Builds a graph representing the biochemical interactions between units of a protein. More...

#include <Tertiary_quaternary_structure_annotator.hpp>

Classes
class	Edge_label_writer
	Functor allowing to write two properties associated to a vertex or an edge into a dot file representing a graph. More...
class	Vertex_label_writer
	Functor allowing to write two properties associated to a vertex into a dot file representing a graph. More...

Public Types
typedef ParticleTraits::Molecular_system	Molecular_system
	Representation of a molecular system of a protein.
typedef MolecularSystemLabelTraits::Primitive_label_classifier	Primitive_label_classifier
	Functor returning the unit identifier associated to an atom.
typedef boost::property< boost::vertex_index_t, int, boost::property< boost::vertex_name_t, Vertex_rep, boost::property< boost::vertex_index1_t, int, boost::property< boost::vertex_index2_t, int > > > >	Vertex_properties
	Attach the identifier of partners to the corresponding vertices in the interfaces graph.
typedef boost::property< boost::edge_name_t, Bond_rep_set, boost::property< boost::edge_weight_t, Bond_type > >	Edge_properties
	Attach two weights (the number of contacts and the number of connected components) to the edges of the interfaces graph.
typedef boost::adjacency_list< boost::listS, boost::listS, boost::undirectedS, Vertex_properties, Edge_properties >	Interfaces_graph
	Representation of the interfaces graph, where vertices are labeled with an identifier, and edges are weighted with the number of c.c and the number of contacts.

Internal Methods
static void	print (const Interfaces_graph &G, std::ostream &out)
	Prints the graph on dot format into an output stream.

Detailed Description

template<class ParticleTraits, class MolecularSystemLabelTraits>
class SBL::CSB::T_Tertiary_quaternary_structure_annotator< ParticleTraits, MolecularSystemLabelTraits >

Builds a graph representing the biochemical interactions between units of a protein.

Vertices are the units of the protein. Units are determined by the labels attached to all input particles. Edges link vertices if :

the units are sequentially linked in the input structure,

there is a disulfide bridge or a salt bridge between the two units.

When bridges involve gaps between the units, the gap is added as a vertex. Annotations are added to the vertices and edges :

for vertices, the total number of residues in the unit / gap, with the number of input residues in the unit / gap.

for sequential edges, if there is a gap that is not represented by a vertex, the interval of residues defining the gap.

for bridge edges, the nature of the bridges (S-S or S-B) and the number of bridges between the two involved units.

Template Parameters

ParticleTraits	Traits class defining geometric particle types endowed with labels.
MolecularSystemLabelTraits	Traits class defining a functor associating a label to a particle.