rbatools.info_matrix module

Classes

class InfoMatrix

Attributes

Reaction_Reaction : pandas.DataFrame

Mapping of model-reactions to unique BiGG IDs (compensation for reaction-duplication for Isozymes). rows: unique BiGG-reactions ; cols: model-reactions

Protein_Enzyme : pandas.DataFrame

Conversion of Enzyme levels to levels of proteins, constituting them. (Gives Proteome of Metabolic Proteins, needs to be added to Process_Protein to obtain full proteome) rows: proteins ; cols: model-enzymes

ProteinWeight : pandas.DataFrame

Molecular weight and number of amino-acids for each protein rows: proteins ; cols: AAnum and weight

Protein_ProcessMachinery : pandas.DataFrame

Conversion of Process levels to levels of proteins, constituting their machineries. (Gives Proteome of Process Proteins, needs to be added to Enzyme_Protein to obtain full proteome) rows: proteins ; cols: model-processes

Process_Protein : pandas.DataFrame

Indication on how much each protein requires of each process rows: processes ; cols: protein

Compartment_Protein : pandas.DataFrame

Logical matrix on which protein is located in which compartment rows: compartments ; cols: proteins

S : pandas.DataFrame

Model stoichiometry-matrix rows: metabolites ; cols: reactions

Methods

def __init__(self, struct)

Initialize self. See help(type(self)) for accurate signature.