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protocols::sewing::data_storage::HashedSmartAssembly Class Reference

an Assembly that makes use of the Hasher More...

#include <HashedSmartAssembly.hh>

Inheritance diagram for protocols::sewing::data_storage::HashedSmartAssembly:
Inheritance graph
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Public Member Functions

 HashedSmartAssembly ()
 
 HashedSmartAssembly (hashing::SegmentVectorCOP)
 
 HashedSmartAssembly (HashedSmartAssembly const &src)
 
 ~HashedSmartAssembly () override
 
HashedSmartAssemblyOP clone () const
 
void set_basis_map_generator (hashing::BasisMapGeneratorOP new_bmg)
 
bool add_segment (bool n_terminus, core::Size seg_ID_to_add, core::Size res_ID_1, core::Size res_ID_2) override
 
core::Size get_window_width () const
 
- Public Member Functions inherited from protocols::sewing::data_storage::SmartAssembly
 SmartAssembly ()
 
 SmartAssembly (hashing::SegmentVectorCOP segment_vector, core::Size window_width=1)
 
 SmartAssembly (SmartAssembly const &src)
 
 ~SmartAssembly () override
 
SmartAssemblyOP clone () const
 
void set_starting_segment (SmartSegmentOP start_segment, std::string start_node_vital_segments)
 
SmartSegmentOP get_n_terminal_segment () const
 
void set_n_terminal_segment (SmartSegmentOP new_segment)
 
bool has_segment (core::Size seg_id)
 
SmartSegmentOP get_segment (core::Size seg_id)
 
SmartSegmentOP get_c_terminal_segment () const
 
void set_c_terminal_segment (SmartSegmentOP new_segment)
 
std::string get_start_node_vital_segments ()
 
void set_start_node_vital_segments (std::string start_node_vital_segments)
 
bool get_last_change_was_n_terminal () const
 
void set_last_change_was_n_terminal (bool)
 
char get_last_change () const
 
SmartSegmentOP get_last_chimaera () const
 
BasisPair get_last_chimaera_deleted () const
 
void set_partner (core::pose::PoseOP partner_pose)
 
core::pose::PoseOP get_partner () const
 
void set_last_change (char)
 
void set_last_chimaera (SmartSegmentOP)
 
void set_last_chimaera_deleted (BasisPair)
 
bool can_delete ()
 
void pdb_segments (std::map< core::Size, data_storage::SmartSegmentOP >)
 
std::map< core::Size,
data_storage::SmartSegmentOP > & 
pdb_segments ()
 
std::map< core::Size,
data_storage::SmartSegmentOP > & 
local_segments ()
 
std::map< core::Size,
data_storage::SmartSegmentOP
const_pdb_segments () const
 
core::Size get_length () const
 
void set_length (core::Size)
 
core::Size get_size () const
 
void set_size (core::Size)
 
hashing::SegmentVectorCOP get_segment_vector () const
 
void set_segment_vector (hashing::SegmentVectorCOP)
 
bool get_modifiable_terminus (char op)
 
char get_modifiable_terminus ()
 
void set_modifiable_terminus (char modifiable_terminus)
 
bool is_continuous () const
 
core::Size get_random_segment_id (bool n_terminus)
 
std::string get_forward_assembly () const
 
std::string get_comprehensive_forward_assembly () const
 
std::string get_reverse_assembly () const
 
std::string get_comprehensive_reverse_assembly () const
 
std::string get_comprehensive_assembly_string () const
 
std::map< core::Size,
LigandResidueCOP
get_partner_ligands () const
 
void set_partner_ligands (std::map< core::Size, LigandResidueCOP >)
 
std::map< core::Size,
LigandResidueOP
get_local_ligands ()
 
std::map< core::Size,
LigandResidueOP
get_local_ligands () const
 
bool add_segment (bool n_terminus)
 
bool delete_segment (bool n_terminus)
 
bool switch_segment (bool n_terminus)
 
bool undelete_segment ()
 
void unswitch_segment ()
 
SmartSegmentOP recurse_revert_far_n_terminal_parent (SmartSegmentOP current_segment)
 
SmartSegmentOP recurse_revert_far_c_terminal_parent (SmartSegmentOP current_segment)
 
void unchimerize_ligand_segment (LigandSegmentOP ligseg)
 
void revert ()
 
void dump_side_chains ()
 
void pick_random_starting_segment ()
 
core::pose::Pose to_pose (std::string)
 
bool transform_segments (BasisPair basis_pair)
 Transforms the segments in the second basis to the coordinate frame of the first basis. Returns the transformed (second) basis segment. More...
 
