sewing

• sampling
• scoring

Bindings for protocols::sewing namespace

class pyrosetta.rosetta.protocols.sewing.Assembly

Bases: pybind11_builtins.pybind11_object

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.sewing.Assembly) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.protocols.sewing.Assembly) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

add_loop_segment(self: pyrosetta.rosetta.protocols.sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop, segment: int) → None

C++: protocols::sewing::Assembly::add_loop_segment(const class core::pose::Pose &, class protocols::loops::Loop, unsigned long) –> void

add_model(*args, **kwargs)

Overloaded function.

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

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

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

align_model(self: pyrosetta.rosetta.protocols.sewing.Assembly, mobile_model: pyrosetta.rosetta.protocols.sewing.Model, atom_alignments: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_model_id: int) → None

C++: protocols::sewing::Assembly::align_model(struct protocols::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.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_sewing_SewSegment_std_allocator_protocols_sewing_SewSegment_t

C++: protocols::sewing::Assembly::all_segments() const –> class utility::vector1<class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> >, class std::allocator<class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> > > >

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

append the given model to the end of the assembly

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

append_segments(self: pyrosetta.rosetta.protocols.sewing.Assembly, segments: pyrosetta.rosetta.utility.vector1_protocols_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::sewing::Assembly::append_segments(const class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> > &) –> void

assign(self: pyrosetta.rosetta.protocols.sewing.Assembly, : pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.protocols.sewing.Assembly

C++: protocols::sewing::Assembly::operator=(const class protocols::sewing::Assembly &) –> class protocols::sewing::Assembly &

atom_map_from_score_result(self: pyrosetta.rosetta.protocols.sewing.Assembly, alignment_scores: Tuple[Tuple[pyrosetta.rosetta.protocols.sewing.Basis, pyrosetta.rosetta.protocols.sewing.Basis], pyrosetta.rosetta.protocols.sewing.HashResult]) → pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID

C++: protocols::sewing::Assembly::atom_map_from_score_result(const struct std::pair<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::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> > >

clone(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.protocols.sewing.Assembly

C++: protocols::sewing::Assembly::clone() –> class std::shared_ptr<class protocols::sewing::Assembly>

create_chimera_segment(self: pyrosetta.rosetta.protocols.sewing.Assembly, reference_segment: pyrosetta.rosetta.protocols.sewing.SewSegment, mobile_segment: pyrosetta.rosetta.protocols.sewing.SewSegment, atom_map: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_is_nter: bool) → pyrosetta.rosetta.protocols.sewing.SewSegment

C++: protocols::sewing::Assembly::create_chimera_segment(const struct protocols::sewing::SewSegment &, const struct protocols::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::sewing::SewSegment

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

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

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

disconnected_segments(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::sewing::Assembly::disconnected_segments() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

ending_node(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.protocols.sewing.ModelNode

C++: protocols::sewing::Assembly::ending_node() const –> const class protocols::sewing::ModelNode *

find_possible_orders(self: pyrosetta.rosetta.protocols.sewing.Assembly, max_loop_distance: float) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

C++: protocols::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.sewing.Assembly, graph: pyrosetta.rosetta.protocols.sewing.SewGraph, edge: pyrosetta.rosetta.protocols.sewing.HashEdge, source_index: int) → None

C++: protocols::sewing::Assembly::follow_edge(class std::shared_ptr<const class protocols::sewing::SewGraph>, const class protocols::sewing::HashEdge *const, unsigned long) –> void

get_model_segments(self: pyrosetta.rosetta.protocols.sewing.Assembly, model_id: int) → pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment

C++: protocols::sewing::Assembly::get_model_segments(int) const –> class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> >

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

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

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

get_partner(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::sewing::Assembly::get_partner() const –> class std::shared_ptr<class core::pose::Pose>

get_score_result(self: pyrosetta.rosetta.protocols.sewing.Assembly, model_1_node: pyrosetta.rosetta.protocols.sewing.ModelNode, cur_edge: pyrosetta.rosetta.protocols.sewing.HashEdge, graph: pyrosetta.rosetta.protocols.sewing.SewGraph) → Tuple[Tuple[pyrosetta.rosetta.protocols.sewing.Basis, pyrosetta.rosetta.protocols.sewing.Basis], pyrosetta.rosetta.protocols.sewing.HashResult]

C++: protocols::sewing::Assembly::get_score_result(const class protocols::sewing::ModelNode *, const class protocols::sewing::HashEdge *const, class std::shared_ptr<const class protocols::sewing::SewGraph>) const –> struct std::pair<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult>

map_residues(self: pyrosetta.rosetta.protocols.sewing.Assembly, reference_model_id: int, mobile_model: pyrosetta.rosetta.protocols.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::sewing::Assembly::map_residues(int, struct protocols::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.sewing.Assembly) → pyrosetta.rosetta.std.set_unsigned_long_t

C++: protocols::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.sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_unsigned_long_t

C++: protocols::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.

