Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.

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. More...  
typedef MolecularSystemLabelTraits::Primitive_label_classifier  Primitive_label_classifier 
Functor returning the unit identifier associated to an atom. More...  
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. More...  
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. More...  
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. More...  
Functor  
Interfaces_graph  operator() (const Molecular_model &model, bool internal=false) const 
Internal Methods  
static void  print (const Interfaces_graph &G, std::ostream &out) 
Prints the graph on dot format into an output stream. More...  
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 :
When bridges involve gaps between the units, the gap is added as a vertex. Annotations are added to the vertices and edges :
ParticleTraits  Traits class defining geometric particle types endowed with labels. 
MolecularSystemLabelTraits  Traits class defining a functor associating a label to a particle. 
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.
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.

inlinestatic 
Prints the graph on dot format into an output stream.