wholecell.utils.enzymeKinetics

EnzymeKinetics

Takes in enzyme kinetics data on initialization, and returns dicts of rate estimates when passed metabolite and enzyme concentrations at runtime.

class wholecell.utils.enzymeKinetics.EnzymeKinetics(reactionRateInfo, kcatsOnly=False, useCustoms=True, moreThanKcat=False)

Bases: object

Returns rate estimates from kinetic equation information stored in reactionRateInfo.

allConstraintsDict(metaboliteConcentrationsDict, enzymeConcentrationsDict)

allReactionsDict(metaboliteConcentrationsDict, enzymeConcentrationsDict)

Create a dict of dicts from reactionID to constraintIDs for that reaction, to rates for each constraintID.

checkKnownSubstratesAndEnzymes(metaboliteSMatrixNamesNoCompartment, metaboliteNamesWithConcentrations, enzymeNames, removeUnknowns=False)

ratesView(reactionIDs, reactionsToConstraintsDict, metaboliteConcentrationsDict, enzymeConcentrationsDict, raiseIfNotFound=False)

Returns an array of rates with units.

Order taken from reactionIDs, rates to estimate come from reactionsToConstraintsDict. When a rate is not found, raises exception if raiseIfNotFound, else returns default rate. A reaction must be in reactionsToConstraintsDict, or it will get the default value.

ratesViewConstraints(constraintIDs, metaboliteConcentrationsDict, enzymeConcentrationsDict, raiseIfNotFound=False)

Returns an array of rates with units, in the same order as the constraintIDs iterable.

ratesViewHighest(reactionIDs, metaboliteConcentrationsDict, enzymeConcentrationsDict, raiseIfNotFound=False)

Returns an array of rates with units, in the same order as the reactionIDs, chosing the minimum estimate when a reactionID has multiple constraintIDs.

ratesViewLowest(reactionIDs, metaboliteConcentrationsDict, enzymeConcentrationsDict, raiseIfNotFound=False)

Returns an array of rates with units, in the same order as the reactionIDs, chosing the minimum estimate when a reactionID has multiple constraintIDs.

ratesViewReactions(reactionIDs, metaboliteConcentrationsDict, enzymeConcentrationsDict, sortFunction, raiseIfNotFound=False)

Returns an array of rates with units, in the same order as the reactionIDs. Uses sortFunction to decide which constraint to use if a reaction has multiple choices.

reactionCustom(reactionInfo, metaboliteConcentrationsDict, enzymeConcentrationsDict)

reactionRate(reactionInfo, metaboliteConcentrationsDict, enzymeConcentrationsDict)

reactionStandard(reactionInfo, metaboliteConcentrationsDict, enzymeConcentrationsDict)

exception wholecell.utils.enzymeKinetics.enzymeKineticsError

Bases: Exception