rbatools.rba_model_structure API documentation

rbatools.rba_model_structure module

Classes

class ModelStructureRBA

Class holding information on model-structure.

Attributes

GeneralInfo : DescriptionBlock
Model description
MetaboliteInfo : MetaboliteBlock
Metabolite information
ModuleInfo : ModuleBlock
Module information
ProcessInfo : ProcessBlock
Process information
ReactionInfo : ReactionBlock
Reaction information
EnzymeInfo : EnzymeBlock
Enzyme information
ProteinInfo : ProteinBlock
Protein information
MacromoleculeInfo : MacromoleculeBlock
Macromolecule (other than protein) information
CompartmentInfo : CompartmentBlock
Compartment information
MetaboliteConstraintsInfo : MetaboliteConstraintBlock
Metabolite-constraint information
DensityConstraintsInfo : DensityConstraintBlock
Density-constraint information
ProcessConstraintsInfo : ProcessConstraintBlock
Process-constraint information
EnzymeConstraintsInfo : EnzymeConstraintBlock
Enzyme-constraint information
ModelStatistics : StatisticsBlock
Statistics on Model
TargetInfo : TargetBlock
Target information
ProteinMatrix : numpy.array
Matrix mapping proteins to consumers (enzymes and process-machineries)
MediumDependencies : dict
Dictionary with boundary metabolites as keys and a list of constraint_IDs, which are affected by its concentration, as values.
MuDependencies : list
List of constraint_IDs, which are affected by the growth-rate

Methods

def export_json(self, path)

Saves model-structure object in JSON-format in specified directory, under the name ModelStructure.json.

Parameters

path : str
Directory, where to save JSON-file
def export_sbtab(self, add_links=False, filename='')

Saves model-structure object in SBtab-format under the specified name (filename).

Parameters

filename : str
Name, under which to save SBtab-file
add_links : str
Wheter to implement entry-format, which allows links between table-elements.
def from_files(self, xml_dir)

Generates model-structure object from model-files and provided auxilliary information.

Parameters

xml_dir : str
Directory, where RBA-model is located
def from_json(self, inputString)

Generates model-structure object from model-structure in JSON-format.

Parameters

inputString : json-str
JSON-string to be parsed in to ModelStructure-object.