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

#include <Tertiary_quaternary_structure_annotator.hpp>

Classes
struct	Bond_rep

struct	Bond_rep_set

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...

struct	Vertex_rep

Public Types
enum	Bond_type { COVALENT_BOND , MISSING_BOND , SS_BOND , SALT_BRIDGE , NONE_BOND }

enum	Vertex_type { SUBDOMAIN_TYPE , GAP_TYPE , NONE_TYPE }

typedef T_Tertiary_quaternary_structure_annotator< ParticleTraits, MolecularSystemLabelTraits >	Self

typedef ParticleTraits::Molecular_system	Molecular_system
	Representation of a molecular system of a protein in ESBTL. More...

typedef Molecular_system::Model	Molecular_model

typedef MolecularSystemLabelTraits::Primitive_label_classifier	Primitive_label_classifier
	Functor returning the unit identifier associated to an atom. More...

typedef SBL::CSB::T_Salt_bridges_finder< ParticleTraits >	Salt_bridges_finder

typedef SBL::CSB::T_Disulfide_bonds_finder< ParticleTraits >	Disulfide_bonds_finder

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...

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.

Member Typedef Documentation

◆ Disulfide_bonds_finder

typedef SBL::CSB::T_Disulfide_bonds_finder<ParticleTraits> Disulfide_bonds_finder

◆ Edge_properties

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.

◆ 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.

◆ Molecular_model

typedef Molecular_system::Model Molecular_model

◆ Molecular_system

typedef ParticleTraits::Molecular_system Molecular_system

Representation of a molecular system of a protein in ESBTL.

◆ Primitive_label_classifier

typedef MolecularSystemLabelTraits::Primitive_label_classifier Primitive_label_classifier

Functor returning the unit identifier associated to an atom.

◆ Salt_bridges_finder

typedef SBL::CSB::T_Salt_bridges_finder<ParticleTraits> Salt_bridges_finder

◆ Self

typedef T_Tertiary_quaternary_structure_annotator<ParticleTraits, MolecularSystemLabelTraits> Self

◆ Vertex_properties

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.

Member Enumeration Documentation

◆ Bond_type

enum Bond_type

Enumerator
COVALENT_BOND
MISSING_BOND
SS_BOND
SALT_BRIDGE
NONE_BOND

◆ Vertex_type

enum Vertex_type

Enumerator
SUBDOMAIN_TYPE
GAP_TYPE
NONE_TYPE

Member Function Documentation

◆ operator()()

T_Tertiary_quaternary_structure_annotator< ParticleTraits, MolecularSystemLabelTraits >::Interfaces_graph operator()	(	const Molecular_model &	model,
		bool	internal = `false`
	)		const

inline

◆ print()

void print	(	const Interfaces_graph &	G,
		std::ostream &	out
	)

inlinestatic

Prints the graph on dot format into an output stream.

Classes

Public Types

Functor

Internal Methods