Index

A

a_e() (NutMEG.culture.base_organism.synthesis.cell_synthesis.cell_synthesis static method) AAreader() (in module NutMEG.culture.base_organism.synthesis.importers) AAsynthCost() (NutMEG.culture.base_organism.synthesis.cell_synthesis.cell_synthesis static method) activity (NutMEG.reaction.reagent.reagent attribute), [1] activity_finder() (NutMEG.reaction.reaction.reaction method) add_AAP_to_db() (NutMEG.culture.base_organism.synthesis.cell_synthesis.cell_synthesis static method) add_map_plot() (NutMEG.plotter.habitabilitymap.habitabilitymap method) add_mechanism() (NutMEG.culture.base_organism.maintainer.maintainer method) add_organism() (NutMEG.culture.colony.colony.colony method) add_reaction() (NutMEG.reactor.reactor.reactor method) add_to_Composition() (NutMEG.reactor.reactor_dbhelper.rdb_helper method)

add_to_Reactions() (NutMEG.reactor.reactor_dbhelper.rdb_helper method) addcolumn() (NutMEG.ecosystem_dbhelper.db_helper method) addlinearplot() (NutMEG.plotter.growthparams.growthparams method) age (NutMEG.culture.base_organism.base_organism.base_organism attribute) all() (NutMEG.culture.culture.culture method) all_activities (NutMEG.reaction.reaction.reaction attribute) appendvals() (NutMEG.culture.colony.colony_output.colony_output method) (NutMEG.culture.culture_output.culture_output method) (NutMEG.culture.horde.horde_output.horde_output method) ATP_production (NutMEG.culture.base_organism.respirator.respirator attribute) avg_org_params() (NutMEG.culture.saved_organisms.TypicalOptimalMethanogen.TypicalOptimalMethanogen static method)

B

backup_r (NutMEG.ecosystem.ecosystem attribute) base (NutMEG.culture.colony.colony.colony attribute) base_life_span (NutMEG.culture.base_organism.base_organism.base_organism attribute) base_organism (class in NutMEG.culture.base_organism.base_organism) base_volume (NutMEG.culture.base_organism.base_organism.base_organism attribute) biomass_cell_ratio (NutMEG.culture.horde.horde.horde attribute) BioMolecule (class in NutMEG.culture.base_organism.synthesis.BioMolecule)

bo_from_db() (NutMEG.culture.base_organism.base_organism.base_organism class method) bodb_helper (class in NutMEG.culture.base_organism.base_organism_dbhelper) bool_rate_constants() (NutMEG.reaction.reaction.reaction method) build_ATP_reaction() (NutMEG.culture.base_organism.respirator.respirator method) buildbaseparams() (NutMEG.culture.colony.colony_output.colony_output method) (NutMEG.culture.culture_output.culture_output method) (NutMEG.culture.horde.horde_output.horde_output method) buildresultsdict() (NutMEG.ecosystem_dbhelper.db_helper method)

C

c (NutMEG.ecosystem.ecosystem attribute), [1] calc_mol_CH4() (NutMEG.reactor.saved_systems.Enceladus.Enceladus method) calc_mol_H2() (NutMEG.reactor.saved_systems.Enceladus.Enceladus method) calculate_rate() (NutMEG.reaction.reaction.reaction method) cell_synthesis (class in NutMEG.culture.base_organism.synthesis.cell_synthesis) CH4Rate_from_GrowthRate() (NutMEG.culture.saved_organisms.TypicalOptimalMethanogen.TypicalOptimalMethanogen static method) change_P() (NutMEG.reactor.reactor.reactor method) change_T() (NutMEG.reactor.reactor.reactor method) change_vol() (NutMEG.reactor.reactor.reactor method) charge (NutMEG.reaction.reagent.reagent attribute), [1] check_nutrients() (NutMEG.culture.base_organism.CHNOPSexchanger.CHNOPSexchanger method) check_stopper() (NutMEG.ecosystem.ecosystem method) check_summary() (NutMEG.ecosystem_dbhelper.db_helper method) CHNOPS (NutMEG.culture.base_organism.base_organism.base_organism attribute) CHNOPSexchanger (class in NutMEG.culture.base_organism.CHNOPSexchanger) CO2origin (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) collection (NutMEG.culture.colony.colony.colony attribute) colonies (NutMEG.culture.culture.culture attribute) colony (class in NutMEG.culture.colony.colony) colony_output (class in NutMEG.culture.colony.colony_output)

