protocols::legacy_sewing::Assembly Class Reference

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

#include <Assembly.hh>

Inheritance diagram for protocols::legacy_sewing::Assembly:

Public Member Functions
	Assembly ()
virtual AssemblyOP	clone ()=0
void	add_model (SewGraphCOP graph, Model const &model, bool available=true)
	Add a model to the Assembly. Only used for first node and special cases. More...
void	update_coords_from_pose (core::pose::Pose const &pose)
std::map< SewSegment, SewSegment >	get_matching_model_segments (Model const &model, ScoreResult const &edge_score) const
ScoreResult	get_score_result (ModelNode const *model_1_node, HashEdge const *const cur_edge, SewGraphCOP graph) const
ModelNode const *	starting_node () const
ModelNode const *	ending_node () const
utility::vector1< boost::tuple< ModelNode const *, ModelNode const *, HashEdge const * > >	edges () const
core::Size	get_next_reference_node (SewGraphOP graph) const
	Pick which model to use as the reference model for the next node additon. More...
utility::vector1< SewSegment >	get_chimera_segments (std::map< SewSegment, SewSegment > const &matching_segments, std::map< SegmentPair, AtomMap > const &segment_matches, Model const &mobile_model)
SewSegment	create_chimera_segment (SewSegment const &reference_segment, SewSegment const &mobile_segment, AtomMap const &atom_map, bool reference_is_nter) const
utility::vector1< SewSegment >	segments () const
utility::vector1< utility::vector1< SewSegment > >	all_segments () const
utility::vector1< SewSegment >	get_model_segments (int model_id) const
std::set< core::Size >	model_ids () const
Model	regenerate_model (int model_id) const
virtual void	append_model (Model const &model, ScoreResult const &edge_score)=0
	append the given model to the end of the assembly More...
void	add_loop_segment (core::pose::Pose const &pose, protocols::loops::Loop loop, core::Size segment)
AtomMap	atom_map_from_score_result (ScoreResult const &alignment_scores) const
void	follow_edge (SewGraphCOP graph, HashEdge const *const edge, core::Size source_index)
void	align_model (Model &mobile_model, AtomMap const &atom_alignments, int reference_model_id) const
void	map_residues (int reference_model_id, Model mobile_model, AtomMap const &atom_alignments)
	create mappings between SewResidues in the Assembly that map to the same pose number More...
NativeRotamersMap	generate_native_rotamers_map () const
void	prepare_for_packing (core::pose::Pose &pose, core::pack::task::TaskFactoryOP task_factory, core::Real base_native_bonus, core::Size neighbor_cutoff) const
	Update the task factory such that the 'native' rotamers are added to the rotamer set, and the native residues are favored. More...
core::pose::Pose	to_pose (std::string residue_type_set, bool create_cuts=true) const
core::pose::Pose	to_multichain_pose (std::string residue_type_set) const
bool	reorder_randomly (core::Real max_loop_distance)
	reorder segments in a random fashion that satisfies the maximum loop distance cutoff If this is not possible then return false, otherwise true More...
void	reorder (utility::vector1< core::Size > new_order)
utility::vector1< utility::vector1< core::Size > >	find_possible_orders (core::Real max_loop_distance) const
core::Size	pose_num (int model_id, core::Size resnum) const
core::Size	total_residue () const
utility::vector1< core::Size >	pose_loop_anchors () const
utility::vector1< core::Size >	disconnected_segments () const
std::set< core::Size >	native_positions (core::pose::Pose const &pose) const
	Records which positions in the given pose match the sequence identify of at least one of the amino acids from the underlying models at that position. More...
core::Real	percent_native (core::pose::Pose const &pose) const
	count the amount of 'native' residues retained in the pose More...
std::string	natives_select (core::pose::Pose const &pose, std::string object_name="") const
	print pymol selection of "native" positions More...
utility::vector1< std::pair< core::Size, core::Size > >	path () const
std::string	string_path () const
std::string	string_blosum (utility::vector1< std::pair< core::Real, core::Size > > blosum_history) const
void	set_partner (core::pose::PoseOP partner_pose)
core::pose::PoseOP	get_partner () const
void	append_segments (utility::vector1< SewSegment > const &segments)
	append the segments to the given assembly. This should be used very infrequently. The normal way to add segments is to follow an edge More...
void	delete_segments (core::Size seg_index)
	delete segments at the given index. This should be used very infrequently More...
ModelConstIterator< SewSegment >	assembly_begin () const
ModelIterator< SewSegment >	assembly_begin ()
ModelConstIterator< SewSegment >	assembly_end () const
ModelIterator< SewSegment >	assembly_end ()

