy_sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::legacy_sewing::Model> > >

pyrosetta.rosetta.protocols.legacy_sewing.read_native_residue_file(filename: str) → pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t¶: C++: protocols::legacy_sewing::read_native_residue_file(const std::string &) –> class std::map<unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > > > > >

pyrosetta.rosetta.protocols.legacy_sewing.remove_models_from_dssp(models: pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model, dssp1: str, dssp2: str) → None¶: C++: protocols::legacy_sewing::remove_models_from_dssp(class std::map<int, struct protocols::legacy_sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::legacy_sewing::Model> > > &, char, char) –> void

pyrosetta.rosetta.protocols.legacy_sewing.see_whether_model_is_H_bonded_by_terminal_strands(model: pyrosetta.rosetta.protocols.legacy_sewing.Model, P_PA: str) → str¶

Return true if given model is H bonded by terminal strands

C++: protocols::legacy_sewing::see_whether_model_is_H_bonded_by_terminal_strands(struct protocols::legacy_sewing::Model, const std::string &) –> std::string

pyrosetta.rosetta.protocols.legacy_sewing.serialize_graph_json(graph: protocols::legacy_sewing::SewGraph, max_nodes: int) → str¶: C++: protocols::legacy_sewing::serialize_graph_json(class std::shared_ptr<const class protocols::legacy_sewing::SewGraph>, unsigned long) –> std::string

pyrosetta.rosetta.protocols.legacy_sewing.write_hashing_scores_to_file(scores: pyrosetta.rosetta.std.map_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_protocols_legacy_sewing_HashResult_std_less_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_std_allocator_std_pair_const_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_protocols_legacy_sewing_HashResult_t, filename: str) → None¶

Take the given StructureScores and save them to disk

C++: protocols::legacy_sewing::write_hashing_scores_to_file(const class std::map<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult, struct std::less<struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::legacy_sewing::Basis, struct protocols::legacy_sewing::Basis>, struct protocols::legacy_sewing::HashResult> > > &, std::string) –> void

pyrosetta.rosetta.protocols.legacy_sewing.write_model_file(comments: str, models: pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model, filename: str) → None¶: C++: protocols::legacy_sewing::write_model_file(const std::string &, class std::map<int, struct protocols::legacy_sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::legacy_sewing::Model> > >, std::string) –> void

pyrosetta.rosetta.protocols.legacy_sewing.write_native_residue_file(native_residue_map: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t, filename: str) → None¶: C++: protocols::legacy_sewing::write_native_residue_file(class std::map<unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> >, class std::allocator<struct std::pair<bool, class std::shared_ptr<class core::conformation::Residue> > > > > > >, const std::string &) –> void