colorpicker() (NutMEG.plotter.growthparams.growthparams method) composition (NutMEG.reactor.reactor.reactor attribute) Composition_db_sqlparams() (NutMEG.reactor.reactor_dbhelper.rdb_helper method) composition_inputs (NutMEG.reactor.reactor.reactor attribute) compute_P_growth() (NutMEG.culture.base_organism.maintainer.maintainer method) conc (NutMEG.reaction.reagent.reagent attribute), [1] conc_mol_per_cell (NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule attribute) conc_mol_per_l (NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule attribute) copies_moles() (in module NutMEG.culture.base_organism.synthesis.importers) copies_per_cell (NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule attribute) counter (NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule attribute) Cp_env (NutMEG.reaction.reagent.reagent attribute) Cp_RTP (NutMEG.reaction.reagent.reagent attribute) Cp_T_poly (NutMEG.reaction.reagent.reagent attribute) create_major_tables() (NutMEG.ecosystem_dbhelper.db_helper static method) createtable() (NutMEG.culture.base_organism.base_organism_dbhelper.bodb_helper method) (NutMEG.ecosystem_dbhelper.db_helper method) (NutMEG.reactor.reactor_dbhelper.rdb_helper method) culture (class in NutMEG.culture.culture) culture_output (class in NutMEG.culture.culture_output)

D

d2E_by_dT2 (NutMEG.reaction.special.solutions.redox_half attribute) db_helper (class in NutMEG.ecosystem_dbhelper) db_select() (NutMEG.reaction.thermo.reagent_thermo.reagent_thermo method) dbdict (NutMEG.culture.base_organism.base_organism_dbhelper.bodb_helper attribute) (NutMEG.reactor.reactor_dbhelper.rdb_helper attribute) dbh (NutMEG.culture.base_organism.base_organism.base_organism attribute) (NutMEG.ecosystem.ecosystem attribute) dbpath (NutMEG.culture.base_organism.base_organism_dbhelper.bodb_helper attribute) (NutMEG.ecosystem_dbhelper.db_helper attribute) (NutMEG.reactor.reactor_dbhelper.rdb_helper attribute)

dE_by_dT (NutMEG.reaction.special.solutions.redox_half attribute) deathnum (NutMEG.culture.horde.horde.horde attribute) denormalise() (NutMEG.plotter.plotter_setup.nutfig static method) depth (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) dict_to_db() (NutMEG.ecosystem_dbhelper.db_helper method) dry_mass (NutMEG.culture.base_organism.base_organism.base_organism attribute)

E

e (NutMEG.ecosystem_dbhelper.db_helper attribute) E (NutMEG.reaction.special.solutions.redox attribute) E_store (NutMEG.culture.base_organism.base_organism.base_organism attribute) E_synth (NutMEG.culture.base_organism.base_organism.base_organism attribute) ecosystem (class in NutMEG.ecosystem) electrolyte (class in NutMEG.reaction.special.solutions) Enceladus (class in NutMEG.reactor.saved_systems.Enceladus) env (NutMEG.reaction.reaction.reaction attribute) (NutMEG.reaction.reagent.reagent attribute) (NutMEG.reaction.special.solutions.redox attribute) (NutMEG.reactor.reactor.reactor attribute) (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) environment (class in NutMEG.environment.environment)

epsilon() (in module NutMEG.reaction.special.plotter) equation (NutMEG.reaction.reaction.reaction attribute) equationbuilder() (NutMEG.reaction.reaction.reaction method) equilibrium (NutMEG.reaction.reaction.reaction attribute) exparam() (NutMEG.applications.NutMEmatcher.NutMEmatcher method) extract_AAP_from_db() (NutMEG.culture.base_organism.synthesis.cell_synthesis.cell_synthesis static method) extract_from_Composition() (NutMEG.reactor.reactor_dbhelper.rdb_helper method) extract_from_Reactions() (NutMEG.reactor.reactor_dbhelper.rdb_helper method) extract_param_db() (NutMEG.culture.base_organism.base_organism_dbhelper.bodb_helper static method) extract_param_db_OrgLoc() (NutMEG.ecosystem_dbhelper.db_helper static method) (NutMEG.plotter.plotter_setup.nutfig static method) extract_param_db_Sim() (NutMEG.ecosystem_dbhelper.db_helper static method) (NutMEG.plotter.plotter_setup.nutfig static method)

