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protocols::sewing::data_storage::SmartSegment Class Reference

a neighbor-aware SewSegment version More...

#include <SmartSegment.hh>

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

 SmartSegment ()
 
 SmartSegment (bool is_vital)
 
 SmartSegment (bool is_vital, core::Size max_segment_length)
 
 SmartSegment (SmartSegment const &src)
 
 ~SmartSegment () override
 
SmartSegmentOP clone () const
 
void set_segment_id (core::Size new_segment_id)
 
core::Size get_segment_id () const
 
void set_n_terminal_neighbor (SmartSegmentOP new_n_terminal_neighbor)
 
SmartSegmentOP get_n_terminal_neighbor () const
 
void set_c_terminal_neighbor (SmartSegmentOP new_c_terminal_neighbor)
 
SmartSegmentOP get_c_terminal_neighbor () const
 
void set_dssp_code (char new_dssp_code)
 
char get_dssp_code () const
 
void set_chimaeric_status (bool is_chimaera)
 
bool is_chimaeric () const
 
void set_n_terminal_parent (SmartSegmentOP new_n_terminal_parent)
 
void set_c_terminal_parent (SmartSegmentOP new_c_terminal_parent)
 
SmartSegmentOP get_n_terminal_parent () const
 
SmartSegmentOP get_c_terminal_parent () const
 
bool is_vital () const
 
void set_is_vital (bool)
 
bool is_in_Assembly () const
 
void set_is_in_Assembly (bool)
 
bool is_n_terminus_fixed () const
 
bool is_c_terminus_fixed () const
 
bool is_hashable () const
 
void set_residue_vector (utility::vector1< SmartSewingResidueOP > new_residue_vector)
 
utility::vector1
< SmartSewingResidueOP > & 
get_residue_vector ()
 
utility::vector1
< SmartSewingResidueOP > const & 
get_const_residue_vector () const
 
SmartSewingResidueOP get_residue (core::Size resnum)
 
void set_length (core::Size new_length)
 
core::Size get_length () const
 
void set_basis_pair (BasisPair basis_pair)
 
BasisPair get_basis_pair () const
 
std::set< core::Sizeget_vital_residues () const
 
void set_vital_residues (std::set< core::Size >)
 
void add_vital_residue (core::Size)
 
void set_const_reference_segment (SmartSegmentCOP ref)
 
SmartSegmentCOP get_const_reference_segment () const
 
void isolate ()
 
bool residue_is_vital (core::Size)
 
virtual std::string get_name () const
 

Static Public Member Functions

static SmartSegmentOP get_far_n_terminal_parent (SmartSegmentOP current_segment)
 
static SmartSegmentOP get_far_c_terminal_parent (SmartSegmentOP current_segment)
 
static SmartSegmentCOP get_n_most_segment (SmartSegmentCOP, bool cross_chimaerae)
 
static SmartSegmentOP get_n_most_segment (SmartSegmentOP, bool cross_chimaerae)
 
static SmartSegmentCOP get_c_most_segment (SmartSegmentCOP, bool cross_chimaerae)
 
static SmartSegmentOP get_c_most_segment (SmartSegmentOP, bool cross_chimaerae)
 
static void link_to (SmartSegmentOP n_term, SmartSegmentOP c_term)
 
static void become (SmartSegmentOP changing_segment, SmartSegmentCOP src_segment)
 

Private Attributes

core::Size segment_id_
 
SmartSegmentOP n_terminal_neighbor_
 
SmartSegmentOP c_terminal_neighbor_
 
utility::vector1
< SmartSewingResidueOP
residues_
 
char dssp_code_
 
bool is_a_chimaera_
 
SmartSegmentOP n_terminal_parent_
 
SmartSegmentOP c_terminal_parent_
 
bool is_vital_
 
bool is_in_Assembly_
 
core::Size length_
 
BasisPair basis_pair_ = std::make_pair( Basis( 0, 0), Basis( 0, 0) )
 
