Connectivity_inference is a package providing programs enumerating the possible pairwise subunits interactions within an assembly from oligomers of this assembly Reference Manual – User Manual . Authors: D. Agarwal and C. Caillouet and F. Cazals and D. Coudert

Main classes:

SBL::Connectivity_inference_analysis::MCI_output_preprocessing : A class to preprocess the output of a connectivity inference problem.

SBL::Connectivity_inference_analysis::MCI_analysis : A class to analyze the solutions of a connectivity inference problem.

SBL::Connectivity_inference_data_structures::MCI_Oligomers : A class to store a set of oligomers of an assembly.

SBL::Connectivity_inference_data_structures::MCI_Contact : A class to store a contact between two subunits of an assembly.

SBL::Connectivity_inference_data_structures::MCI_specification : A class to specify the input of a connectivity inference problem.

SBL::Connectivity_inference_data_structures::MCI_set_of_contacts : A class to specify a set of contacts.

SBL::Connectivity_inference_data_structures::MCI_solutions : A class to store solutions, each as a triple (cost, set of contacts, running time per solution)

SBL::Connectivity_inference_engine::MCI_MILP_engine : A class implementing the Mixed Integer Linear Program (MILP) to solve Connectivity inference problems.

SBL::mcibootstrap_iterative::MCI_bootstrap : A class to enrich set of initial consensus contacts by bootstraping procedure.