Public Attributes
utility::vector1< std::pair< core::Real, core::Size > >	blosum_history_

Protected Attributes
SegmentGraph	segments_
core::pose::PoseOP	partner_pose_
std::set< core::Size >	available_nodes_
utility::vector1< utility::vector1< SewSegment > >	all_segments_
utility::vector1< boost::tuple< ModelNode const *, ModelNode const *, HashEdge const * > >	edge_path_
utility::vector1< std::pair< core::Size, core::Size > >	path_

Friends
std::ostream &	operator<< (std::ostream &out, Assembly const &atom)

Detailed Description

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

Constructor & Destructor Documentation

Assembly()

protocols::legacy_sewing::Assembly::Assembly ( )

default

Member Function Documentation

add_loop_segment()

void protocols::legacy_sewing::Assembly::add_loop_segment	(	core::pose::Pose const &	pose,
		protocols::loops::Loop	loop,
		core::Size	segment
	)

References all_segments_, core::conformation::Residue::atom(), protocols::legacy_sewing::SewAtom::atomno_, protocols::legacy_sewing::SewResidue::basis_atoms_, protocols::legacy_sewing::SewAtom::coords_, protocols::legacy_sewing::SegmentGraph::insert_connected_segment(), protocols::legacy_sewing::SewSegment::model_id_, core::chemical::ResidueTypeBase::name(), core::pose::Pose::residue(), protocols::legacy_sewing::SewResidue::residue_type_, protocols::legacy_sewing::SewSegment::residues_, protocols::legacy_sewing::SewResidue::resnum_, protocols::legacy_sewing::SewSegment::segment_id_, segments_, protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

add_model()

void protocols::legacy_sewing::Assembly::add_model	(	SewGraphCOP	graph,
		Model const &	model,
		bool	available = true
	)

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

Only used to add the first model to the Assembly, subsequent models should be added using the follow_edge function.

References protocols::legacy_sewing::SegmentGraph::add_connection(), all_segments_, available_nodes_, protocols::legacy_sewing::SegmentGraph::forward_connections(), protocols::legacy_sewing::Model::model_id_, segments_, and protocols::legacy_sewing::Model::segments_.

align_model()

void protocols::legacy_sewing::Assembly::align_model	(	Model &	mobile_model,
		AtomMap const &	atom_alignments,
		int	reference_model_id
	)		const

References all_segments_, protocols::legacy_sewing::ModelIterator< T >::atom(), protocols::legacy_sewing::SewAtom::atomno_, protocols::legacy_sewing::SewResidue::basis_atoms_, core::pose::center_of_mass(), protocols::legacy_sewing::SewSegment::chimera_, protocols::legacy_sewing::SewAtom::coords_, protocols::legacy_sewing::Model::model_begin(), protocols::legacy_sewing::Model::model_end(), protocols::legacy_sewing::SewSegment::model_id_, protocols::legacy_sewing::ModelIterator< T >::residue(), protocols::legacy_sewing::SewSegment::residues_, and protocols::legacy_sewing::SewResidue::resnum_.

Referenced by follow_edge().

all_segments()

utility::vector1< utility::vector1< SewSegment > > protocols::legacy_sewing::Assembly::all_segments

(

)

const

References all_segments_.

append_model()

virtual void protocols::legacy_sewing::Assembly::append_model ( Model const &  model, ScoreResult const &  edge_score  )

pure virtual

append the given model to the end of the assembly

Implemented in protocols::legacy_sewing::DisembodiedAssembly, and protocols::legacy_sewing::ContinuousAssembly.