std::set< core::Sizevital_residues_
 
SmartSegmentCOP const_reference_segment_ = nullptr
 

Detailed Description

a neighbor-aware SewSegment version

Constructor & Destructor Documentation

protocols::sewing::data_storage::SmartSegment::SmartSegment ( )
protocols::sewing::data_storage::SmartSegment::SmartSegment ( bool  is_vital)
protocols::sewing::data_storage::SmartSegment::SmartSegment ( bool  is_vital,
core::Size  max_segment_length 
)
protocols::sewing::data_storage::SmartSegment::SmartSegment ( SmartSegment const &  src)
protocols::sewing::data_storage::SmartSegment::~SmartSegment ( )
override

Member Function Documentation

void protocols::sewing::data_storage::SmartSegment::add_vital_residue ( core::Size  resnum)
void protocols::sewing::data_storage::SmartSegment::become ( SmartSegmentOP  changing_segment,
SmartSegmentCOP  src_segment 
)
static
SmartSegmentOP protocols::sewing::data_storage::SmartSegment::clone ( ) const
BasisPair protocols::sewing::data_storage::SmartSegment::get_basis_pair ( ) const

References basis_pair_.

Referenced by SmartSegment().

SmartSegmentCOP protocols::sewing::data_storage::SmartSegment::get_c_most_segment ( SmartSegmentCOP  start_segment,
bool  cross_chimaerae 
)
static
SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_c_most_segment ( SmartSegmentOP  start_segment,
bool  cross_chimaerae 
)
static

References get_c_most_segment().

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_c_terminal_neighbor ( ) const
SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_c_terminal_parent ( ) const
SmartSegmentCOP protocols::sewing::data_storage::SmartSegment::get_const_reference_segment ( ) const

References const_reference_segment_.

Referenced by SmartSegment().

utility::vector1< SmartSewingResidueOP > const & protocols::sewing::data_storage::SmartSegment::get_const_residue_vector ( ) const

References residues_.

Referenced by SmartSegment().

char protocols::sewing::data_storage::SmartSegment::get_dssp_code ( ) const

References dssp_code_.

Referenced by SmartSegment().

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_far_c_terminal_parent ( SmartSegmentOP  current_segment)
static
SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_far_n_terminal_parent ( SmartSegmentOP  current_segment)
static
core::Size protocols::sewing::data_storage::SmartSegment::get_length ( ) const

References residues_.

Referenced by become(), and SmartSegment().

SmartSegmentCOP protocols::sewing::data_storage::SmartSegment::get_n_most_segment ( SmartSegmentCOP  start_segment,
bool  cross_chimaerae 
)
static
SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_n_most_segment ( SmartSegmentOP  start_segment,
bool  cross_chimaerae 
)
static

References get_n_most_segment().

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_n_terminal_neighbor ( ) const

References n_terminal_neighbor_.

Referenced by isolate().

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_n_terminal_parent ( ) const
virtual std::string protocols::sewing::data_storage::SmartSegment::get_name ( ) const
inlinevirtual
SmartSewingResidueOP protocols::sewing::data_storage::SmartSegment::get_residue ( core::Size  resnum)

References residues_, and protocols::TR().

utility::vector1< SmartSewingResidueOP > & protocols::sewing::data_storage::SmartSegment::get_residue_vector ( )

References residues_.

core::Size protocols::sewing::data_storage::SmartSegment::get_segment_id ( ) const
std::set< core::Size > protocols::sewing::data_storage::SmartSegment::get_vital_residues ( ) const

References vital_residues_.

bool protocols::sewing::data_storage::SmartSegment::is_c_terminus_fixed ( ) const

References c_terminal_neighbor_.

Referenced by is_hashable(), and isolate().

bool protocols::sewing::data_storage::SmartSegment::is_chimaeric ( ) const
bool protocols::sewing::data_storage::SmartSegment::is_hashable ( ) const
bool protocols::sewing::data_storage::SmartSegment::is_in_Assembly ( ) const

References is_in_Assembly_.

bool protocols::sewing::data_storage::SmartSegment::is_n_terminus_fixed ( ) const

References n_terminal_neighbor_.

