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EnzymeSectors

Sector Objects​

class Sector(Object)

__copy__​

def __copy__() -> "Sector"

Copy the Sector.

Returns:

  • Sector - A new Sector that is a copy of the original Sector.

__deepcopy__​

def __deepcopy__(memo: dict) -> "Sector"

Copy the Sector with memo.

Arguments:

  • memo dict - Automatically passed parameter.

Returns:

  • Sector - A new Sector that is a copy of the original Sector with memo.

EnzymeSector Objects​

class EnzymeSector(Sector)

DEFAULT_MOL_MASS​

mean enzymes mass E.coli [g/mol]

ActiveEnzymeSector Objects​

class ActiveEnzymeSector(Sector)

DEFAULT_MOL_MASS​

mean enzymes mass E.coli [g/mol]

__init__​

def __init__(rxn2protein: dict,
             protein2gene: dict = {},
             configuration: Config = Config)

summary

Arguments:

  • rxn2protein dict - A dictionary with reaction ID, enzymes_dict key, value pairs for each reaction in the active_enzyme sector. The enzymes_dict contains the enzyme identifiers of the enzymes related to the specific reaction as keys, and a dict with information about the enzyme as values. The information included in this dict includes the turnover number for the forward and backward reaction (1/s), molar mass of the enzyme (mol/g), gene identifiers related to the enzyme, and with which other enzymes it forms a complex.
  • protein2gene - dict enzyme_id, gene_list key, value pairs for each enzyme.The gene_list value is a list of lists which indicates 'and' or 'or' relationships between the genes which code for the enzyme(complex).

Example:

For the Parameter rxn2protein a dictionary may look like this:
{
    'R1':
        {E1:
                    {'f': forward kcat, 'b': backward kcat, 'molmass': molar mass, 'genes': [G1, G2],
                    'protein_reaction_association': [[E1, E2]]
                    },
                E2:
                    {'f': forward kcat, 'b': backward kcat, 'molmass': molar mass, 'genes': [G3, G4],
                     'protein_reaction_association': [[E1, E2]]
        }
}

For the Parameter protein2gene a dictionary may look like this:
{E1:
        [[gene1], [gene2, gene3]],
E2:
        [[gene4]]
}
where the gene-protein-reaction associations are the following:
E1: gene1 or (gene2 and gene3)
E2: gene4

Arguments:

rxn2protein : nested dict reaction id, enzymes_dict key, value pairs for each reaction in the active_enzyme sector. The enzymes_dict contains the enzyme identifiers of the enzymes which are related to the specific reaction as keys and a dict with information about the enzyme as values. The information included in this dict is: turnover number for forward and backward reaction [1/s], molar mass of the enzyme [mol/g], gene identifiers related to the enzyme, with which other enzymes it forms a complex.

  • protein2gene - dict enzyme_id, gene_list key, value pairs for each enzyme.The gene_list value is a list of lists which indicates 'and' or 'or' relationships between the genes which code for the enzyme(complex).

  • configuration - Config object, optional Information about general configuration of the model including identifier conventions. Default as defined in the PAModelpy.configuration script for the E.coli iML1515 model.

check_kcat_values​

def check_kcat_values(model, reaction, enzyme_dict)

Function to check if the kcat values provided for an enzyme are consistent with the direction of the reaction

Arguments:

  • model cobra.Model or PAModel - Model to which the kcat values should be added.
  • reaction cobra.Reaction - Reaction that is catalyzed with the enzyme related to the kcats.
  • enzyme_dict dict - A dictionary with the turnover values for the forward and/or backward reaction for different enzymes [/s].

Example:

Example dictionary for the enzyme_dict parameter

{'E1': {'f': forward kcat, 'b': backward kcat}}

TransEnzymeSector Objects​

class TransEnzymeSector(EnzymeSector)

DEFAULT_MOL_MASS​

default E. coli ribosome molar mass [g/mol]

UnusedEnzymeSector Objects​

class UnusedEnzymeSector(EnzymeSector)

DEFAULT_MOL_MASS​

mean enzymes mass E.coli [g/mol]

CustomSector Objects​

class CustomSector(EnzymeSector)

DEFAULT_ENZYME_MOL_MASS​

mean enzymes mass E.coli [g/mol]