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
None
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
float
