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protocols::sewing::data_storage::SmartAssembly Class Reference

a SEWING Assembly composed of SmartSegments More...

#include <SmartAssembly.hh>

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

 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)
 
virtual bool add_segment (bool n_terminus, core::Size seg_ID_to_add, core::Size res_ID_1, core::Size res_ID_2)
 
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)
 

Protected Member Functions

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
 

Private Attributes

hashing::SegmentVectorCOP segment_vector_
 
std::map< core::Size,
SmartSegmentOP
local_segments_
 
std::map< core::Size,
data_storage::SmartSegmentOP
pdb_segments_
 
std::map< core::Size,
LigandResidueCOP
const_ligands_
 
std::map< core::Size,
LigandResidueCOP
partner_ligands_
 
std::map< core::Size,
LigandResidueOP
local_ligands_
 
std::map< core::Size,
utility::vector1
< LigandResidueOP > > 
ligand_conformers_
 
std::pair< core::Size,
LigandResidueOP
last_sampled_ligand_
 
utility::vector1< core::Sizec_terminal_segments_
 
utility::vector1< core::Sizen_terminal_segments_
 
core::Size window_width_
 
SmartSegmentOP first_segment_
 
SmartSegmentOP n_terminal_segment_
 
SmartSegmentOP c_terminal_segment_
 
bool last_change_was_n_terminal_
 
SmartSegmentOP last_chimaera_
 
BasisPair last_chimaera_deleted_
 
SmartSegmentOP last_reverted_parent_chimaera_
 
char last_change_
 
core::Size size_
 
core::Size length_
 
SmartSegmentOP counter_segment_
 
core::Size segID_1_
 
core::Size segID_2_
 
core::Size resID_1_
 
core::Size resID_2_
 
BasisPair current_basis_pair_
 
utility::vector1< std::pair
< core::Size, core::Size > > 
all_basis_pairs_
 
core::pose::PoseOP partner_
 
bool output_partner_
 
char modifiable_terminus_
 
std::string start_node_vital_segments_
 

Detailed Description

a SEWING Assembly composed of SmartSegments

Constructor & Destructor Documentation

protocols::sewing::data_storage::SmartAssembly::SmartAssembly ( )

References all_basis_pairs_.

protocols::sewing::data_storage::SmartAssembly::SmartAssembly ( hashing::SegmentVectorCOP  segment_vector,
core::Size  window_width = 1 
)
protocols::sewing::data_storage::SmartAssembly::SmartAssembly ( SmartAssembly const &  src)
protocols::sewing::data_storage::SmartAssembly::~SmartAssembly ( )
override

Member Function Documentation

bool protocols::sewing::data_storage::SmartAssembly::add_segment ( bool  n_terminus)
bool protocols::sewing::data_storage::SmartAssembly::add_segment ( bool  n_terminus,
core::Size  seg_ID_to_add,
core::Size  res_ID_1,
core::Size  res_ID_2 
)
virtual
void protocols::sewing::data_storage::SmartAssembly::add_segment_and_neighbors_to_local_segments ( SmartSegmentCOP  ref_seg,
core::Size  new_id = 0 
)
bool protocols::sewing::data_storage::SmartAssembly::can_delete ( )
bool protocols::sewing::data_storage::SmartAssembly::chimerize ( BasisPair  basis_pair,
bool  n_terminus 
)
SmartAssemblyOP protocols::sewing::data_storage::SmartAssembly::clone ( ) const
std::map< core::Size, data_storage::SmartSegmentOP > protocols::sewing::data_storage::SmartAssembly::const_pdb_segments ( ) const

References pdb_segments_.

Referenced by SmartAssembly().

bool protocols::sewing::data_storage::SmartAssembly::delete_segment ( bool  n_terminus)
void protocols::sewing::data_storage::SmartAssembly::dump_side_chains ( )
SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::get_c_terminal_segment ( ) const
std::string protocols::sewing::data_storage::SmartAssembly::get_comprehensive_assembly_string ( ) const
std::string protocols::sewing::data_storage::SmartAssembly::get_comprehensive_forward_assembly ( ) const
std::string protocols::sewing::data_storage::SmartAssembly::get_comprehensive_reverse_assembly ( ) const
std::string protocols::sewing::data_storage::SmartAssembly::get_forward_assembly ( ) const
char protocols::sewing::data_storage::SmartAssembly::get_last_change ( ) const

References last_change_.

bool protocols::sewing::data_storage::SmartAssembly::get_last_change_was_n_terminal ( ) const
SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::get_last_chimaera ( ) const
BasisPair protocols::sewing::data_storage::SmartAssembly::get_last_chimaera_deleted ( ) const
core::Size protocols::sewing::data_storage::SmartAssembly::get_length ( ) const
std::map< core::Size, LigandResidueOP > protocols::sewing::data_storage::SmartAssembly::get_local_ligands ( )

References local_ligands_.

std::map< core::Size, LigandResidueOP > protocols::sewing::data_storage::SmartAssembly::get_local_ligands ( ) const

References local_ligands_.

bool protocols::sewing::data_storage::SmartAssembly::get_modifiable_terminus ( char  op)
char protocols::sewing::data_storage::SmartAssembly::get_modifiable_terminus ( )

References modifiable_terminus_.

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::get_n_terminal_segment ( ) const
bool protocols::sewing::data_storage::SmartAssembly::get_output_partner ( ) const

References output_partner_.

core::pose::PoseOP protocols::sewing::data_storage::SmartAssembly::get_partner ( ) const

References partner_.

Referenced by SmartAssembly().

std::map< core::Size, LigandResidueCOP > protocols::sewing::data_storage::SmartAssembly::get_partner_ligands ( ) const

References partner_ligands_.

Referenced by SmartAssembly().

core::Size protocols::sewing::data_storage::SmartAssembly::get_random_segment_id ( bool  n_terminus)
core::Size protocols::sewing::data_storage::SmartAssembly::get_resID_1 ( ) const
protected

References resID_1_.

core::Size protocols::sewing::data_storage::SmartAssembly::get_resID_2 ( ) const
protected

References resID_2_.

std::string protocols::sewing::data_storage::SmartAssembly::get_reverse_assembly ( ) const
core::Size protocols::sewing::data_storage::SmartAssembly::get_segID_1 ( ) const
protected
core::Size protocols::sewing::data_storage::SmartAssembly::get_segID_2 ( ) const
protected
SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::get_segment ( core::Size  seg_id)

References n_terminal_segment_.

hashing::SegmentVectorCOP protocols::sewing::data_storage::SmartAssembly::get_segment_vector ( ) const
core::Size protocols::sewing::data_storage::SmartAssembly::get_size ( ) const
std::string protocols::sewing::data_storage::SmartAssembly::get_start_node_vital_segments ( )
core::Size protocols::sewing::data_storage::SmartAssembly::get_window_width ( ) const

References window_width_.

bool protocols::sewing::data_storage::SmartAssembly::has_segment ( core::Size  seg_id)

References n_terminal_segment_.

bool protocols::sewing::data_storage::SmartAssembly::is_continuous ( ) const
std::pair< bool, core::Size > protocols::sewing::data_storage::SmartAssembly::iterate_over_basis_pairs ( data_storage::SmartSegmentCOP  segment_1,
data_storage::SmartSegmentCOP  segment_2,
bool  n_terminus 
)
void protocols::sewing::data_storage::SmartAssembly::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.

