ecoli.analysis.causality_network.network_components
Classes for the Nodes and Edges of a causality network.
- class ecoli.analysis.causality_network.network_components.Edge(process)[source]
Bases:
object
Class definition for an edge in the causality network.
- Parameters:
process (str)
- edge_type
Type of edge (type of the process node the edge is attached to), string, e.g. “Complexation”, “Metabolism”
- src_id
ID of the source node, string, e.g. “RXN0-2382”
- dst_id
ID of the destination node, string, e.g. “WATER[c]”
- stoichiometry
(Only for metabolism edges) Stoichiometric coefficient of reaction-metabolite pair, integer, e.g. 1
- class ecoli.analysis.causality_network.network_components.Node[source]
Bases:
object
Class definition for a node in the causality network.
- node_class
Class of node, string, either “State” or “Process”
- node_type
Type of node, string, e.g. “Gene”, “Metabolism”
- node_id
Unique ID of node, string, e.g. “EG11274”, “CPLX-125[c]”
- name
Generic name of node, string, e.g. “trpL”, “pyruvate”
- synonyms
List of synonyms of node, list of strings e.g. [“anth”, “tryD”, tryp-4”]
- constants
Dictionary with constant names as keys and constants as values, dictionary, e.g. {“reversibility”: 0, “Km”: 1e-6}
- dynamics
Dictionary with dynamics data type as keys and list of time-series data as values, dictionary. For example:
{ "counts": [8151, 8525, ...], "concentration": [1.151e-7, 1.155e-7, ...], }
- dynamics_units
Dictionary with dynamics data type as keys and its units as values (must share same keys with dynamics), dictionary, e.g. {“counts”: “N”, “concentration”: “mol/L”}
- url
URL to EcoCyc page, string, eg. “https://ecocyc.org/ECOLI/ substring-search?type=NIL&object=EG11028&quickSearch=Quick+ Search”
- _format_dynamics_string(dynamics, datatype)[source]
Formats the string of dynamics data that is printed out to the dynamics file. If datatype is “int”, print all numbers as full decimal integers. If datatype is “float”, print all numbers in the general format with the precision set by DYNAMICS_PRECISION. If datatype is “time”, print all numbers in the floating point format with the precision set by TIME_PRECISION.
- read_attributes(node_class, node_type, node_id, name='', synonyms='', constants='', url='', location='')[source]
Sets the attribute variables of the node. Argument can be in the form of a single dictionary with names of each argument names as keys.
- read_attributes_from_tsv(tsv_line)[source]
Reads attributes (node type and node id) from a tab-delimited line in the node_list.tsv file.