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Rosetta
2021.16
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Rosetta
2021.16
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An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher. More...
#include <ContinuousAssembly.hh>
Public Member Functions | |
| ContinuousAssembly () | |
| default constructor More... | |
| AssemblyOP | clone () override |
| void | append_model (Model const &model, ScoreResult const &edge_score) override |
| Needs to be implemented. 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, 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 |
| 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 () |
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::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_ |
An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher.
| protocols::legacy_sewing::ContinuousAssembly::ContinuousAssembly | ( | ) |
default constructor
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overridevirtual |
Needs to be implemented.
add a model to assembly
Implements protocols::legacy_sewing::Assembly.
References protocols::legacy_sewing::SegmentGraph::add_connection(), protocols::legacy_sewing::Assembly::all_segments_, protocols::legacy_sewing::SegmentGraph::clear_connections(), protocols::legacy_sewing::Assembly::get_chimera_segments(), protocols::legacy_sewing::Assembly::get_matching_model_segments(), protocols::legacy_sewing::SegmentGraph::has_next(), protocols::legacy_sewing::SegmentGraph::has_previous(), protocols::legacy_sewing::Assembly::regenerate_model(), protocols::legacy_sewing::Assembly::segments_, protocols::legacy_sewing::Model::segments_, protocols::legacy_sewing::TR(), and protocols::legacy_sewing::write_model_file().
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overridevirtual |
Implements protocols::legacy_sewing::Assembly.
1.8.7