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

print pymol selection of “native” positions

C++: protocols::sewing::Assembly::natives_select(const class core::pose::Pose &, class std::basic_string<char>) const –> std::string

path(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

C++: protocols::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.sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → float

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

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

pose_loop_anchors(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::sewing::Assembly::pose_loop_anchors() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pose_num(self: pyrosetta.rosetta.protocols.sewing.Assembly, model_id: int, resnum: int) → int

C++: protocols::sewing::Assembly::pose_num(int, unsigned long) const –> unsigned long

prepare_for_packing(self: pyrosetta.rosetta.protocols.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::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.sewing.Assembly, model_id: int) → pyrosetta.rosetta.protocols.sewing.Model

C++: protocols::sewing::Assembly::regenerate_model(int) const –> struct protocols::sewing::Model

reorder(self: pyrosetta.rosetta.protocols.sewing.Assembly, new_order: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::sewing::Assembly::reorder(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

reorder_randomly(self: pyrosetta.rosetta.protocols.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::sewing::Assembly::reorder_randomly(double) –> bool

segments(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment

C++: protocols::sewing::Assembly::segments() const –> class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> >

set_partner(self: pyrosetta.rosetta.protocols.sewing.Assembly, partner_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::sewing::Assembly::set_partner(class std::shared_ptr<class core::pose::Pose>) –> void

starting_node(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.protocols.sewing.ModelNode

C++: protocols::sewing::Assembly::starting_node() const –> const class protocols::sewing::ModelNode *

string_blosum(self: pyrosetta.rosetta.protocols.sewing.Assembly, blosum_history: pyrosetta.rosetta.utility.vector1_std_pair_double_unsigned_long_t) → str

C++: protocols::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.sewing.Assembly) → str

C++: protocols::sewing::Assembly::string_path() const –> std::string

to_multichain_pose(self: pyrosetta.rosetta.protocols.sewing.Assembly, residue_type_set: str) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::sewing::Assembly::to_multichain_pose(class std::basic_string<char>) const –> class core::pose::Pose

to_pose(*args, **kwargs)

Overloaded function.

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

C++: protocols::sewing::Assembly::to_pose(class std::basic_string<char>, bool) const –> class core::pose::Pose

total_residue(self: pyrosetta.rosetta.protocols.sewing.Assembly) → int

C++: protocols::sewing::Assembly::total_residue() const –> unsigned long

update_coords_from_pose(self: pyrosetta.rosetta.protocols.sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::sewing::Assembly::update_coords_from_pose(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

///////////AssemblyConstraintsMover/////////////////

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover, arg0: pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

apply(self: pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::sewing::AssemblyConstraintsMover::apply(class core::pose::Pose &) –> void

apply_repeat(self: pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::sewing::AssemblyConstraintsMover::apply_repeat(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover, : pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover) → pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover

C++: protocols::sewing::AssemblyConstraintsMover::operator=(const class protocols::sewing::AssemblyConstraintsMover &) –> class protocols::sewing::AssemblyConstraintsMover &

base_native_bonus(self: pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover, base_native_bonus: float) → None

C++: protocols::sewing::AssemblyConstraintsMover::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.sewing.AssemblyConstraintsMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::sewing::AssemblyConstraintsMover::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.sewing.AssemblyConstraintsMover) → pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

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

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

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover) → str

C++: protocols::sewing::AssemblyConstraintsMover::get_name() const –> std::string

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

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

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

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mover_name() → str

C++: protocols::sewing::AssemblyConstraintsMover::mover_name() –> std::string

name() → str

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

neighbor_cutoff(self: pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover, neighbor_cutoff: float) → None

C++: protocols::sewing::AssemblyConstraintsMover::neighbor_cutoff(double) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::sewing::AssemblyConstraintsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

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

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

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

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

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

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

setter for poses contained for rms

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

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

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

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

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

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

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
2. 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(class std::basic_ostream<char> &) const –> void

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

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

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

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

class pyrosetta.rosetta.protocols.sewing.AssemblyFactory

Bases: pybind11_builtins.pybind11_object

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.sewing.AssemblyFactory) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

create_assembly(assembly_name: str) → pyrosetta.rosetta.protocols.sewing.Assembly

C++: protocols::sewing::AssemblyFactory::create_assembly(class std::basic_string<char>) –> class std::shared_ptr<class protocols::sewing::Assembly>

class pyrosetta.rosetta.protocols.sewing.Basis

Bases: pybind11_builtins.pybind11_object

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.sewing.Basis) -> None
2. __init__(self: pyrosetta.rosetta.protocols.sewing.Basis, model_id_temp: int, resnum_temp: int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.sewing.Basis, arg0: pyrosetta.rosetta.protocols.sewing.Basis) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.sewing.Basis, : pyrosetta.rosetta.protocols.sewing.Basis) → pyrosetta.rosetta.protocols.sewing.Basis

C++: protocols::sewing::Basis::operator=(const struct protocols::sewing::Basis &) –> struct protocols::sewing::Basis &

class pyrosetta.rosetta.protocols.sewing.ContinuousAssembly

Bases: pyrosetta.rosetta.protocols.sewing.Assembly

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.sewing.ContinuousAssembly) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.protocols.sewing.Assembly) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

add_loop_segment(self: pyrosetta.rosetta.protocols.sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop, segment: int) → None

C++: protocols::sewing::Assembly::add_loop_segment(const class core::pose::Pose &, class protocols::loops::Loop, unsigned long) –> void

add_model(*args, **kwargs)

Overloaded function.

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

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

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

align_model(self: pyrosetta.rosetta.protocols.sewing.Assembly, mobile_model: pyrosetta.rosetta.protocols.sewing.Model, atom_alignments: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_model_id: int) → None

C++: protocols::sewing::Assembly::align_model(struct protocols::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.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_sewing_SewSegment_std_allocator_protocols_sewing_SewSegment_t

C++: protocols::sewing::Assembly::all_segments() const –> class utility::vector1<class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> >, class std::allocator<class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> > > >

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

Needs to be implemented.

