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)

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

get_dst_id()

Return ID of destination node.

get_process()

Return process associated with the edge.

get_src_id()

Return ID of source node.

read_attributes(src_id, dst_id, stoichiometry='')

Sets the remaining attribute variables of the node. Argument can be in the form of a single dictionary with names of each argument names as keys.

Parameters:

• src_id (str)

• dst_id (str)

• stoichiometry (str | int | None)

write_edgelist(edgelist_file)

Writes a single row specifying the given edge to the edgelist file.

class ecoli.analysis.causality_network.network_components.Node

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)

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.

dynamics_dict()

get_node_id()

Return ID of node.

read_attributes(node_class, node_type, node_id, name='', synonyms='', constants='', url='', location='')

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)

Reads attributes (node type and node id) from a tab-delimited line in the node_list.tsv file.

read_dynamics(dynamics, dynamics_units)

Sets the dynamics variable of the node.

to_dict()

write_dynamics(dynamics_file)

Writes a single row of dynamics data for each dynamics variable associated with the node.

write_nodelist(nodelist_file)

Writes a single row specifying the given node to the nodelist file.