Referenced by follow_edge().

append_segments()

void protocols::legacy_sewing::Assembly::append_segments

(

utility::vector1< SewSegment > const &

segments

)

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

References all_segments_, segments(), and segments_.

assembly_begin() [1/2]

ModelIterator< SewSegment > protocols::legacy_sewing::Assembly::assembly_begin

(

)

References segments_.

assembly_begin() [2/2]

ModelConstIterator< SewSegment > protocols::legacy_sewing::Assembly::assembly_begin

(

)

const

References segments_.

Referenced by update_coords_from_pose().

assembly_end() [1/2]

ModelIterator< SewSegment > protocols::legacy_sewing::Assembly::assembly_end

(

)

References segments_.

assembly_end() [2/2]

ModelConstIterator< SewSegment > protocols::legacy_sewing::Assembly::assembly_end

(

)

const

References segments_.

Referenced by update_coords_from_pose().

atom_map_from_score_result()

AtomMap protocols::legacy_sewing::Assembly::atom_map_from_score_result

(

ScoreResult const &

alignment_scores

)

const

Referenced by follow_edge().

clone()

virtual AssemblyOP protocols::legacy_sewing::Assembly::clone ( )

pure virtual

Implemented in protocols::legacy_sewing::DisembodiedAssembly, and protocols::legacy_sewing::ContinuousAssembly.

create_chimera_segment()

SewSegment protocols::legacy_sewing::Assembly::create_chimera_segment	(	SewSegment const &	reference_segment,
		SewSegment const &	mobile_segment,
		AtomMap const &	atom_map,
		bool	reference_is_nter
	)		const

References protocols::legacy_sewing::SewSegment::chimera_, protocols::legacy_sewing::CHIMERA_SEGMENT, protocols::legacy_sewing::SewSegment::dssp_, protocols::legacy_sewing::largest_continuous_atom_map(), protocols::legacy_sewing::SewSegment::model_id_, protocols::legacy_sewing::SewSegment::parent_segments_, protocols::legacy_sewing::SewSegment::residues_, protocols::legacy_sewing::SewSegment::segment_id_, and protocols::legacy_sewing::TR().

Referenced by get_chimera_segments().

delete_segments()

void protocols::legacy_sewing::Assembly::delete_segments

(

core::Size

seg_index

)

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

References all_segments_, and segments_.

disconnected_segments()

utility::vector1< core::Size > protocols::legacy_sewing::Assembly::disconnected_segments

(

)

const

References protocols::legacy_sewing::SegmentGraph::has_next(), and segments_.

edges()

utility::vector1< boost::tuple< ModelNode const *, ModelNode const *, HashEdge const * > > protocols::legacy_sewing::Assembly::edges

(

)

const

References edge_path_.

ending_node()

ModelNode const * protocols::legacy_sewing::Assembly::ending_node

(

)

const

References edge_path_.

find_possible_orders()

utility::vector1< utility::vector1< core::Size > > protocols::legacy_sewing::Assembly::find_possible_orders

(

core::Real

max_loop_distance

)

const

find all possible segment orders where the CA-CA distance of all unclosed loops is less than the max distance respect any current connections.

References protocols::legacy_sewing::SewResidue::basis_atoms_, protocols::legacy_sewing::SegmentGraph::c_segment(), protocols::legacy_sewing::SegmentGraph::has_previous(), protocols::legacy_sewing::SewSegment::model_id_, pose_num(), protocols::legacy_sewing::SewSegment::residues_, protocols::legacy_sewing::SewResidue::resnum_, segments_, and protocols::legacy_sewing::TR().

