Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer > Class Template Reference

Note that all methods are static – no member data. More...

#include <Transition_graph_traits_compressed.hpp>

Public Types

typedef SampleRep Sample_rep
 
typedef SampleWeight Sample_weight
 
typedef VertexContainer Vertex_container
 
typedef EdgeContainer Edge_container
 
typedef T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer > Self
 
typedef boost::property< boost::vertex_name_t, std::pair< bool, SampleWeight >, SampleRep > Vertex_property
 
typedef boost::property< boost::edge_name_t, bool, SampleRep > Edge_property
 
typedef boost::adjacency_list< EdgeContainer, VertexContainer, boost::undirectedS, Vertex_property, Edge_propertyGraph
 
typedef boost::graph_traits< GraphGraph_traits
 
typedef Graph_traits::vertex_descriptor Vertex
 
typedef Graph_traits::vertex_descriptor Minimum
 
typedef Graph_traits::edge_descriptor Transition_state
 
typedef Graph_traits::vertex_iterator Minima_iterator
 
typedef Graph_traits::edge_iterator Transition_states_iterator
 
typedef Graph_traits::out_edge_iterator Incident_transition_states_iterator
 

Static Public Member Functions

static Minimum add_minimum (Graph &G)
 
static Minimum add_minimum (SampleRep &sample, Graph &G)
 
static void remove_minimum (Minimum u, Graph &G)
 
static unsigned num_minima (Graph &G)
 
static std::pair< Transition_state, bool > add_transition_state (Minimum u, Minimum v, Graph &G)
 
static std::pair< Transition_state, bool > add_transition_state (Minimum u, Minimum v, SampleRep &sample, Graph &G)
 
static void remove_transition_state (Transition_state t, Graph &G)
 
static unsigned num_transition_states (Graph &G)
 
static const SampleWeight & get_weight (Graph &G, Minimum u)
 
static void set_weight (Graph &G, Minimum u, const SampleWeight &w)
 
static bool has_sample (Graph &G, Minimum u)
 
static bool has_sample (Graph &G, Transition_state t)
 
static SampleRep & get_sample (Graph &G, Minimum u)
 
static SampleRep & get_sample (Graph &G, Transition_state t)
 
static std::pair< Minimum, Minimumminima (Transition_state t, Graph &G)
 
static std::pair< Minima_iterator, Minima_iteratorminima (Graph &G)
 
static std::pair< Transition_states_iterator, Transition_states_iteratortransition_states (Graph &G)
 
static std::pair< Incident_transition_states_iterator, Incident_transition_states_iteratortransition_states (Minimum u, Graph &G)
 
static bool is_minimum (Vertex u, Graph &G)
 

Detailed Description

template<class SampleRep, class SampleWeight, class VertexContainer = boost::vecS, class EdgeContainer = boost::vecS>
class SBL::CSB::T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >

Note that all methods are static – no member data.

TG representation without explicit storage of the transitions as vertices of the TG.

A std TG traits means that minima and saddles are explicitely represented as vertices of the graph so that each transition state yields two edges to the connected minina.

Template Parameters
SampleRep
SampleWeight
VertexContainer
EdgeContainer

Member Typedef Documentation

◆ Edge_container

typedef EdgeContainer Edge_container

◆ Edge_property

typedef boost::property<boost::edge_name_t, bool, SampleRep> Edge_property

◆ Graph

typedef boost::adjacency_list<EdgeContainer, VertexContainer, boost::undirectedS, Vertex_property, Edge_property> Graph

◆ Graph_traits

typedef boost::graph_traits<Graph> Graph_traits

◆ Incident_transition_states_iterator

typedef Graph_traits::out_edge_iterator Incident_transition_states_iterator

◆ Minima_iterator

typedef Graph_traits::vertex_iterator Minima_iterator

◆ Minimum

typedef Graph_traits::vertex_descriptor Minimum

◆ Sample_rep

typedef SampleRep Sample_rep

◆ Sample_weight

typedef SampleWeight Sample_weight

◆ Self

typedef T_Transition_graph_traits_compressed<SampleRep, SampleWeight, VertexContainer, EdgeContainer> Self

◆ Transition_state

typedef Graph_traits::edge_descriptor Transition_state

◆ Transition_states_iterator

typedef Graph_traits::edge_iterator Transition_states_iterator

◆ Vertex

typedef Graph_traits::vertex_descriptor Vertex

◆ Vertex_container

typedef VertexContainer Vertex_container

◆ Vertex_property

typedef boost::property<boost::vertex_name_t, std::pair<bool, SampleWeight>, SampleRep> Vertex_property

Member Function Documentation

◆ add_minimum() [1/2]

T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >::Minimum add_minimum ( Graph G)
inlinestatic

◆ add_minimum() [2/2]

T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >::Minimum add_minimum ( SampleRep &  sample,
Graph G 
)
inlinestatic

◆ add_transition_state() [1/2]

std::pair< typename T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >::Transition_state, bool > add_transition_state ( Minimum  u,
Minimum  v,
Graph G 
)
inlinestatic

◆ add_transition_state() [2/2]

std::pair< typename T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >::Transition_state, bool > add_transition_state ( Minimum  u,
Minimum  v,
SampleRep &  sample,
Graph G 
)
inlinestatic

◆ get_sample() [1/2]

SampleRep & get_sample ( Graph G,
Minimum  u 
)
inlinestatic

◆ get_sample() [2/2]

SampleRep & get_sample ( Graph G,
Transition_state  t 
)
inlinestatic

◆ get_weight()

const SampleWeight & get_weight ( Graph G,
Minimum  u 
)
inlinestatic

◆ has_sample() [1/2]

bool has_sample ( Graph G,
Minimum  u 
)
inlinestatic

◆ has_sample() [2/2]

bool has_sample ( Graph G,
Transition_state  t 
)
inlinestatic

◆ is_minimum()

bool is_minimum ( Vertex  u,
Graph G 
)
inlinestatic

◆ minima() [1/2]

std::pair< typename T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >::Minima_iterator, typename T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >::Minima_iterator > minima ( Graph G)
inlinestatic

◆ minima() [2/2]

std::pair< typename T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >::Minimum, typename T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >::Minimum > minima ( Transition_state  t,
Graph G 
)
inlinestatic

◆ num_minima()

unsigned num_minima ( Graph G)
inlinestatic

◆ num_transition_states()

unsigned num_transition_states ( Graph G)
inlinestatic

◆ remove_minimum()

void remove_minimum ( Minimum  u,
Graph G 
)
inlinestatic

◆ remove_transition_state()

void remove_transition_state ( Transition_state  t,
Graph G 
)
inlinestatic

◆ set_weight()

void set_weight ( Graph G,
Minimum  u,
const SampleWeight &  w 
)
inlinestatic

◆ transition_states() [1/2]

std::pair< typename T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >::Transition_states_iterator, typename T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >::Transition_states_iterator > transition_states ( Graph G)
inlinestatic

◆ transition_states() [2/2]

std::pair< typename T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >::Incident_transition_states_iterator, typename T_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >::Incident_transition_states_iterator > transition_states ( Minimum  u,
Graph G 
)
inlinestatic