F

F_T (NutMEG.culture.base_organism.respirator.respirator attribute) Fcons (NutMEG.reaction.special.solutions.redox attribute) (NutMEG.reaction.special.solutions.redox_half attribute) fig (NutMEG.plotter.plotter_setup.nutfig attribute) find_nutrients() (NutMEG.culture.base_organism.CHNOPSexchanger.CHNOPSexchanger method) findOrgIDsLocID() (NutMEG.ecosystem_dbhelper.db_helper static method) findSimID() (NutMEG.ecosystem_dbhelper.db_helper static method) forward (NutMEG.reaction.special.solutions.redox attribute)

frac_dict (NutMEG.culture.base_organism.maintainer.maintainer attribute) frequency (NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule attribute) frequency_factor (NutMEG.reaction.reaction.reaction attribute) from_db() (NutMEG.culture.base_organism.base_organism_dbhelper.bodb_helper static method) (NutMEG.reactor.reactor_dbhelper.rdb_helper static method) fromOrgLoc() (NutMEG.applications.theory_estimates.theory_estimates class method) fromSim() (NutMEG.applications.theory_estimates.theory_estimates class method) full_output() (NutMEG.culture.culture.culture method) full_output_datatypes() (NutMEG.culture.culture.culture method)

G

G_A (NutMEG.culture.base_organism.respirator.respirator attribute) G_C (NutMEG.culture.base_organism.respirator.respirator attribute) G_P (NutMEG.culture.base_organism.respirator.respirator attribute) gamma (NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule attribute) (NutMEG.reaction.reagent.reagent attribute), [1] get_a_salt() (NutMEG.reaction.special.solutions.electrolyte method) get_average_maintenance_fraction() (NutMEG.culture.colony.colony.colony method) get_CO2_from_HTHeating() (NutMEG.reactor.saved_systems.Enceladus.Enceladus static method) get_CO2_from_pH() (NutMEG.reactor.saved_systems.Enceladus.Enceladus method) get_comp_activities() (NutMEG.reactor.reactor_dbhelper.rdb_helper method) get_db_sqlparams() (NutMEG.culture.base_organism.base_organism_dbhelper.bodb_helper method) (NutMEG.reactor.reactor_dbhelper.rdb_helper method) get_default_nutrients() (NutMEG.culture.base_organism.CHNOPSexchanger.CHNOPSexchanger method) get_equation() (NutMEG.reaction.reaction.reaction method) (NutMEG.reaction.special.solutions.redox method) get_ESynth() (NutMEG.culture.base_organism.base_organism.base_organism method) get_ESynth_density() (NutMEG.culture.base_organism.synthesis.cell_synthesis.cell_synthesis static method) get_exp_T() (NutMEG.reactor.saved_systems.Enceladus.Enceladus method) get_growth_rates() (NutMEG.culture.culture.culture method) get_ionic_strength_c() (NutMEG.reaction.special.solutions.electrolyte method) get_ionic_strength_m() (NutMEG.reaction.special.solutions.electrolyte method) get_maintenance_fractions() (NutMEG.culture.culture.culture method) get_mass() (NutMEG.culture.colony.colony.colony method) (NutMEG.culture.horde.horde.horde method) get_metabolic_rates() (NutMEG.culture.culture.culture method) get_netdictstr() (NutMEG.culture.base_organism.maintainer.maintainer method) get_P_pH() (NutMEG.culture.base_organism.maintainer.maintainer method) get_P_store() (NutMEG.culture.base_organism.maintainer.maintainer method) get_P_T() (NutMEG.culture.base_organism.maintainer.maintainer method) get_permittivity() (NutMEG.reaction.special.solutions.electrolyte method) get_phase_str() (NutMEG.reaction.reagent.reagent static method) get_population() (NutMEG.culture.colony.colony.colony method) (NutMEG.culture.culture.culture method) (NutMEG.culture.horde.horde.horde method)