Referenced by reorder_randomly().

follow_edge()

void protocols::legacy_sewing::Assembly::follow_edge	(	SewGraphCOP	graph,
		HashEdge const *const	edge,
		core::Size	source_index
	)

References align_model(), append_model(), atom_map_from_score_result(), available_nodes_, edge_path_, protocols::legacy_sewing::Model::get_residue(), protocols::legacy_sewing::Model::model_id_, protocols::legacy_sewing::HashEdge::model_resnum(), path_, regenerate_model(), protocols::legacy_sewing::Hasher::score_one(), and protocols::legacy_sewing::TR().

generate_native_rotamers_map()

NativeRotamersMap protocols::legacy_sewing::Assembly::generate_native_rotamers_map

(

)

const

create a map of sequence positions to ResidueOP objects for each of the 'natives' seen during the Assembly process. Ensure that if a residue is the first or last in the Assembly then we create lower and upper terminus types for that residues at tha position.

References core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, core::chemical::LOWER_TERMINUS_VARIANT, segments_, total_residue(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by prepare_for_packing().

get_chimera_segments()

utility::vector1< SewSegment > protocols::legacy_sewing::Assembly::get_chimera_segments	(	std::map< SewSegment, SewSegment > const &	matching_segments,
		std::map< SegmentPair, AtomMap > const &	segment_matches,
		Model const &	mobile_model
	)

References create_chimera_segment(), protocols::legacy_sewing::SegmentGraph::has_next(), protocols::legacy_sewing::SegmentGraph::has_previous(), segments_, and protocols::legacy_sewing::Model::segments_.

Referenced by protocols::legacy_sewing::ContinuousAssembly::append_model().

get_matching_model_segments()

std::map< SewSegment, SewSegment > protocols::legacy_sewing::Assembly::get_matching_model_segments	(	Model const &	model,
		ScoreResult const &	edge_score
	)		const

References all_segments_, protocols::legacy_sewing::Model::segments_, and protocols::legacy_sewing::TR().

Referenced by protocols::legacy_sewing::ContinuousAssembly::append_model(), and protocols::legacy_sewing::DisembodiedAssembly::append_model().

get_model_segments()

utility::vector1< SewSegment > protocols::legacy_sewing::Assembly::get_model_segments

(

int

model_id

)

const

References all_segments_.

Referenced by regenerate_model(), and to_multichain_pose().

get_next_reference_node()

core::Size protocols::legacy_sewing::Assembly::get_next_reference_node

(

SewGraphOP

graph

)

const

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

TODO remove logic for picking nodes and just return available nodes! we are convoluting sampling and the conformation itself by not doing that

References available_nodes_.

get_partner()

core::pose::PoseOP protocols::legacy_sewing::Assembly::get_partner

(

)

const

References partner_pose_.

get_score_result()

ScoreResult protocols::legacy_sewing::Assembly::get_score_result	(	ModelNode const *	model_1_node,
		HashEdge const *const	cur_edge,
		SewGraphCOP	graph
	)		const

References protocols::legacy_sewing::Model::get_residue(), protocols::legacy_sewing::ModelNode::model(), protocols::legacy_sewing::Model::model_id_, protocols::legacy_sewing::HashEdge::model_resnum(), regenerate_model(), and protocols::legacy_sewing::Hasher::score_one().

map_residues()

void protocols::legacy_sewing::Assembly::map_residues	(	int	reference_model_id,
		Model	mobile_model,
		AtomMap const &	atom_alignments
	)

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

Use the given atom alignments to create mappings between SewResidues in the Assembly. These mappings will be used to generate 'Native' Rotamers for positions in the final Pose

References all_segments_, protocols::legacy_sewing::SewAtom::atomno_, protocols::legacy_sewing::SewResidue::basis_atoms_, protocols::legacy_sewing::SewResidue::matched_residues_, protocols::legacy_sewing::SewSegment::model_id_, protocols::legacy_sewing::SewSegment::residues_, protocols::legacy_sewing::SewResidue::resnum_, protocols::legacy_sewing::Model::segments_, and protocols::legacy_sewing::TR().

model_ids()

std::set< core::Size > protocols::legacy_sewing::Assembly::model_ids

(

)

const

References all_segments_.