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

append_segments(self: pyrosetta.rosetta.protocols.sewing.Assembly, segments: pyrosetta.rosetta.utility.vector1_protocols_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::sewing::Assembly::append_segments(const class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> > &) –> void

assign(self: pyrosetta.rosetta.protocols.sewing.ContinuousAssembly, : pyrosetta.rosetta.protocols.sewing.ContinuousAssembly) → pyrosetta.rosetta.protocols.sewing.ContinuousAssembly

C++: protocols::sewing::ContinuousAssembly::operator=(const class protocols::sewing::ContinuousAssembly &) –> class protocols::sewing::ContinuousAssembly &

atom_map_from_score_result(self: pyrosetta.rosetta.protocols.sewing.Assembly, alignment_scores: Tuple[Tuple[pyrosetta.rosetta.protocols.sewing.Basis, pyrosetta.rosetta.protocols.sewing.Basis], pyrosetta.rosetta.protocols.sewing.HashResult]) → pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID

C++: protocols::sewing::Assembly::atom_map_from_score_result(const struct std::pair<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::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> > >

clone(self: pyrosetta.rosetta.protocols.sewing.ContinuousAssembly) → pyrosetta.rosetta.protocols.sewing.Assembly

C++: protocols::sewing::ContinuousAssembly::clone() –> class std::shared_ptr<class protocols::sewing::Assembly>

create_chimera_segment(self: pyrosetta.rosetta.protocols.sewing.Assembly, reference_segment: pyrosetta.rosetta.protocols.sewing.SewSegment, mobile_segment: pyrosetta.rosetta.protocols.sewing.SewSegment, atom_map: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_is_nter: bool) → pyrosetta.rosetta.protocols.sewing.SewSegment

C++: protocols::sewing::Assembly::create_chimera_segment(const struct protocols::sewing::SewSegment &, const struct protocols::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::sewing::SewSegment

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

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

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

disconnected_segments(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::sewing::Assembly::disconnected_segments() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

ending_node(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.protocols.sewing.ModelNode

C++: protocols::sewing::Assembly::ending_node() const –> const class protocols::sewing::ModelNode *

find_possible_orders(self: pyrosetta.rosetta.protocols.sewing.Assembly, max_loop_distance: float) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

C++: protocols::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.sewing.Assembly, graph: pyrosetta.rosetta.protocols.sewing.SewGraph, edge: pyrosetta.rosetta.protocols.sewing.HashEdge, source_index: int) → None

C++: protocols::sewing::Assembly::follow_edge(class std::shared_ptr<const class protocols::sewing::SewGraph>, const class protocols::sewing::HashEdge *const, unsigned long) –> void

get_model_segments(self: pyrosetta.rosetta.protocols.sewing.Assembly, model_id: int) → pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment

C++: protocols::sewing::Assembly::get_model_segments(int) const –> class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> >

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

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

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

get_partner(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::sewing::Assembly::get_partner() const –> class std::shared_ptr<class core::pose::Pose>

get_score_result(self: pyrosetta.rosetta.protocols.sewing.Assembly, model_1_node: pyrosetta.rosetta.protocols.sewing.ModelNode, cur_edge: pyrosetta.rosetta.protocols.sewing.HashEdge, graph: pyrosetta.rosetta.protocols.sewing.SewGraph) → Tuple[Tuple[pyrosetta.rosetta.protocols.sewing.Basis, pyrosetta.rosetta.protocols.sewing.Basis], pyrosetta.rosetta.protocols.sewing.HashResult]

C++: protocols::sewing::Assembly::get_score_result(const class protocols::sewing::ModelNode *, const class protocols::sewing::HashEdge *const, class std::shared_ptr<const class protocols::sewing::SewGraph>) const –> struct std::pair<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult>

map_residues(self: pyrosetta.rosetta.protocols.sewing.Assembly, reference_model_id: int, mobile_model: pyrosetta.rosetta.protocols.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::sewing::Assembly::map_residues(int, struct protocols::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.sewing.Assembly) → pyrosetta.rosetta.std.set_unsigned_long_t

C++: protocols::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.sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_unsigned_long_t

C++: protocols::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.

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

print pymol selection of “native” positions

C++: protocols::sewing::Assembly::natives_select(const class core::pose::Pose &, class std::basic_string<char>) const –> std::string

path(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

C++: protocols::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.sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → float

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

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

pose_loop_anchors(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::sewing::Assembly::pose_loop_anchors() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pose_num(self: pyrosetta.rosetta.protocols.sewing.Assembly, model_id: int, resnum: int) → int

C++: protocols::sewing::Assembly::pose_num(int, unsigned long) const –> unsigned long

prepare_for_packing(self: pyrosetta.rosetta.protocols.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::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.sewing.Assembly, model_id: int) → pyrosetta.rosetta.protocols.sewing.Model

C++: protocols::sewing::Assembly::regenerate_model(int) const –> struct protocols::sewing::Model

reorder(self: pyrosetta.rosetta.protocols.sewing.Assembly, new_order: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::sewing::Assembly::reorder(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

reorder_randomly(self: pyrosetta.rosetta.protocols.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::sewing::Assembly::reorder_randomly(double) –> bool

segments(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment

C++: protocols::sewing::Assembly::segments() const –> class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> >

set_partner(self: pyrosetta.rosetta.protocols.sewing.Assembly, partner_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::sewing::Assembly::set_partner(class std::shared_ptr<class core::pose::Pose>) –> void

starting_node(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.protocols.sewing.ModelNode

