Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Seeder_DP_score< StructureType, ScoreComputer > Class Template Reference

Given two structures, align them using Seeder_DP_score. More...

#include <Seeder_DP_score.hpp>

Classes

struct  DP_matrix_item
 

Public Types

enum  DP_direction { U , L , UL , S }
 
typedef StructureType Structure_type
 
typedef Structure_type::Residue Residue
 
typedef Structure_type::Alignment_residue Alignment_residue
 
typedef SBL::CSB::T_Alignment_sequence< Alignment_residueAlignment_sequence
 
typedef SBL::CSB::T_Alignment_engine_sequences_seqan< Structure_typeAlignment_sequence_engine
 
typedef Alignment_sequence_engine::Alignment_type Alignment_type
 
typedef ScoreComputer Score_computer
 
typedef T_Seeder_DP_score< Structure_type, Score_computerSelf
 
typedef Structure_type::value_type Canonized_residue
 
typedef Canonized_residue::Canonized_segment Canonized_segment
 
typedef Canonized_residue::SSE_Type SSE_Type
 
typedef Score_computer::K K
 
typedef Score_computer::Score_type Score_type
 
typedef K::Point_3 Point_3
 
typedef K::Point_2 Point_2
 
typedef std::pair< int, int > Aligned_pair
 
typedef std::pair< Score_type, Aligned_pairSeed_pair
 
typedef std::vector< Seed_pairSeed_type
 
typedef std::vector< Seed_type >::iterator Seed_iterator
 
typedef std::vector< DP_matrix_itemDP_matrix
 
typedef std::vector< Score_typeScore_matrix
 

Constructors

 T_Seeder_DP_score ()
 Default constructor. More...
 
 T_Seeder_DP_score (const Self &other)
 Copy constructor. More...
 

Internal public methods

Score_type operator() (const Structure_type &struct_1, const Structure_type &struct_2)
 
Seed_iterator seeds_begin ()
 
Seed_iterator seeds_end ()
 
std::size_t get_num_seeds ()
 
static void add_options (boost::program_options::options_description &options)
 

Detailed Description

template<class StructureType, class ScoreComputer>
class SBL::CSB::T_Seeder_DP_score< StructureType, ScoreComputer >

Given two structures, align them using Seeder_DP_score.

Given two structures, align them using Seeder_DP_score.

Member Typedef Documentation

◆ Aligned_pair

typedef std::pair<int, int> Aligned_pair

◆ Alignment_residue

typedef Structure_type::Alignment_residue Alignment_residue

◆ Alignment_sequence

◆ Alignment_sequence_engine

◆ Alignment_type

◆ Canonized_residue

typedef Structure_type::value_type Canonized_residue

◆ Canonized_segment

typedef Canonized_residue::Canonized_segment Canonized_segment

◆ DP_matrix

typedef std::vector<DP_matrix_item> DP_matrix

◆ K

typedef Score_computer::K K

◆ Point_2

typedef K::Point_2 Point_2

◆ Point_3

typedef K::Point_3 Point_3

◆ Residue

typedef Structure_type::Residue Residue

◆ Score_computer

typedef ScoreComputer Score_computer

◆ Score_matrix

typedef std::vector<Score_type> Score_matrix

◆ Score_type

typedef Score_computer::Score_type Score_type

◆ Seed_iterator

typedef std::vector<Seed_type>::iterator Seed_iterator

◆ Seed_pair

typedef std::pair<Score_type, Aligned_pair> Seed_pair

◆ Seed_type

typedef std::vector<Seed_pair> Seed_type

◆ Self

◆ SSE_Type

typedef Canonized_residue::SSE_Type SSE_Type

◆ Structure_type

typedef StructureType Structure_type

Member Enumeration Documentation

◆ DP_direction

Enumerator
UL 

Constructor & Destructor Documentation

◆ T_Seeder_DP_score() [1/2]

Default constructor.

◆ T_Seeder_DP_score() [2/2]

T_Seeder_DP_score ( const Self other)
inline

Copy constructor.

Member Function Documentation

◆ add_options()

void add_options ( boost::program_options::options_description &  options)
inlinestatic

◆ get_num_seeds()

std::size_t get_num_seeds ( )
inline

◆ operator()()

T_Seeder_DP_score< StructureType, ScoreComputer >::Score_type operator() ( const Structure_type struct_1,
const Structure_type struct_2 
)
inline

◆ seeds_begin()

Seed_iterator seeds_begin ( )
inline

◆ seeds_end()

Seed_iterator seeds_end ( )
inline