Referenced by to_multichain_pose().

native_positions()

std::set< core::Size > protocols::legacy_sewing::Assembly::native_positions

(

core::pose::Pose const &

pose

)

const

Records which positions in the given pose match the sequence identify of at least one of the amino acids from the underlying models at that position.

References core::chemical::CENTROID, core::chemical::FA_STANDARD, core::pose::Pose::is_centroid(), core::pose::Pose::is_fullatom(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue(), segments_, protocols::legacy_sewing::TR(), and core::conformation::Residue::type().

Referenced by natives_select(), and percent_native().

natives_select()

std::string protocols::legacy_sewing::Assembly::natives_select	(	core::pose::Pose const &	pose,
		std::string	object_name = ""
	)		const

print pymol selection of "native" positions

References native_positions().

path()

utility::vector1< std::pair< core::Size, core::Size > > protocols::legacy_sewing::Assembly::path

(

)

const

References path_.

percent_native()

core::Real protocols::legacy_sewing::Assembly::percent_native

(

core::pose::Pose const &

pose

)

const

count the amount of 'native' residues retained in the pose

References native_positions(), and core::pose::Pose::size().

pose_loop_anchors()

utility::vector1< core::Size > protocols::legacy_sewing::Assembly::pose_loop_anchors

(

)

const

References protocols::legacy_sewing::SegmentGraph::has_next(), pose_num(), and segments_.

pose_num()

core::Size protocols::legacy_sewing::Assembly::pose_num	(	int	model_id,
		core::Size	resnum
	)		const

References segments_, and core::id::to_string().

Referenced by find_possible_orders(), pose_loop_anchors(), and to_pose().

prepare_for_packing()

void protocols::legacy_sewing::Assembly::prepare_for_packing	(	core::pose::Pose &	pose,
		core::pack::task::TaskFactoryOP	task_factory,
		core::Real	base_native_bonus,
		core::Size	neighbor_cutoff
	)		const

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

prepare the pose for packing by adding all the rotmaers defined by the chi-angles in SewResidue. Also, add residue type constraints to the Pose for each of the 'native' residue types for each position in the pose.

References core::chemical::FA_STANDARD, generate_native_rotamers_map(), and core::pose::Pose::update_residue_neighbors().

regenerate_model()

Model protocols::legacy_sewing::Assembly::regenerate_model

(

int

model_id

)

const

References get_model_segments(), protocols::legacy_sewing::Model::model_id_, and protocols::legacy_sewing::Model::segments_.

Referenced by protocols::legacy_sewing::ContinuousAssembly::append_model(), follow_edge(), and get_score_result().

reorder()

void protocols::legacy_sewing::Assembly::reorder

(

utility::vector1< core::Size >

new_order

)

References core::chemical::CENTROID, core::pose::Pose::dump_pdb(), protocols::legacy_sewing::SegmentGraph::reorder(), segments_, and to_pose().

reorder_randomly()

bool protocols::legacy_sewing::Assembly::reorder_randomly

(

core::Real

max_loop_distance

)

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

References find_possible_orders(), protocols::legacy_sewing::SegmentGraph::reorder(), and segments_.

segments()

utility::vector1< SewSegment > protocols::legacy_sewing::Assembly::segments

(

)

const

References segments_.

Referenced by append_segments().

set_partner()

void protocols::legacy_sewing::Assembly::set_partner

(

core::pose::PoseOP

partner_pose

)

References partner_pose_.

starting_node()

ModelNode const * protocols::legacy_sewing::Assembly::starting_node

(

)

const

References edge_path_.

string_blosum()

std::string protocols::legacy_sewing::Assembly::string_blosum

(

utility::vector1< std::pair< core::Real, core::Size > >

blosum_history

)

const

string_path()

std::string protocols::legacy_sewing::Assembly::string_path

(

)

const

References path_.

to_multichain_pose()

core::pose::Pose protocols::legacy_sewing::Assembly::to_multichain_pose

(

std::string

residue_type_set

)

const

for testing purposes, create a pose that includes all untrimmed segments. These will (or at least, should) heavily overlap with one another. Make each model a new chain