C++: protocols::sewing::Assembly::starting_node() const –> const class protocols::sewing::ModelNode *

string_blosum(self: pyrosetta.rosetta.protocols.sewing.Assembly, blosum_history: pyrosetta.rosetta.utility.vector1_std_pair_double_unsigned_long_t) → str

C++: protocols::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.sewing.Assembly) → str

C++: protocols::sewing::Assembly::string_path() const –> std::string

to_multichain_pose(self: pyrosetta.rosetta.protocols.sewing.Assembly, residue_type_set: str) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::sewing::Assembly::to_multichain_pose(class std::basic_string<char>) const –> class core::pose::Pose

to_pose(*args, **kwargs)

Overloaded function.

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

C++: protocols::sewing::Assembly::to_pose(class std::basic_string<char>, bool) const –> class core::pose::Pose

total_residue(self: pyrosetta.rosetta.protocols.sewing.Assembly) → int

C++: protocols::sewing::Assembly::total_residue() const –> unsigned long

update_coords_from_pose(self: pyrosetta.rosetta.protocols.sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::sewing::Assembly::update_coords_from_pose(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly

Bases: pyrosetta.rosetta.protocols.sewing.Assembly

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.protocols.sewing.Assembly) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

add_loop_segment(self: pyrosetta.rosetta.protocols.sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop, segment: int) → None

C++: protocols::sewing::Assembly::add_loop_segment(const class core::pose::Pose &, class protocols::loops::Loop, unsigned long) –> void

add_model(*args, **kwargs)

Overloaded function.

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

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

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

align_model(self: pyrosetta.rosetta.protocols.sewing.Assembly, mobile_model: pyrosetta.rosetta.protocols.sewing.Model, atom_alignments: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_model_id: int) → None

C++: protocols::sewing::Assembly::align_model(struct protocols::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.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_sewing_SewSegment_std_allocator_protocols_sewing_SewSegment_t

C++: protocols::sewing::Assembly::all_segments() const –> class utility::vector1<class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> >, class std::allocator<class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> > > >

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

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

append_segments(self: pyrosetta.rosetta.protocols.sewing.Assembly, segments: pyrosetta.rosetta.utility.vector1_protocols_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::sewing::Assembly::append_segments(const class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> > &) –> void

assign(self: pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly, : pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly) → pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly

C++: protocols::sewing::DisembodiedAssembly::operator=(const class protocols::sewing::DisembodiedAssembly &) –> class protocols::sewing::DisembodiedAssembly &

atom_map_from_score_result(self: pyrosetta.rosetta.protocols.sewing.Assembly, alignment_scores: Tuple[Tuple[pyrosetta.rosetta.protocols.sewing.Basis, pyrosetta.rosetta.protocols.sewing.Basis], pyrosetta.rosetta.protocols.sewing.HashResult]) → pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID

C++: protocols::sewing::Assembly::atom_map_from_score_result(const struct std::pair<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::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> > >

clone(self: pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly) → pyrosetta.rosetta.protocols.sewing.Assembly

C++: protocols::sewing::DisembodiedAssembly::clone() –> class std::shared_ptr<class protocols::sewing::Assembly>

create_chimera_segment(self: pyrosetta.rosetta.protocols.sewing.Assembly, reference_segment: pyrosetta.rosetta.protocols.sewing.SewSegment, mobile_segment: pyrosetta.rosetta.protocols.sewing.SewSegment, atom_map: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_is_nter: bool) → pyrosetta.rosetta.protocols.sewing.SewSegment

C++: protocols::sewing::Assembly::create_chimera_segment(const struct protocols::sewing::SewSegment &, const struct protocols::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::sewing::SewSegment

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

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

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

disconnected_segments(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::sewing::Assembly::disconnected_segments() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

ending_node(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.protocols.sewing.ModelNode

C++: protocols::sewing::Assembly::ending_node() const –> const class protocols::sewing::ModelNode *

find_possible_orders(self: pyrosetta.rosetta.protocols.sewing.Assembly, max_loop_distance: float) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

C++: protocols::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.sewing.Assembly, graph: pyrosetta.rosetta.protocols.sewing.SewGraph, edge: pyrosetta.rosetta.protocols.sewing.HashEdge, source_index: int) → None

C++: protocols::sewing::Assembly::follow_edge(class std::shared_ptr<const class protocols::sewing::SewGraph>, const class protocols::sewing::HashEdge *const, unsigned long) –> void

get_model_segments(self: pyrosetta.rosetta.protocols.sewing.Assembly, model_id: int) → pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment

C++: protocols::sewing::Assembly::get_model_segments(int) const –> class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> >

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

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

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

get_partner(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::sewing::Assembly::get_partner() const –> class std::shared_ptr<class core::pose::Pose>

get_score_result(self: pyrosetta.rosetta.protocols.sewing.Assembly, model_1_node: pyrosetta.rosetta.protocols.sewing.ModelNode, cur_edge: pyrosetta.rosetta.protocols.sewing.HashEdge, graph: pyrosetta.rosetta.protocols.sewing.SewGraph) → Tuple[Tuple[pyrosetta.rosetta.protocols.sewing.Basis, pyrosetta.rosetta.protocols.sewing.Basis], pyrosetta.rosetta.protocols.sewing.HashResult]

C++: protocols::sewing::Assembly::get_score_result(const class protocols::sewing::ModelNode *, const class protocols::sewing::HashEdge *const, class std::shared_ptr<const class protocols::sewing::SewGraph>) const –> struct std::pair<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult>

map_residues(self: pyrosetta.rosetta.protocols.sewing.Assembly, reference_model_id: int, mobile_model: pyrosetta.rosetta.protocols.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::sewing::Assembly::map_residues(int, struct protocols::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.sewing.Assembly) → pyrosetta.rosetta.std.set_unsigned_long_t

C++: protocols::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.sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_unsigned_long_t

C++: protocols::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.

