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	Vertex_property
	Vertex property for the motif graph. More...

Public Types
typedef Structure::value_type	Residue
	Representation of a molecular residue. More...
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 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).

Member Typedef Documentation

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

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_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_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...)