References const_ligands_, ligand_conformers_, protocols::sewing::data_storage::LigandDescription::ligand_id, local_ligands_, and protocols::sewing::data_storage::LigandDescription::pdb_conformers.

std::map< core::Size, data_storage::SmartSegmentOP > & protocols::sewing::data_storage::SmartAssembly::local_segments ( )
void protocols::sewing::data_storage::SmartAssembly::pdb_segments ( std::map< core::Size, data_storage::SmartSegmentOP pdbsegs)
std::map< core::Size, data_storage::SmartSegmentOP > & protocols::sewing::data_storage::SmartAssembly::pdb_segments ( )
void protocols::sewing::data_storage::SmartAssembly::pick_random_starting_segment ( )
void protocols::sewing::data_storage::SmartAssembly::reconstitute_assembly_from_string ( std::string  assembly_string)
SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::recurse_revert_far_c_terminal_parent ( SmartSegmentOP  current_segment)
SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::recurse_revert_far_n_terminal_parent ( SmartSegmentOP  current_segment)
void protocols::sewing::data_storage::SmartAssembly::reset_chimaera_contacts ( LigandResidueOP  ligand,
LigandSegmentOP  ligand_chimaera,
Basis  nterm_basis,
Basis  cterm_basis,
bool  nterm 
)
void protocols::sewing::data_storage::SmartAssembly::revert ( )
bool protocols::sewing::data_storage::SmartAssembly::sample_ligand ( )
void protocols::sewing::data_storage::SmartAssembly::set_c_terminal_segment ( SmartSegmentOP  new_segment)
void protocols::sewing::data_storage::SmartAssembly::set_last_change ( char  last_change)
void protocols::sewing::data_storage::SmartAssembly::set_last_change_was_n_terminal ( bool  last_change_n)
void protocols::sewing::data_storage::SmartAssembly::set_last_chimaera ( SmartSegmentOP  last_chimaera)

References last_chimaera_.

void protocols::sewing::data_storage::SmartAssembly::set_last_chimaera_deleted ( BasisPair  last_chimaera_deleted)
void protocols::sewing::data_storage::SmartAssembly::set_length ( core::Size  new_length)
void protocols::sewing::data_storage::SmartAssembly::set_modifiable_terminus ( char  modifiable_terminus)

References modifiable_terminus_.

void protocols::sewing::data_storage::SmartAssembly::set_n_terminal_segment ( SmartSegmentOP  new_segment)
void protocols::sewing::data_storage::SmartAssembly::set_output_partner ( bool  output_partner)

References output_partner_.

void protocols::sewing::data_storage::SmartAssembly::set_partner ( core::pose::PoseOP  partner_pose)

References partner_.

Referenced by SmartAssembly().

void protocols::sewing::data_storage::SmartAssembly::set_partner_ligands ( std::map< core::Size, LigandResidueCOP ligs)

References local_ligands_, and partner_ligands_.

Referenced by SmartAssembly().

void protocols::sewing::data_storage::SmartAssembly::set_resID_1 ( core::Size  id)
protected
void protocols::sewing::data_storage::SmartAssembly::set_resID_2 ( core::Size  id)
protected
void protocols::sewing::data_storage::SmartAssembly::set_segID_1 ( core::Size  id)
protected
void protocols::sewing::data_storage::SmartAssembly::set_segID_2 ( core::Size  id)
protected
void protocols::sewing::data_storage::SmartAssembly::set_segment_vector ( hashing::SegmentVectorCOP  segment_vector)
void protocols::sewing::data_storage::SmartAssembly::set_size ( core::Size  new_size)
void protocols::sewing::data_storage::SmartAssembly::set_start_node_vital_segments ( std::string  start_node_vital_segments)
void protocols::sewing::data_storage::SmartAssembly::set_starting_segment ( SmartSegmentOP  start_segment,
std::string  start_node_vital_segments 
)
void protocols::sewing::data_storage::SmartAssembly::set_window_width ( core::Size  width)

References window_width_.

bool protocols::sewing::data_storage::SmartAssembly::switch_segment ( bool  n_terminus)
core::pose::Pose protocols::sewing::data_storage::SmartAssembly::to_pose ( std::string  residue_type_set)
bool protocols::sewing::data_storage::SmartAssembly::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.