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

print pymol selection of “native” positions

C++: protocols::sewing::Assembly::natives_select(const class core::pose::Pose &, class std::basic_string<char>) const –> std::string

path(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

C++: protocols::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.sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → float

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

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

pose_loop_anchors(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::sewing::Assembly::pose_loop_anchors() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pose_num(self: pyrosetta.rosetta.protocols.sewing.Assembly, model_id: int, resnum: int) → int

C++: protocols::sewing::Assembly::pose_num(int, unsigned long) const –> unsigned long

prepare_for_packing(self: pyrosetta.rosetta.protocols.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::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.sewing.Assembly, model_id: int) → pyrosetta.rosetta.protocols.sewing.Model

C++: protocols::sewing::Assembly::regenerate_model(int) const –> struct protocols::sewing::Model

reorder(self: pyrosetta.rosetta.protocols.sewing.Assembly, new_order: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::sewing::Assembly::reorder(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

reorder_randomly(self: pyrosetta.rosetta.protocols.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::sewing::Assembly::reorder_randomly(double) –> bool

segments(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment

C++: protocols::sewing::Assembly::segments() const –> class utility::vector1<struct protocols::sewing::SewSegment, class std::allocator<struct protocols::sewing::SewSegment> >

set_partner(self: pyrosetta.rosetta.protocols.sewing.Assembly, partner_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::sewing::Assembly::set_partner(class std::shared_ptr<class core::pose::Pose>) –> void

starting_node(self: pyrosetta.rosetta.protocols.sewing.Assembly) → pyrosetta.rosetta.protocols.sewing.ModelNode

C++: protocols::sewing::Assembly::starting_node() const –> const class protocols::sewing::ModelNode *

string_blosum(self: pyrosetta.rosetta.protocols.sewing.Assembly, blosum_history: pyrosetta.rosetta.utility.vector1_std_pair_double_unsigned_long_t) → str

C++: protocols::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.sewing.Assembly) → str

C++: protocols::sewing::Assembly::string_path() const –> std::string

to_multichain_pose(self: pyrosetta.rosetta.protocols.sewing.Assembly, residue_type_set: str) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::sewing::Assembly::to_multichain_pose(class std::basic_string<char>) const –> class core::pose::Pose

to_pose(*args, **kwargs)

Overloaded function.

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

C++: protocols::sewing::Assembly::to_pose(class std::basic_string<char>, bool) const –> class core::pose::Pose

total_residue(self: pyrosetta.rosetta.protocols.sewing.Assembly) → int

C++: protocols::sewing::Assembly::total_residue() const –> unsigned long

update_coords_from_pose(self: pyrosetta.rosetta.protocols.sewing.Assembly, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::sewing::Assembly::update_coords_from_pose(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.sewing.HashEdge

Bases: pyrosetta.rosetta.utility.graph.Edge

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.sewing.HashEdge, owner: protocols::sewing::SewGraph, n1: int, n2: int) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.protocols.sewing.HashEdge) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

basis_pair(*args, **kwargs)

Overloaded function.

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

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

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

C++: protocols::sewing::HashEdge::basis_pair() const –> const struct std::pair<struct protocols::sewing::Basis, struct protocols::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.sewing.HashEdge, model_id: int) → int

C++: protocols::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.sewing.Hasher

Bases: pybind11_builtins.pybind11_object

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.sewing.Hasher) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.sewing.Hasher, : pyrosetta.rosetta.protocols.sewing.Hasher) → pyrosetta.rosetta.protocols.sewing.Hasher

C++: protocols::sewing::Hasher::operator=(const class protocols::sewing::Hasher &) –> class protocols::sewing::Hasher &

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

Create the HashKey from a SewAtom

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

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

Hash the transformed residues into the HashMap

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

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

Insert this model into the hash table

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

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

Populate the hash table from one on disk.

C++: protocols::sewing::Hasher::read_from_disk(class std::basic_string<char>) –> void

remove_connection_inconsistencies(self: pyrosetta.rosetta.protocols.sewing.Hasher, models: pyrosetta.rosetta.std.map_int_protocols_sewing_Model, scores: pyrosetta.rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult) → None

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

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

remove_duplicates(self: pyrosetta.rosetta.protocols.sewing.Hasher, scores: pyrosetta.rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult) → pyrosetta.rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult

keep only best scoring alignment between two models

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

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.sewing.Hasher, model: pyrosetta.rosetta.protocols.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_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult

C++: protocols::sewing::Hasher::score(const struct protocols::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::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult, struct std::less<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult> > >

2. score(self: pyrosetta.rosetta.protocols.sewing.Hasher, model: pyrosetta.rosetta.protocols.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_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult

Score the given model against the models in the hash table

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

score_basis(self: pyrosetta.rosetta.protocols.sewing.Hasher, alignment_scores: pyrosetta.rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult, transformed_model: pyrosetta.rosetta.protocols.sewing.Model, basis_residue: pyrosetta.rosetta.protocols.sewing.SewResidue, store_atoms: bool) → None

