Metabolic network
Class that represents a network.
A network is a collection of reconstructed metabolic pathways.
Constructor, please do not overwrite this method, use the init method instead Leave the constructor without parameters.
Adds a compound
Compound
Adds a product
Reaction
Adds a simulation
SimulationDict
Add technical information on the resource. Technical info are useful to set additional information on the resource.
TechnicalInfo
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
Union[str, NoneType]
Clone the resource to create a new instance with a new id. It copies the RFields.
ResourceType
Check that a compound exists in the network
Compound
bool
Returns a deep copy
Network
Create the input stoichiometric matrix of the network
We define by input stoichiometric matrix, the submatrix of the stoichimetric matrix involving the consumed compounds
bool
- True
bool
- False
DataFrame
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)
bool
- True
bool
- False
DataFrame
Create the output stoichiometric matrix of the network
We define by input stoichiometric matrix, the submatrix of the stoichimetric matrix involving the excreted compounds
bool
- True
bool
- False
DataFrame
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)
bool
- False
DataFrame
Create the full stoichiometric matrix of the network
DataFrame
Dumps the network
bool
- False
NetworkDict
Flatten the id of a compartment
Compartment
str
Flatten the id of a compound
Compound
str
Flatten the id of a reaction
Reaction
str
Get the biomass compounds if it exists
Compound
Get the biomass reaction if it exists
Reaction
Get a compound by its id.
str
Compound
Get all compound ids
List
Get compound stats as JSON
dict
Get compound stats as table
Table
Get a compound by its chebi id and compartment.
str
Union[str, NoneType]
- None
List
Get the compounds in a compartments
List
- None
Dict
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
str
Get the non-steady compounds
bool
- False
Dict
Get number of compounds
int
Get number of reactions
int
Get the reaction bounds [lb, ub]
DataFrame
Get a reaction by its ec number.
str
Reaction
Get a reaction by its id.
str
Reaction
Get a reaction by its rhea id.
str
Reaction
Get all reaction ids
List
Gather and return networks stats
dict
Get stats as JSON
dict
Get the steady compounds
bool
- False
Dict
Return the summary of the network
dict
Get the technical information of the resource
str
TechnicalInfo
Get the total absolute flux as table
Table
Return True if the network has sink reaction, False otherwise
bool
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
Network
bool
- False
Check that a reaction exists in the network
Reaction
bool
Remove a compound from the network
str
Remove a reaction from the network
str
Set simulations
Dict
Returns a CSV representation of the network
str
Returns a DataFrame representation of the network
DataFrame
Returns a string representation of the network
str
Returns a Table representation of the network
Table
Set a compound recon tag
Any
dict
Set a ec recon tag
Any
dict
Set a reaction recon tag
Any
dict
View as json
ConfigParams
JSONView
View as table
ConfigParams
TableView
View compound stats as table
ConfigParams
TableView
View gaps as table
ConfigParams
TableView