T_RMSD_comb_edge_weighted< Structure, MolecularDistance > Class Template Reference

Given a set of motifs instantiates the motif graph and computes the associated combined RMSD. More...

#include <RMSD_comb_edge_weighted.hpp>

Classes
struct	Component_statistics
struct	Vertex_property
	Vertex property for the motif graph. More...

Public Types
typedef MolecularDistance	Molecular_distance
typedef T_RMSD_comb_edge_weighted< Structure, Molecular_distance >	Self
typedef std::pair< int, int >	Aligned_pair
typedef double	Score_type
typedef std::pair< Score_type, Aligned_pair >	Seed_pair
typedef std::vector< Seed_pair >	Seed_type
typedef std::vector< Seed_type >::iterator	Seed_iterator
typedef Structure::value_type	Residue
	Representation of a molecular residue. More...
typedef Molecular_distance::Point	Conformation
typedef Molecular_distance::Conformation_traits	Conformation_traits
typedef boost::property< boost::edge_weight_t, int >	Edge_weight_property
	The weight for the motif graph edges. More...
typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, Vertex_property, Edge_weight_property >	Motif_graph
	The so called Motif_graph. More...
typedef boost::graph_traits< Motif_graph >::vertex_descriptor	Motif_graph_vertex
typedef boost::graph_traits< Motif_graph >::edge_descriptor	Motif_graph_edge
typedef boost::property_map< Motif_graph, boost::edge_weight_t >::type	Edge_weight_map
typedef std::vector< Motif_graph_vertex >	Motif_graph_part
	A part of a motif graph. More...
typedef std::map< Motif_graph_vertex, Motif_graph_vertex >	Motif_pairings
	A map keeping track of the motif pairings. More...

Internal Methods
unsigned	get_num_components ()
void	statistics (std::ostream &out)
void	add_structural_motif (Structure *motif_one, Structure *motif_two)
double	compute_distance (void)
template<class Archive >
void	serialize (Archive &ar, const unsigned BOOST_PFTO int version)
template<class OutputIterator >
void	get_all_motifs (OutputIterator out)
template<class OutputIterator >
void	get_component_motifs (unsigned i, OutputIterator out)

Detailed Description

template<class Structure, class MolecularDistance>
class SBL::CSB::T_RMSD_comb_edge_weighted< Structure, MolecularDistance >

Given a set of motifs instantiates the motif graph and computes the associated combined RMSD.

Uses a boost graph for encoding the motif graph. The vertex properties allow a mapping from a vertex to its associated motif and graph part.

Template Parameters

Structure	Representation of a molecular structure. Basically a vector of residues.
MolecularDistance	Model of the distance between two structures. Typically the lRMSD.

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Class Documentation

SBL::CSB::T_RMSD_comb_edge_weighted::Vertex_property

struct SBL::CSB::T_RMSD_comb_edge_weighted::Vertex_property

template<class Structure, class MolecularDistance>
struct SBL::CSB::T_RMSD_comb_edge_weighted< Structure, MolecularDistance >::Vertex_property

Vertex property for the motif graph.

Contains a part identifier (to determine which structure the motif is from) as well as a Structure (containing the structural motif associated with the vertex).

Class Members
unsigned	part
Structure *	structural_motif

Member Typedef Documentation

Aligned_pair

typedef std::pair<int, int> Aligned_pair

Conformation

typedef Molecular_distance::Point Conformation

Conformation_traits

typedef Molecular_distance::Conformation_traits Conformation_traits

Edge_weight_map

typedef boost::property_map<Motif_graph, boost::edge_weight_t>::type Edge_weight_map

Edge_weight_property

typedef boost::property<boost::edge_weight_t, int> Edge_weight_property

The weight for the motif graph edges.

An integer which represents the size of the intersection between two different motifs

Molecular_distance

typedef MolecularDistance Molecular_distance

Motif_graph

typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, Vertex_property, Edge_weight_property> Motif_graph

The so called Motif_graph.

Implemented with boost graph. The Motif_graph is a 2-colored edge weighted graph. Each color represents a structure. The edge weights correspond to the size of the intersection between two motifs.

Motif_graph_edge

typedef boost::graph_traits<Motif_graph>::edge_descriptor Motif_graph_edge

Motif_graph_part

typedef std::vector<Motif_graph_vertex> Motif_graph_part

A part of a motif graph.

Here we refer to the set of vertices associated to a color (or one of the two structures) as a graph part.

Motif_graph_vertex

typedef boost::graph_traits<Motif_graph>::vertex_descriptor Motif_graph_vertex

Motif_pairings

typedef std::map<Motif_graph_vertex, Motif_graph_vertex> Motif_pairings

A map keeping track of the motif pairings.

We use this structure to ease the access of pairs of motifs which were found together.

Residue

typedef Structure::value_type Residue

Representation of a molecular residue.

Must provide access to all residue information, notably an iterator over its atoms and all the usual information (i.e. residue name, sequence number...)

Score_type

typedef double 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

typedef T_RMSD_comb_edge_weighted<Structure, Molecular_distance> Self

Member Function Documentation

add_structural_motif()

void add_structural_motif ( Structure *  motif_one, Structure *  motif_two  )

inline

compute_distance()

double compute_distance ( void  )

inline

get_all_motifs()

void get_all_motifs ( OutputIterator  out )

inline

get_component_motifs()

void get_component_motifs ( unsigned  i, OutputIterator  out  )

inline

get_num_components()

unsigned get_num_components ( )

inline

serialize()

void serialize ( Archive &  ar, const unsigned BOOST_PFTO int  version  )

inline

statistics()

void statistics ( std::ostream &  out )

inline