C++: protocols::sewing::Hasher::score_basis(class std::map<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult, struct std::less<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult> > > &, const struct protocols::sewing::Model &, const struct protocols::sewing::SewResidue &, bool) const –> void

score_basis_125(self: pyrosetta.rosetta.protocols.sewing.Hasher, alignment_scores: pyrosetta.rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult, transformed_model: pyrosetta.rosetta.protocols.sewing.Model, basis_residue: pyrosetta.rosetta.protocols.sewing.SewResidue, store_atoms: bool) → None

C++: protocols::sewing::Hasher::score_basis_125(class std::map<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult, struct std::less<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult> > > &, const struct protocols::sewing::Model &, const struct protocols::sewing::SewResidue &, bool) const –> void

score_one(self: pyrosetta.rosetta.protocols.sewing.Hasher, m1: pyrosetta.rosetta.protocols.sewing.Model, m1_basis: pyrosetta.rosetta.protocols.sewing.SewResidue, m2: pyrosetta.rosetta.protocols.sewing.Model, m2_basis: pyrosetta.rosetta.protocols.sewing.SewResidue, box_length: int) → Tuple[Tuple[pyrosetta.rosetta.protocols.sewing.Basis, pyrosetta.rosetta.protocols.sewing.Basis], pyrosetta.rosetta.protocols.sewing.HashResult]

C++: protocols::sewing::Hasher::score_one(const struct protocols::sewing::Model &, const struct protocols::sewing::SewResidue &, const struct protocols::sewing::Model &, const struct protocols::sewing::SewResidue &, unsigned long) –> struct std::pair<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult>

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

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

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

trim_scores(self: pyrosetta.rosetta.protocols.sewing.Hasher, scores: pyrosetta.rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult, num_segment_matches: int, min_segment_score: int, max_clash_score: int) → None

Trim the ScoreResults to remove weak hits

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

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

Serialize hash table to disk

C++: protocols::sewing::Hasher::write_to_disk(class std::basic_string<char>) const –> void

class pyrosetta.rosetta.protocols.sewing.ModelNode

Bases: pyrosetta.rosetta.utility.graph.Node

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.sewing.ModelNode, owner: pyrosetta.rosetta.utility.graph.Graph, index: int) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.protocols.sewing.ModelNode) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

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.sewing.ModelNode, source: pyrosetta.rosetta.utility.graph.Node) → None

C++: protocols::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.

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

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

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

C++: protocols::sewing::ModelNode::model(const struct protocols::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.

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

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

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

C++: protocols::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.sewing.ReadNativeRotamersFile

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperation

///////////ReadNativeRotamersFile/////////////////

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

apply(self: pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: protocols::sewing::ReadNativeRotamersFile::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile, : pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile) → pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile

C++: protocols::sewing::ReadNativeRotamersFile::operator=(const class protocols::sewing::ReadNativeRotamersFile &) –> class protocols::sewing::ReadNativeRotamersFile &

clone(self: pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: protocols::sewing::ReadNativeRotamersFile::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname() → str

C++: protocols::sewing::ReadNativeRotamersFile::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::sewing::ReadNativeRotamersFile::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile

Bases: pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile

///////////ReadRepeatNativeRotamersFile/////////////////

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

apply(self: pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: protocols::sewing::ReadRepeatNativeRotamersFile::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile, : pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile) → pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile

C++: protocols::sewing::ReadRepeatNativeRotamersFile::operator=(const class protocols::sewing::ReadRepeatNativeRotamersFile &) –> class protocols::sewing::ReadRepeatNativeRotamersFile &

clone(self: pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: protocols::sewing::ReadRepeatNativeRotamersFile::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname() → str

C++: protocols::sewing::ReadRepeatNativeRotamersFile::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::sewing::ReadRepeatNativeRotamersFile::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.sewing.SegmentGraph

Bases: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment

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

__bool__(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment) → bool

Check whether the list is nonempty

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment, arg0: int) → protocols::sewing::SewSegment

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph, arg0: pyrosetta.rosetta.protocols.sewing.SegmentGraph) -> None
2. __init__(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__iter__(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment) → iterator

__le__

Return self<=value.

__len__(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment) → int

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__setitem__(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment, arg0: int, arg1: protocols::sewing::SewSegment) → None

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

add_connection(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph, i: int, j: int) → None

C++: protocols::sewing::SegmentGraph::add_connection(unsigned long, unsigned long) –> void

append(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment, arg0: protocols::sewing::SewSegment) → None

adds an element to the end

assign(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph, : pyrosetta.rosetta.protocols.sewing.SegmentGraph) → pyrosetta.rosetta.protocols.sewing.SegmentGraph

C++: protocols::sewing::SegmentGraph::operator=(const class protocols::sewing::SegmentGraph &) –> class protocols::sewing::SegmentGraph &

back(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment) → protocols::sewing::SewSegment

access the last element

c_segment(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph, ind: int) → int

C++: protocols::sewing::SegmentGraph::c_segment(unsigned long) const –> unsigned long

capacity(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment) → int

returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment) → None

clears the contents

clear_connections(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph) → None

C++: protocols::sewing::SegmentGraph::clear_connections() –> void

erase(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment, arg0: int) → None

erases element at index

forward_connections(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph) → pyrosetta.rosetta.std.map_unsigned_long_unsigned_long