get_rate() (NutMEG.culture.base_organism.respirator.respirator method) get_RTP_params() (NutMEG.reaction.thermo.reagent_thermo.reagent_thermo method) get_stdG_lnK() (NutMEG.reaction.thermo.reaction_thermo.reaction_thermo method) get_supplied_power() (NutMEG.culture.base_organism.base_organism.base_organism method) get_table_as_dataframe() (NutMEG.ecosystem_dbhelper.db_helper method) get_thermo_params() (NutMEG.reaction.thermo.reagent_thermo.reagent_thermo method) get_tigerstripe_CO2() (NutMEG.reactor.saved_systems.Enceladus.Enceladus method) get_total_mass() (NutMEG.culture.culture.culture method) get_total_volume() (NutMEG.culture.culture.culture method) get_uptake() (NutMEG.culture.base_organism.CHNOPSexchanger.CHNOPSexchanger method) get_volume() (NutMEG.culture.colony.colony.colony method) (NutMEG.culture.horde.horde.horde method) getCHNOPSut() (NutMEG.culture.colony.colony.colony method) getconcs() (NutMEG.reactor.reactor.reactor method) getEnergyPump() (in module NutMEG.culture.base_organism.adaptations.pHadaptations) getfluxH() (in module NutMEG.culture.base_organism.adaptations.pHadaptations) getfluxOH() (in module NutMEG.culture.base_organism.adaptations.pHadaptations) getFluxPerm_MP() (NutMEG.culture.base_organism.adaptations.pHadaptations.pHadaptations method) getgasconc() (NutMEG.reactor.saved_systems.VenusDrop.VenusDrop static method) getHsuT() (NutMEG.reactor.saved_systems.Enceladus.Enceladus static method) getLeverME() (NutMEG.culture.base_organism.adaptations.Tadaptations.Tadaptations method) getmin_timestep() (NutMEG.culture.culture.culture method) getOrgdetails() (NutMEG.ecosystem_dbhelper.db_helper method) getreplistAA() (NutMEG.culture.base_organism.synthesis.cell_synthesis.cell_synthesis static method) GetThermoParams() (NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule method) (NutMEG.reaction.reagent.reagent method) getTijuisME() (NutMEG.culture.base_organism.adaptations.Tadaptations.Tadaptations method) grow_with_nutrients() (NutMEG.culture.base_organism.CHNOPSexchanger.CHNOPSexchanger method) growthparams (class in NutMEG.plotter.growthparams) guess_name_from_ID() (NutMEG.ecosystem_dbhelper.db_helper static method)

H

H2 (NutMEG.reaction.special.solutions.redox_half attribute) H2O (NutMEG.reaction.special.solutions.electrolyte attribute) (NutMEG.reaction.special.solutions.redox attribute) H2Oact (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) habitabilitymap (class in NutMEG.plotter.habitabilitymap) higherorlower() (NutMEG.applications.NutMEmatcher.NutMEmatcher method) horde (class in NutMEG.culture.horde.horde)

horde_output (class in NutMEG.culture.horde.horde_output) hordes (NutMEG.culture.culture.culture attribute) host (NutMEG.culture.base_organism.base_organism_dbhelper.bodb_helper attribute) (NutMEG.culture.base_organism.CHNOPSexchanger.CHNOPSexchanger attribute) (NutMEG.culture.base_organism.maintainer.maintainer attribute) (NutMEG.culture.base_organism.respirator.respirator attribute) (NutMEG.reactor.reactor_dbhelper.rdb_helper attribute) hosthorde (NutMEG.culture.horde.horde_output.horde_output attribute)

I

import_params_db() (NutMEG.reaction.reagent.reagent method) import_RTP_params() (NutMEG.reaction.reagent.reagent method) inactive (NutMEG.culture.colony.colony.colony attribute) initial_conditions() (NutMEG.reactor.saved_systems.Enceladus.Enceladus method) (NutMEG.reactor.saved_systems.VenusDrop.VenusDrop method)

interpo_CO2_H2O() (NutMEG.reactor.saved_systems.Enceladus.Enceladus static method) isactive (NutMEG.culture.base_organism.base_organism.base_organism attribute) iterate_to_target() (NutMEG.applications.NutMEmatcher.NutMEmatcher method) iterateMF() (NutMEG.applications.NutMEmatcher.NutMEmatcher method)

K

kappa (NutMEG.reaction.special.solutions.electrolyte attribute)

kappa_cons (NutMEG.reaction.special.solutions.electrolyte attribute) kT1P1_to_kT2P2() (NutMEG.culture.saved_organisms.TypicalOptimalMethanogen.TypicalOptimalMethanogen static method)

L

limter (NutMEG.culture.base_organism.CHNOPSexchanger.CHNOPSexchanger attribute) linearplot() (NutMEG.plotter.growthparams.growthparams method) lite (NutMEG.culture.culture.culture attribute), [1]

lnK (NutMEG.reaction.reaction.reaction attribute) lnProteinReactionQuotient() (NutMEG.culture.base_organism.synthesis.cell_synthesis.cell_synthesis static method) loc (NutMEG.applications.theory_estimates.theory_estimates attribute) locale (NutMEG.culture.base_organism.base_organism.base_organism attribute)

