cameo.network_analysis package¶
Submodules¶
cameo.network_analysis.networkx_based module¶

cameo.network_analysis.networkx_based.
model_to_network
(model, *args, **kwargs)[source]¶ Convert a model into a networkx graph.
Calls reactions_to_network with model.reactions.
Parameters: model (cobra.Model) – The model. Returns: Return type: networkx.MultiDiGraph See also

cameo.network_analysis.networkx_based.
reactions_to_network
(reactions, max_distance=0.3)[source]¶ Convert a list of reactions into a networkx graph.
Parameters:  reactions (list) – The list of reactions.
 max_distance (float, optional) – A threshold on the normalized distance between two compounds. If distance is above this threshold, no edge between those compounds will be created.
Returns: Return type: networkx.MultiDiGraph
See also
distance_based_on_molecular_formula()

cameo.network_analysis.networkx_based.
remove_highly_connected_nodes
(network, max_degree=10, ignore=[])[source]¶ Remove highly connected nodes (changes network in place).
Parameters:  network (networkx graph) –
 max_degree (int (default 10)) – Remove nodes with degree > max_degree
 ignore (list) – List of nodes to ignore.
Returns: Return type:
cameo.network_analysis.util module¶

cameo.network_analysis.util.
distance_based_on_molecular_formula
(metabolite1, metabolite2, normalize=True)[source]¶ Calculate the distance of two metabolites bases on the molecular formula
Parameters:  metabolite1 (Metabolite) – The first metabolite.
 metabolite2 (Metabolite) – The second metabolite.
 normalize (bool, optional) – If the distance should be normalized by the total number of elements in both metabolites (defaults to True).
Returns: The distance between metabolite1 and metabolite2.
Return type: