NutMEG.culture.saved_organisms package¶
Submodules¶
NutMEG.culture.saved_organisms.TypicalOptimalMethanogen module¶
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class
NutMEG.culture.saved_organisms.TypicalOptimalMethanogen.TypicalOptimalMethanogen(R, orgtype='horde', paramchange={}, dbpath='/Users/pete/github2/NutMEG/NutMEG/util/../../NutMEG_db', workoutID=False, fromdata=False, **kwargs)¶ Bases:
NutMEG.culture.horde.horde.hordeClass for the typical optimal methanogen [TOM] as defined in Higgins & Cockell 2020. The TOM mimicks a methanogen’s behavior in optimal conditions for a given temperature T.
Currently the TOM can only be initialised as a horde. kwargs can be any initialisation parameter for a horde object.
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CH4Rate_from_GrowthRate(growthrate, CH4conc=1e-08)¶ Estimate the rate of CH4 production using the growth rate. ref Powell 1983.
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avg_org_params(locale, paramchange={}, fromdata=False)¶ Get the ‘average’ methanogen parameters from the methanogens csv. Built from methods and application code in Higgins and Cockell 2020.
Commented out code is for generating TOM data, which should be saved in NutMEG’s data directory so isn’t needed. Will leave here for future use if needed.
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kT1P1_to_kT2P2(kT1P1, T1, P1, T2, P2, S=0, headspace=0.2, 0.8)¶ Convert between rate constants at different temperatures and pressures. Uses dissolved gas conc method in Cockell et al. 2021 Venus paper.
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setup_methanogenesis(R, k_RTP=1.0)¶ Return a methanogenesis reaction object in reactor R.
Optional argument k_RTP is used to set the rate constant. For most TOMs this can be left to the default as it is updated seperately in the initialisation.
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