Network

Constructor, please do not overwrite this method, use the init method instead Leave the constructor without parameters.

Adds a compound

Adds a product

Adds a simulation

Add a technical information to the resource

You can redefine this method to define custom logic to check this resource. If there is a problem with the resource, return a string that define the error, otherwise return None This method is called on output resources of a task. If there is an error returned, the task will be set to error and next proceses will not be run. It is also call when uploading a resource (usually for files or folder), if there is an error returned, the resource will not be uploaded

Clone the resource to create a new instance with a new id It copies the RFields

Check that a compound exists in the network

Returns a deep copy

Create the input stoichiometric matrix of the network

We define by input stoichiometric matrix, the submatrix of the stoichimetric matrix involving the consumed compounds

Create the non-steady stoichiometric matrix of the network

We define by non-steady stoichiometric matrix, the submatrix of the stoichimetric matrix involving the non-steady compounds (e.g. extra-cellular, biomass compounds)

Create the output stoichiometric matrix of the network

We define by input stoichiometric matrix, the submatrix of the stoichimetric matrix involving the excreted compounds

Create the steady stoichiometric matrix of the network

We define by steady stoichiometric matrix, the submatrix of the stoichimetric matrix involving the steady compounds (e.g. intra-cellular compounds)

Create the full stoichiometric matrix of the network

Dumps the network

Flatten the id of a compartment

Flatten the id of a compound

Flatten the id of a reaction

Get the biomass compounds if it exists

Get the biomass reaction if it exists

Get a compound by its id.

Get all compound ids

Get compound stats as JSON

Get compound stats as table

Get a compound by its chebi id and compartment.

Get the compounds in a compartments

You can redefine this method to set a name of the resource. When saving the resource the name will be saved automatically This can be useful to distinguish this resource from another one or to search for the resource

Get the non-steady compounds

Get number of compounds

Get number of reactions

Get the reaction bounds [lb, ub]

Get a reaction by its ec number.

Get a reaction by its id.

Get a reaction by its rhea id.

Get all reaction ids

Get the reactions related to a compound with having a given CheBI ID

Gather and return networks stats

Get stats as JSON

Get the steady compounds

Return the summary of the network

Get the technical information of the resource

Get the total absolute flux as table

Return True if the network has sink reaction, False otherwise

This can be overwritten to perform custom initialization of the resource. This method is called just after the init (constructor) of the resource. The default values of RFields are set before this method is called.

Merge with another network

Check that a reaction exists in the network

Remove a compound from the network

Remove a reaction from the network

Set simulations

Returns a CSV representation of the network

Returns a DataFrame representation of the network

Returns a string representation of the network

Returns a Table representation of the network

Set a compound recon tag

Set a ec recon tag

Set a reaction recon tag

View as json

View as table

View compound stats as table

View gaps as table