References protocols::sewing::data_storage::SmartSegment::get_n_most_segment(), core::pose::full_model_info::get_residue(), protocols::sewing::data_storage::ligand, local_segments_, protocols::TR(), window_width_, and protocols::kinmatch::xyz().

Referenced by chimerize(), and reconstitute_assembly_from_string().

void protocols::sewing::data_storage::SmartAssembly::trim_terminal_segments ( char  terminus,
core::Size  number 
)
void protocols::sewing::data_storage::SmartAssembly::unchimerize_ligand_segment ( LigandSegmentOP  ligseg)
bool protocols::sewing::data_storage::SmartAssembly::undelete_segment ( )
void protocols::sewing::data_storage::SmartAssembly::unsample_ligand ( )
void protocols::sewing::data_storage::SmartAssembly::unswitch_segment ( )

Member Data Documentation

utility::vector1< std::pair< core::Size, core::Size > > protocols::sewing::data_storage::SmartAssembly::all_basis_pairs_
private
SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::c_terminal_segment_
private
utility::vector1<core::Size> protocols::sewing::data_storage::SmartAssembly::c_terminal_segments_
private
std::map< core::Size, LigandResidueCOP > protocols::sewing::data_storage::SmartAssembly::const_ligands_
private
SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::counter_segment_
private

Referenced by set_starting_segment().

BasisPair protocols::sewing::data_storage::SmartAssembly::current_basis_pair_
private
SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::first_segment_
private

Referenced by add_segment().

char protocols::sewing::data_storage::SmartAssembly::last_change_
private
bool protocols::sewing::data_storage::SmartAssembly::last_change_was_n_terminal_
private
SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::last_chimaera_
private
BasisPair protocols::sewing::data_storage::SmartAssembly::last_chimaera_deleted_
private
SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::last_reverted_parent_chimaera_
private
std::pair< core::Size, LigandResidueOP > protocols::sewing::data_storage::SmartAssembly::last_sampled_ligand_
private

Referenced by sample_ligand(), and unsample_ligand().

core::Size protocols::sewing::data_storage::SmartAssembly::length_
private
std::map< core::Size, utility::vector1< LigandResidueOP > > protocols::sewing::data_storage::SmartAssembly::ligand_conformers_
private
std::map< core::Size, LigandResidueOP > protocols::sewing::data_storage::SmartAssembly::local_ligands_
private
std::map< core::Size, SmartSegmentOP > protocols::sewing::data_storage::SmartAssembly::local_segments_
private
char protocols::sewing::data_storage::SmartAssembly::modifiable_terminus_
private
SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::n_terminal_segment_
private
utility::vector1<core::Size> protocols::sewing::data_storage::SmartAssembly::n_terminal_segments_
private
bool protocols::sewing::data_storage::SmartAssembly::output_partner_
private
core::pose::PoseOP protocols::sewing::data_storage::SmartAssembly::partner_
private

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

std::map< core::Size, LigandResidueCOP > protocols::sewing::data_storage::SmartAssembly::partner_ligands_
private
std::map< core::Size, data_storage::SmartSegmentOP > protocols::sewing::data_storage::SmartAssembly::pdb_segments_
private
core::Size protocols::sewing::data_storage::SmartAssembly::resID_1_
private
core::Size protocols::sewing::data_storage::SmartAssembly::resID_2_
private
core::Size protocols::sewing::data_storage::SmartAssembly::segID_1_
private
core::Size protocols::sewing::data_storage::SmartAssembly::segID_2_
private
hashing::SegmentVectorCOP protocols::sewing::data_storage::SmartAssembly::segment_vector_
private
core::Size protocols::sewing::data_storage::SmartAssembly::size_
private
std::string protocols::sewing::data_storage::SmartAssembly::start_node_vital_segments_
private
core::Size protocols::sewing::data_storage::SmartAssembly::window_width_
private

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