6.1.1.3.1.1. pytfa.io.base
¶
Input/Output tools to import or export pytfa models
6.1.1.3.1.1.1. Module Contents¶
6.1.1.3.1.1.1.1. Functions¶
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Convert at matlab cobra_model to a pyTFA cobra_model, with Thermodynamic values |
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Writes the Thermo Model to a Matlab-compatible structure |
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Dumps the thermodynamic information in a mat-compatible dictionary |
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Transforms reaction variable pairs from ('ACALD','ACALD_reverse_xxxxx') to |
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Dumps the the MILP formulation for TFA in a mat-compatible dictionary |
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Returns the generalized stoichiomatric matrix used for TFA |
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Load a thermodynamic database |
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Print the LP file corresponding to the cobra_model |
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Write the LP file of the specified cobra_model to the file indicated by path. |
- pytfa.import_matlab_model(path, variable_name=None)¶
Convert at matlab cobra_model to a pyTFA cobra_model, with Thermodynamic values
- Parameters
variable_name –
path (string) – The path of the file to import
- Returns
The converted cobra_model
- Return type
cobra.thermo.model.Model
- pytfa.recover_compartments(model, compartments_list)¶
- pytfa.write_matlab_model(tmodel, path, varname='tmodel')¶
Writes the Thermo Model to a Matlab-compatible structure
- Parameters
varname –
tmodel –
path –
- Returns
None
- pytfa.create_thermo_dict(tmodel)¶
Dumps the thermodynamic information in a mat-compatible dictionary (similar to the output of cobra.io.mat.create_mat_dict)
- Parameters
tmodel – pytfa.thermo.tmodel.ThermoModel
- Returns
dict object
- pytfa.varnames2matlab(name, tmodel)¶
Transforms reaction variable pairs from (‘ACALD’,’ACALD_reverse_xxxxx’) to (‘F_ACALD’,’B_ACALD’) if it is a reaction, else leaves is as is
- Returns
- pytfa.create_problem_dict(tmodel)¶
Dumps the the MILP formulation for TFA in a mat-compatible dictionary (similar to the output of cobra.io.mat.create_mat_dict)
- Parameters
tmodel – pytfa.thermo.tmodel.ThermoModel
:ret
- pytfa.create_generalized_matrix(tmodel, array_type='dense')¶
Returns the generalized stoichiomatric matrix used for TFA
- Parameters
array_type –
tmodel – pytfa.ThermoModel
- Returns
matrix.
- pytfa.load_thermoDB(path)¶
Load a thermodynamic database
- Parameters
path (string) – The path of the file to load
- Returns
The thermodynamic database
- Return type
- pytfa.printLP(model)¶
Print the LP file corresponding to the cobra_model
- Parameters
model (cobra.thermo.model.Model) – The cobra_model to output the LP file for
- Returns
The content of the LP file
- Return type
Usually, you pass the result of this function to
file.write()
to write it on disk. If you prefer, you can usepytfa.io.writeLP()
to write the result directly to a file.
- pytfa.writeLP(model, path=None)¶
Write the LP file of the specified cobra_model to the file indicated by path.
- Parameters
model (cobra.thermo.model.Model) – The COBRApy cobra_model to write the LP file for
path (string) – Optional The path of the file to be written. If not specified, the name of the COBRApy cobra_model will be used.