References protocols::legacy_sewing::SewResidue::basis_atoms_, core::conformation::Conformation::chain_endings(), protocols::legacy_sewing::SewResidue::chi_angles_, core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), get_model_segments(), core::conformation::idealize_hydrogens(), core::pose::make_pose_from_sequence(), model_ids(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::type().

to_pose()

core::pose::Pose protocols::legacy_sewing::Assembly::to_pose	(	std::string	residue_type_set,
		bool	create_cuts = true
	)		const

convert this assembly to a pose. This involves creating ideal residues and placing them on the backbone atom coordinates held by the assembly. This function assembles the pose residues in the order they are contained in the segments_ vector to re-order segments, use the reorder function

References core::kinematics::FoldTree::add_edge(), core::pose::append_pose_to_pose(), protocols::legacy_sewing::SewResidue::basis_atoms_, protocols::legacy_sewing::SewResidue::chi_angles_, core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), core::conformation::idealize_hydrogens(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::make_pose_from_sequence(), partner_pose_, core::kinematics::Edge::PEPTIDE, pose_num(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), segments_, core::pose::Pose::size(), core::util::switch_to_residue_type_set(), core::conformation::Residue::type(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by reorder().

total_residue()

core::Size protocols::legacy_sewing::Assembly::total_residue

(

)

const

References segments_, and core::simple_metrics::metrics::sum.

Referenced by generate_native_rotamers_map().

update_coords_from_pose()

void protocols::legacy_sewing::Assembly::update_coords_from_pose

(

core::pose::Pose const &

pose

)

References assembly_begin(), assembly_end(), protocols::legacy_sewing::ModelIterator< T >::atom(), core::conformation::Residue::chi(), protocols::legacy_sewing::ModelIterator< T >::residue(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Friends And Related Function Documentation

operator<<

std::ostream& operator<< ( std::ostream &  out, Assembly const &  atom  )

friend

Member Data Documentation

all_segments_

utility::vector1< utility::vector1<SewSegment> > protocols::legacy_sewing::Assembly::all_segments_

protected

Referenced by add_loop_segment(), add_model(), align_model(), all_segments(), protocols::legacy_sewing::ContinuousAssembly::append_model(), protocols::legacy_sewing::DisembodiedAssembly::append_model(), append_segments(), delete_segments(), get_matching_model_segments(), get_model_segments(), map_residues(), and model_ids().

available_nodes_

std::set<core::Size> protocols::legacy_sewing::Assembly::available_nodes_

protected

Referenced by add_model(), follow_edge(), and get_next_reference_node().

blosum_history_

utility::vector1< std::pair<core::Real, core::Size> > protocols::legacy_sewing::Assembly::blosum_history_

edge_path_

utility::vector1< boost::tuple<ModelNode const *, ModelNode const *, HashEdge const *> > protocols::legacy_sewing::Assembly::edge_path_

protected

Referenced by edges(), ending_node(), follow_edge(), and starting_node().

partner_pose_

core::pose::PoseOP protocols::legacy_sewing::Assembly::partner_pose_

protected

Referenced by get_partner(), set_partner(), and to_pose().

path_

utility::vector1< std::pair<core::Size, core::Size> > protocols::legacy_sewing::Assembly::path_

protected

Referenced by follow_edge(), path(), and string_path().

segments_

SegmentGraph protocols::legacy_sewing::Assembly::segments_

protected

Referenced by add_loop_segment(), add_model(), protocols::legacy_sewing::ContinuousAssembly::append_model(), protocols::legacy_sewing::DisembodiedAssembly::append_model(), append_segments(), assembly_begin(), assembly_end(), delete_segments(), disconnected_segments(), find_possible_orders(), generate_native_rotamers_map(), get_chimera_segments(), native_positions(), pose_loop_anchors(), pose_num(), reorder(), reorder_randomly(), segments(), to_pose(), and total_residue().

---

The documentation for this class was generated from the following files:

• src/protocols/legacy_sewing/conformation/Assembly.hh
• src/protocols/legacy_sewing/conformation/Assembly.cc