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protocols::legacy_sewing::DisembodiedAssembly Class Reference

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

#include <DisembodiedAssembly.hh>

Inheritance diagram for protocols::legacy_sewing::DisembodiedAssembly:
Inheritance graph
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Public Member Functions

 DisembodiedAssembly ()
 default constructor More...
 
AssemblyOP clone () override
 
void append_model (Model const &model, ScoreResult const &edge_score) override
 append the given model to the end of the assembly More...
 
- Public Member Functions inherited from protocols::legacy_sewing::Assembly
 Assembly ()
 
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, SewSegmentget_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< SewSegmentget_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< SewSegmentsegments () const
 
utility::vector1
< utility::vector1< SewSegment > > 
all_segments () const
 
utility::vector1< SewSegmentget_model_segments (int model_id) const
 
std::set< core::Sizemodel_ids () const
 
Model regenerate_model (int model_id) const
 
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::Sizepose_loop_anchors () const
 
utility::vector1< core::Sizedisconnected_segments () const
 
std::set< core::Sizenative_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< SewSegmentassembly_begin () const
 
ModelIterator< SewSegmentassembly_begin ()
 
ModelConstIterator< SewSegmentassembly_end () const
 
ModelIterator< SewSegmentassembly_end ()
 

Additional Inherited Members

- Public Attributes inherited from protocols::legacy_sewing::Assembly
utility::vector1< std::pair
< core::Real, core::Size > > 
blosum_history_
 
- Protected Attributes inherited from protocols::legacy_sewing::Assembly
SegmentGraph segments_
 
core::pose::PoseOP partner_pose_
 
std::set< core::Sizeavailable_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_
 

Detailed Description

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

Constructor & Destructor Documentation

protocols::legacy_sewing::DisembodiedAssembly::DisembodiedAssembly ( )

default constructor

Member Function Documentation

void protocols::legacy_sewing::DisembodiedAssembly::append_model ( Model const &  model,
ScoreResult const &  edge_score 
)
overridevirtual
AssemblyOP protocols::legacy_sewing::DisembodiedAssembly::clone ( )
overridevirtual

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