Potential Cooperation (PC) & Biological Interaction Type (BIT)

pc()

The relative growth of the members between their isolate growth and their growth in the pairwise community, which can optionally generate the member-level PC scores and the BIT score, depending on the specified arguments:

CommScores.pc(member_models=None, modelutils=None, com_model=None, isolate_growths=None, comm_sol=None,
               environment=None, comm_effects=True, community=None, interaction_threshold=0.1, compatibilized=False)

  • member_models list|set: The models from which the MSModelUtil objects and the community model can be constructed.

  • modelutils list|set: The MSModeulUtils objects of the member models that can be provided as an alternative to member_models for quicker execution time or to conserve additional constraints in the models.

  • com_model cobrakbase.core.kbasefba.fbamodel.FBAModel: The community model that will be simulated, which can alternatively be constructed from the member_models or model_utils arguments when comm_model remains None.

  • isolate_growth dict: The maximal growth of the member isolates, keyed by their IDs, which can be directly provided through this argument to circumvent external simulation.

  • com_sol cobra.core.solution.Solution: The flux solution of the community at maximal growth, which is computed when com_sol is left as None.

  • environment dict|cobrakbase.core.kbasebiochem.media.Media: The media environment in which the member models will be simulated.

  • comm_effects bool: specifies whether the biological interaction type will be approximated based on the PC score for each member, otherwise the community PC score is returned.

  • community modelseedpy.community.mscommunity.MSCommunity: The MSCommunity object that encapsulates the com_model.

  • interaction_threshold float: The deviation threshold from a PC score of 1 is that used to identify a positive or negative effect on a given member, which is used to compute the BIT score.

  • compatibilized bool: specifies whether the member models have been compatibilized to ModelSEED conventions, which is necessary to appropriately simulate the community growth and behaviors.

Returns float|tuple: The function returns the community PC score when comm_effects is False. A comm_effects of True returns instead a tuple of the community PC score, a dictionary with the PC score of each member, and the string BIT score prediction based on the member PC scores.