`rbatools.protein_block` module

Classes

class ProteinBlock (ancestors: InformationBlock)

Class holding information on the proteins in the model.

Elements : dict: Each model-protein is represented by a key. The values, holding information on each protein, are dicts with predefined keys: 'ID' : protein ID in model (type str). May be compartment_isoform. 'ProtoID' : location independent protein ID in model (type str). Equals ID without compartment-specific ending. 'ExternalIDs' : identifiers of this protein in other namespaces (Locus-tag, Gene-symbol, …) (type dict) 'Function' : associated function, according to Uniprot (type str) 'Name' : name, according to Uniprot (type list) 'associatedReactions' : Reactions, this protein is a subunit of (type list) 'associatedEnzymes' : Enzymes, this protein is a subunit of (type list) 'Compartment' : Location of the protein (type str) 'AAcomposition' : Which amino-acids the protein is composed of and what is the stoichiometry(type dict) 'AAnumber' : Length of protein (type int) 'Weight' : Weight of protein (type float) 'ProcessRequirements' : Which processes the protein requires for synthesis and maintenance and how much (type dict) 'SupportsProcess' : Process-machineries, this protein is a subunit of (type list) 'AssociatedTarget' : Wheter protein represents a (translation) target.

def from_files(self, model, IDmap, Info, UniprotData='Not There'): Derive reaction-info from RBA-model.

Input

RBA-model Dataframe, holding uniprot-file information. Dataframe, holding ID-map information.

Returns

Dictionary with protein-info.
def overview(self): Derive statistics on proteins.

Returns

Dictionary with general numbers on proteins.
def return_protein_iso_form_map(self)