T_Energy_landscape_analysis_workflow< Traits > Class Template Reference

Generic workflow of Energy_landscape_analysis for reading the command line options of the applications and running the calculations.
More...

#include <Energy_landscape_analysis_workflow.hpp>

Public Types
typedef SBL::IO::T_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >	Transition_graph_loader
	Loader for one or more boost archive files More...
typedef SBL::Modules::T_Energy_landscape_transition_graph_topology_module< Traits >	Transition_graph_topology_module
	Module analyzingthe topology of a transition graph. More...
typedef SBL::Modules::T_Energy_landscape_transition_graph_landmarks_paths_module< Traits >	Landmark_paths_module
	Module computing shortes paths in a graph passing through selected landmarks. More...
typedef SBL::Modules::T_Morse_theory_based_analyzer_for_NNG_module< Traits >	MTB_analyzer_module
	Generic manager for reading arguments of the program and run the calculations More...

Workflow
void	start (int argc, char *argv[])
	Starts the workflow by reading the command line options, and pushing on the stack the start vertex. More...

Detailed Description

template<class Traits>
class T_Energy_landscape_analysis_workflow< Traits >

Generic workflow of Energy_landscape_analysis for reading the command line options of the applications and running the calculations.

This workflow instantiates one loader and three modules:

• T_Energy_landscape_analysis_workflow::Transition_graph_loader : loads a transition graph stored in an XML archive.
• T_Energy_landscape_analysis_workflow::Transition_graph_topology_module (optional): runs analysis on the topology of the transition graph.
• T_Energy_landscape_analysis_workflow::Landmark_paths_module (optional): runs shortest paths analysis w.r.t given landmarks.
• T_Energy_landscape_analysis_workflow::MTB_analyzer_module (optional): runs Morse theory based analysis on the transition graph elevated by weights on the vertices.

  Template Parameters

  Traits

  Traits class defining the types used in the applications of Energy_landscape_analysis (see T_Energy_landscape_analysis_traits).

Member Typedef Documentation

Landmark_paths_module

typedef SBL::Modules::T_Energy_landscape_transition_graph_landmarks_paths_module<Traits> Landmark_paths_module

Module computing shortes paths in a graph passing through selected landmarks.

Module computing shortes paths in a graph passing through selected landmarks

Template Parameters

ModuleTraits

Traits class defining the type Transition_graph_traits defining types related to the transition graph, and the type Distance defining a functor returning the distance between two conformations.

MTB_analyzer_module

typedef SBL::Modules::T_Morse_theory_based_analyzer_for_NNG_module<Traits> MTB_analyzer_module

Generic manager for reading arguments of the program and run the calculations

Template Parameters

ModuleTraits

Model of a traits class defining the types used in the manager (see T_Conformational_clustering_traits).

Transition_graph_loader

typedef SBL::IO::T_Transition_graph_loader<boost::archive::xml_iarchive, typename Traits::Transition_graph_traits> Transition_graph_loader

Loader for one or more boost archive files

Template Parameters

Sphere3	Representation of a 3D sphere.
Point3	Representation of the center of a 3D sphere.

Transition_graph_topology_module

typedef SBL::Modules::T_Energy_landscape_transition_graph_topology_module<Traits> Transition_graph_topology_module

Module analyzingthe topology of a transition graph.

Module analyzingthe topology of a transition graph

Template Parameters

ModuleTraits

Traits class defining the type Transition_graph_traits defining types related to the transition graph, and the type Distance defining a functor returning the distance between two conformations.

Member Function Documentation

start()

void start ( int  argc, char *  argv[]  )

inline

Starts the workflow by reading the command line options, and pushing on the stack the start vertex.