C++: protocols::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_sewing_SewSegment) → protocols::sewing::SewSegment

access the first element

has_next(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph, ind: int) → bool

C++: protocols::sewing::SegmentGraph::has_next(unsigned long) const –> bool

has_previous(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph, ind: int) → bool

C++: protocols::sewing::SegmentGraph::has_previous(unsigned long) const –> bool

insert_connected_segment(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph, segment: pyrosetta.rosetta.protocols.sewing.SewSegment, ind: int) → None

C++: protocols::sewing::SegmentGraph::insert_connected_segment(struct protocols::sewing::SewSegment, unsigned long) –> void

l(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment) → int

lower index

max_size(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment) → int

returns the maximum possible number of elements

n_segment(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph, ind: int) → int

C++: protocols::sewing::SegmentGraph::n_segment(unsigned long) const –> unsigned long

next(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph, ind: int) → int

C++: protocols::sewing::SegmentGraph::next(unsigned long) const –> unsigned long

pop(*args, **kwargs)

Overloaded function.

1. pop(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment) -> protocols::sewing::SewSegment

remove and return last item

2. pop(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment, arg0: int) -> protocols::sewing::SewSegment

remove and return item at index

previous(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph, ind: int) → int

C++: protocols::sewing::SegmentGraph::previous(unsigned long) const –> unsigned long

reorder(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph, new_order: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::sewing::SegmentGraph::reorder(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

reserve(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment, arg0: int) → None

reserves storage

resize(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment, arg0: int) → None

changes the number of elements stored

reverse_connections(self: pyrosetta.rosetta.protocols.sewing.SegmentGraph) → pyrosetta.rosetta.std.map_unsigned_long_unsigned_long

C++: protocols::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_sewing_SewSegment) → None

reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector1_protocols_sewing_SewSegment) → int

upper index

class pyrosetta.rosetta.protocols.sewing.SewGraph

Bases: pyrosetta.rosetta.utility.graph.Graph

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.sewing.SewGraph) -> None
2. __init__(self: pyrosetta.rosetta.protocols.sewing.SewGraph, arg0: pyrosetta.rosetta.protocols.sewing.SewGraph) -> None
3. __init__(self: pyrosetta.rosetta.protocols.sewing.SewGraph, models: pyrosetta.rosetta.std.map_int_protocols_sewing_Model, segment_matches_per_edge: int) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

add_all_model_edges_from_binary(self: pyrosetta.rosetta.protocols.sewing.SewGraph, filename: str, model_id: int) → None

C++: protocols::sewing::SewGraph::add_all_model_edges_from_binary(class std::basic_string<char>, int) –> void

add_edge(*args, **kwargs)

Overloaded function.

1. 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 *

2. 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.sewing.SewGraph, filename: str, node_id: int) → None

C++: protocols::sewing::SewGraph::add_edges_from_binary(class std::basic_string<char>, unsigned long) –> void

add_special_edges(self: pyrosetta.rosetta.protocols.sewing.SewGraph) → None

C++: protocols::sewing::SewGraph::add_special_edges() –> void

all_pairs_shortest_paths(self: pyrosetta.rosetta.utility.graph.Graph) → ObjexxFCL::FArray2D<int>

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.sewing.SewGraph, : pyrosetta.rosetta.protocols.sewing.SewGraph) → pyrosetta.rosetta.protocols.sewing.SewGraph

C++: protocols::sewing::SewGraph::operator=(const class protocols::sewing::SewGraph &) –> class protocols::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.sewing.SewGraph, index1: int, index2: int) → pyrosetta.rosetta.utility.graph.Edge

Factory method for edge creation

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

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

Factory method for node creation

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

delete_edge(self: pyrosetta.rosetta.protocols.sewing.SewGraph, edge: pyrosetta.rosetta.utility.graph.Edge) → None

C++: protocols::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.sewing.SewGraph, n1: int, n2: int) → pyrosetta.rosetta.protocols.sewing.HashEdge

C++: protocols::sewing::SewGraph::find_hash_edge(unsigned long, unsigned long) –> class protocols::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.sewing.SewGraph, score_filename: str, binary_filename: str) → None

C++: protocols::sewing::SewGraph::generate_binary_score_file(class std::basic_string<char>, class std::basic_string<char>) –> 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.

1. get_model_node(self: pyrosetta.rosetta.protocols.sewing.SewGraph, n: int) -> pyrosetta.rosetta.protocols.sewing.ModelNode

C++: protocols::sewing::SewGraph::get_model_node(unsigned long) const –> const class protocols::sewing::ModelNode *

2. get_model_node(self: pyrosetta.rosetta.protocols.sewing.SewGraph, model_id: int, segment_ids: pyrosetta.rosetta.std.set_unsigned_long_t) -> pyrosetta.rosetta.protocols.sewing.ModelNode

C++: protocols::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::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.sewing.SewGraph, model_id: int) → pyrosetta.rosetta.std.set_unsigned_long_t

C++: protocols::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.sewing.SewGraph) → pyrosetta.rosetta.protocols.sewing.ModelNode

get a random node from the graph

C++: protocols::sewing::SewGraph::get_random_node() const –> const class protocols::sewing::ModelNode *

get_random_node_with_edges(self: pyrosetta.rosetta.protocols.sewing.SewGraph) → pyrosetta.rosetta.protocols.sewing.ModelNode

get a random node involved in at least one edge from the graph

C++: protocols::sewing::SewGraph::get_random_node_with_edges() const –> const class protocols::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(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &) 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.sewing.SewGraph, models: pyrosetta.rosetta.std.map_int_protocols_sewing_Model, filename: str) → None