Referenced by is_hashable(), and isolate().

bool protocols::sewing::data_storage::SmartSegment::is_vital ( ) const

References is_vital_.

Referenced by set_is_vital(), and SmartSegment().

void protocols::sewing::data_storage::SmartSegment::isolate ( )
void protocols::sewing::data_storage::SmartSegment::link_to ( SmartSegmentOP  n_term,
SmartSegmentOP  c_term 
)
static
bool protocols::sewing::data_storage::SmartSegment::residue_is_vital ( core::Size  resnum)

References vital_residues_.

void protocols::sewing::data_storage::SmartSegment::set_basis_pair ( BasisPair  basis_pair)

References basis_pair_.

void protocols::sewing::data_storage::SmartSegment::set_c_terminal_neighbor ( SmartSegmentOP  new_c_terminal_neighbor)

References c_terminal_neighbor_.

Referenced by isolate().

void protocols::sewing::data_storage::SmartSegment::set_c_terminal_parent ( SmartSegmentOP  new_c_terminal_parent)

References c_terminal_parent_.

void protocols::sewing::data_storage::SmartSegment::set_chimaeric_status ( bool  is_chimaera)

References is_a_chimaera_.

void protocols::sewing::data_storage::SmartSegment::set_const_reference_segment ( SmartSegmentCOP  ref)
void protocols::sewing::data_storage::SmartSegment::set_dssp_code ( char  new_dssp_code)

References dssp_code_.

void protocols::sewing::data_storage::SmartSegment::set_is_in_Assembly ( bool  is_in_assembly)

References is_in_Assembly_.

void protocols::sewing::data_storage::SmartSegment::set_is_vital ( bool  is_vital)
void protocols::sewing::data_storage::SmartSegment::set_length ( core::Size  new_length)

References length_.

void protocols::sewing::data_storage::SmartSegment::set_n_terminal_neighbor ( SmartSegmentOP  new_n_terminal_neighbor)
void protocols::sewing::data_storage::SmartSegment::set_n_terminal_parent ( SmartSegmentOP  new_n_terminal_parent)

References n_terminal_parent_.

void protocols::sewing::data_storage::SmartSegment::set_residue_vector ( utility::vector1< SmartSewingResidueOP new_residue_vector)

References length_, and residues_.

void protocols::sewing::data_storage::SmartSegment::set_segment_id ( core::Size  new_segment_id)

References segment_id_.

void protocols::sewing::data_storage::SmartSegment::set_vital_residues ( std::set< core::Size vital)

References vital_residues_.

Member Data Documentation

BasisPair protocols::sewing::data_storage::SmartSegment::basis_pair_ = std::make_pair( Basis( 0, 0), Basis( 0, 0) )
private
SmartSegmentOP protocols::sewing::data_storage::SmartSegment::c_terminal_neighbor_
private
SmartSegmentOP protocols::sewing::data_storage::SmartSegment::c_terminal_parent_
private
SmartSegmentCOP protocols::sewing::data_storage::SmartSegment::const_reference_segment_ = nullptr
private
char protocols::sewing::data_storage::SmartSegment::dssp_code_
private
bool protocols::sewing::data_storage::SmartSegment::is_a_chimaera_
private
bool protocols::sewing::data_storage::SmartSegment::is_in_Assembly_
private
bool protocols::sewing::data_storage::SmartSegment::is_vital_
private
core::Size protocols::sewing::data_storage::SmartSegment::length_
private
SmartSegmentOP protocols::sewing::data_storage::SmartSegment::n_terminal_neighbor_
private
SmartSegmentOP protocols::sewing::data_storage::SmartSegment::n_terminal_parent_
private
utility::vector1<SmartSewingResidueOP> protocols::sewing::data_storage::SmartSegment::residues_
private
core::Size protocols::sewing::data_storage::SmartSegment::segment_id_
private
std::set< core::Size > protocols::sewing::data_storage::SmartSegment::vital_residues_
private

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