bool chimerize (BasisPair basis_pair, bool n_terminus)
 
std::pair< bool, core::Sizeiterate_over_basis_pairs (SmartSegmentCOP segment_1, SmartSegmentCOP segment_2, bool n_terminus)
 
void reset_chimaera_contacts (LigandResidueOP ligand, LigandSegmentOP ligand_chimaera, Basis nterm_basis, Basis cterm_basis, bool nterm)
 
void add_segment_and_neighbors_to_local_segments (SmartSegmentCOP ref_seg, core::Size new_id=0)
 
bool sample_ligand ()
 
void unsample_ligand ()
 
void load_initial_conformers (data_storage::LigandDescription ligdes)
 NOTE This method MUST be called after pdb_segments() is set and before the starting segment is picked for this to work. More...
 
core::Size get_window_width () const
 
void set_window_width (core::Size)
 
bool get_output_partner () const
 
void set_output_partner (bool)
 
void reconstitute_assembly_from_string (std::string)
 
void trim_terminal_segments (char, core::Size)
 

Private Attributes

hashing::BasisMapGeneratorOP existing_alignments_
 
SmartSegmentOP first_segment_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::sewing::data_storage::SmartAssembly
void set_resID_1 (core::Size)
 
void set_resID_2 (core::Size)
 
core::Size get_resID_1 () const
 
core::Size get_resID_2 () const
 
void set_segID_1 (core::Size)
 
void set_segID_2 (core::Size)
 
core::Size get_segID_1 () const
 
core::Size get_segID_2 () const
 

Detailed Description

an Assembly that makes use of the Hasher

Constructor & Destructor Documentation

protocols::sewing::data_storage::HashedSmartAssembly::HashedSmartAssembly ( )
protocols::sewing::data_storage::HashedSmartAssembly::HashedSmartAssembly ( hashing::SegmentVectorCOP  segment_vector)
protocols::sewing::data_storage::HashedSmartAssembly::HashedSmartAssembly ( HashedSmartAssembly const &  src)
protocols::sewing::data_storage::HashedSmartAssembly::~HashedSmartAssembly ( )
override

Member Function Documentation

bool protocols::sewing::data_storage::HashedSmartAssembly::add_segment ( bool  n_terminus,
core::Size  seg_ID_to_add,
core::Size  res_ID_1,
core::Size  res_ID_2 
)
overridevirtual

Reimplemented from protocols::sewing::data_storage::SmartAssembly.

References protocols::sewing::data_storage::SmartAssembly::add_segment_and_neighbors_to_local_segments(), protocols::sewing::data_storage::SmartAssembly::chimerize(), existing_alignments_, protocols::sewing::data_storage::SmartAssembly::get_c_terminal_segment(), protocols::sewing::data_storage::SmartAssembly::get_last_chimaera(), protocols::sewing::data_storage::SmartAssembly::get_length(), protocols::sewing::data_storage::SmartAssembly::get_n_terminal_segment(), protocols::sewing::data_storage::SmartAssembly::get_random_segment_id(), protocols::sewing::data_storage::SmartAssembly::get_segID_1(), protocols::sewing::data_storage::SmartAssembly::get_segID_2(), protocols::features::strand_assembly::get_segment_id(), protocols::sewing::data_storage::SmartAssembly::get_segment_vector(), protocols::sewing::data_storage::SmartAssembly::get_size(), get_window_width(), protocols::sewing::data_storage::SmartAssembly::local_segments(), protocols::mean_field::max(), protocols::sewing::data_storage::SmartAssembly::pdb_segments(), protocols::sewing::data_storage::SmartAssembly::set_c_terminal_segment(), protocols::sewing::data_storage::SmartAssembly::set_last_change(), protocols::sewing::data_storage::SmartAssembly::set_last_change_was_n_terminal(), protocols::sewing::data_storage::SmartAssembly::set_length(), protocols::sewing::data_storage::SmartAssembly::set_n_terminal_segment(), protocols::sewing::data_storage::SmartAssembly::set_resID_1(), protocols::sewing::data_storage::SmartAssembly::set_resID_2(), protocols::sewing::data_storage::SmartAssembly::set_segID_1(), protocols::sewing::data_storage::SmartAssembly::set_segID_2(), protocols::sewing::data_storage::SmartAssembly::set_size(), and protocols::TR().

HashedSmartAssemblyOP protocols::sewing::data_storage::HashedSmartAssembly::clone ( ) const
core::Size protocols::sewing::data_storage::HashedSmartAssembly::get_window_width ( ) const

References existing_alignments_.

Referenced by add_segment().

void protocols::sewing::data_storage::HashedSmartAssembly::set_basis_map_generator ( hashing::BasisMapGeneratorOP  new_bmg)

References existing_alignments_.

Member Data Documentation

hashing::BasisMapGeneratorOP protocols::sewing::data_storage::HashedSmartAssembly::existing_alignments_
private
SmartSegmentOP protocols::sewing::data_storage::HashedSmartAssembly::first_segment_
private

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