C++: protocols::sewing::SewGraph::report_binary_stats(const class std::map<int, struct protocols::sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::sewing::Model> > > &, class std::basic_string<char>) –> 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.sewing.SewGraph, scores: pyrosetta.rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult) → None

C++: protocols::sewing::SewGraph::set_special_edges(const class std::map<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult, struct std::less<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult> > > &) –> void

pyrosetta.rosetta.protocols.sewing.add_linker_segments(models: pyrosetta.rosetta.std.map_int_protocols_sewing_Model) → None

C++: protocols::sewing::add_linker_segments(class std::map<int, struct protocols::sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::sewing::Model> > > &) –> void

pyrosetta.rosetta.protocols.sewing.add_num_neighbors(models: pyrosetta.rosetta.std.map_int_protocols_sewing_Model) → None

C++: protocols::sewing::add_num_neighbors(class std::map<int, struct protocols::sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::sewing::Model> > > &) –> void

pyrosetta.rosetta.protocols.sewing.create_alpha_beta_models_table() → None

C++: protocols::sewing::create_alpha_beta_models_table() –> void

pyrosetta.rosetta.protocols.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.sewing.Model

create a Model from the pose

C++: protocols::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::sewing::Model

pyrosetta.rosetta.protocols.sewing.get_5_ss_models_from_db(hash_between: str) → pyrosetta.rosetta.std.map_int_protocols_sewing_Model

C++: protocols::sewing::get_5_ss_models_from_db(class std::basic_string<char>) –> class std::map<int, struct protocols::sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::sewing::Model> > >

pyrosetta.rosetta.protocols.sewing.get_alpha_beta_models_from_db() → pyrosetta.rosetta.std.map_int_protocols_sewing_Model

C++: protocols::sewing::get_alpha_beta_models_from_db() –> class std::map<int, struct protocols::sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::sewing::Model> > >

pyrosetta.rosetta.protocols.sewing.get_continuous_models_from_db(hash_between: str) → pyrosetta.rosetta.std.map_int_protocols_sewing_Model

C++: protocols::sewing::get_continuous_models_from_db(class std::basic_string<char>) –> class std::map<int, struct protocols::sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::sewing::Model> > >

pyrosetta.rosetta.protocols.sewing.get_discontinuous_models_from_db() → pyrosetta.rosetta.std.map_int_protocols_sewing_Model

C++: protocols::sewing::get_discontinuous_models_from_db() –> class std::map<int, struct protocols::sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::sewing::Model> > >

pyrosetta.rosetta.protocols.sewing.get_strand_sew_models_from_db() → pyrosetta.rosetta.std.map_int_protocols_sewing_Model

C++: protocols::sewing::get_strand_sew_models_from_db() –> class std::map<int, struct protocols::sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::sewing::Model> > >

pyrosetta.rosetta.protocols.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::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> > >

pyrosetta.rosetta.protocols.sewing.read_model_file(filename: str) → pyrosetta.rosetta.std.map_int_protocols_sewing_Model

C++: protocols::sewing::read_model_file(class std::basic_string<char>) –> class std::map<int, struct protocols::sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::sewing::Model> > >

pyrosetta.rosetta.protocols.sewing.remove_models_from_dssp(models: pyrosetta.rosetta.std.map_int_protocols_sewing_Model, dssp1: str, dssp2: str) → None

C++: protocols::sewing::remove_models_from_dssp(class std::map<int, struct protocols::sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::sewing::Model> > > &, char, char) –> void

pyrosetta.rosetta.protocols.sewing.see_whether_model_is_H_bonded_by_terminal_strands(model: pyrosetta.rosetta.protocols.sewing.Model, P_PA: str) → str

Return true if given model is H bonded by terminal strands

C++: protocols::sewing::see_whether_model_is_H_bonded_by_terminal_strands(struct protocols::sewing::Model, class std::basic_string<char>) –> std::string

pyrosetta.rosetta.protocols.sewing.serialize_graph_json(graph: pyrosetta.rosetta.protocols.sewing.SewGraph, max_nodes: int) → str

C++: protocols::sewing::serialize_graph_json(class std::shared_ptr<const class protocols::sewing::SewGraph>, unsigned long) –> std::string

pyrosetta.rosetta.protocols.sewing.write_hashing_scores_to_file(scores: pyrosetta.rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult, filename: str) → None

Take the given StructureScores and save them to disk

C++: protocols::sewing::write_hashing_scores_to_file(const class std::map<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult, struct std::less<struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis> >, class std::allocator<struct std::pair<const struct std::pair<struct protocols::sewing::Basis, struct protocols::sewing::Basis>, struct protocols::sewing::HashResult> > > &, class std::basic_string<char>) –> void

pyrosetta.rosetta.protocols.sewing.write_model_file(comments: str, models: pyrosetta.rosetta.std.map_int_protocols_sewing_Model, filename: str) → None

C++: protocols::sewing::write_model_file(const class std::basic_string<char> &, class std::map<int, struct protocols::sewing::Model, struct std::less<int>, class std::allocator<struct std::pair<const int, struct protocols::sewing::Model> > >, class std::basic_string<char>) –> void