M

maintainer (class in NutMEG.culture.base_organism.maintainer) maintenance (NutMEG.culture.base_organism.base_organism.base_organism attribute) mapcolorbarh() (NutMEG.plotter.habitabilitymap.habitabilitymap method) mapdata_orgloc() (NutMEG.plotter.habitabilitymap.habitabilitymap method) mass (NutMEG.culture.base_organism.base_organism.base_organism attribute) mass_activation_E (NutMEG.reaction.reaction.reaction attribute) mass_gibbs (NutMEG.reaction.reaction.reaction attribute) match() (NutMEG.applications.NutMEmatcher.NutMEmatcher method) max_metabolic_rate (NutMEG.culture.base_organism.base_organism.base_organism attribute) mean_gamma (NutMEG.reaction.special.solutions.electrolyte attribute) memb_pot (NutMEG.culture.base_organism.base_organism.base_organism attribute) metabolism (NutMEG.culture.base_organism.base_organism.base_organism attribute) mixingratios (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) module NutMEG NutMEG.applications NutMEG.applications.NutMEmatcher NutMEG.applications.theory_estimates NutMEG.culture NutMEG.culture.base_organism NutMEG.culture.base_organism.adaptations NutMEG.culture.base_organism.adaptations.pHadaptations NutMEG.culture.base_organism.adaptations.Tadaptations NutMEG.culture.base_organism.base_organism NutMEG.culture.base_organism.base_organism_dbhelper NutMEG.culture.base_organism.CHNOPSexchanger NutMEG.culture.base_organism.maintainer NutMEG.culture.base_organism.respirator NutMEG.culture.base_organism.synthesis NutMEG.culture.base_organism.synthesis.BioMolecule NutMEG.culture.base_organism.synthesis.cell_synthesis NutMEG.culture.base_organism.synthesis.importers NutMEG.culture.colony NutMEG.culture.colony.colony NutMEG.culture.colony.colony_output NutMEG.culture.culture NutMEG.culture.culture_output NutMEG.culture.horde NutMEG.culture.horde.horde NutMEG.culture.horde.horde_output NutMEG.culture.organism NutMEG.culture.organism.organism NutMEG.culture.saved_organisms NutMEG.culture.saved_organisms.TypicalOptimalMethanogen NutMEG.ecosystem NutMEG.ecosystem_dbhelper NutMEG.environment NutMEG.environment.environment NutMEG.plotter NutMEG.plotter.growthparams NutMEG.plotter.habitabilitymap NutMEG.plotter.plotter_setup NutMEG.reaction NutMEG.reaction.reaction NutMEG.reaction.reagent NutMEG.reaction.special NutMEG.reaction.special.plotter NutMEG.reaction.special.solutions NutMEG.reaction.special.Tdep NutMEG.reaction.thermo NutMEG.reaction.thermo.reaction_thermo NutMEG.reaction.thermo.reagent_thermo NutMEG.reactor NutMEG.reactor.reactor NutMEG.reactor.reactor_dbhelper NutMEG.reactor.saved_systems NutMEG.reactor.saved_systems.Enceladus NutMEG.reactor.saved_systems.VenusDrop

mol_CO2 (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) mol_CO2_oc (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) molal (NutMEG.reaction.reagent.reagent attribute), [1] molar_activation_E (NutMEG.reaction.reaction.reaction attribute) molar_gibbs (NutMEG.reaction.reaction.reaction attribute) Mr (NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule attribute)

N

n (NutMEG.reaction.special.solutions.redox attribute) (NutMEG.reaction.special.solutions.redox_half attribute) n_ATP (NutMEG.culture.base_organism.respirator.respirator attribute) n_HP (NutMEG.culture.base_organism.respirator.respirator attribute) n_HR (NutMEG.culture.base_organism.respirator.respirator attribute) n_P (NutMEG.culture.base_organism.respirator.respirator attribute) name (NutMEG.culture.base_organism.base_organism.base_organism attribute) (NutMEG.culture.base_organism.respirator.respirator attribute) (NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule attribute) (NutMEG.culture.colony.colony.colony attribute) (NutMEG.reaction.reagent.reagent attribute) (NutMEG.reactor.reactor.reactor attribute) net_dict (NutMEG.culture.base_organism.maintainer.maintainer attribute) net_pathway (NutMEG.culture.base_organism.respirator.respirator attribute) net_powers() (NutMEG.applications.NutMEmatcher.NutMEmatcher method) neutralsol (class in NutMEG.reaction.special.solutions) nominals (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) normalise() (NutMEG.plotter.plotter_setup.nutfig static method) num (NutMEG.culture.horde.horde.horde attribute) nutfig (class in NutMEG.plotter.plotter_setup) NutMEG module NutMEG.applications module NutMEG.applications.NutMEmatcher module NutMEG.applications.theory_estimates module NutMEG.culture module NutMEG.culture.base_organism module NutMEG.culture.base_organism.adaptations module NutMEG.culture.base_organism.adaptations.pHadaptations module NutMEG.culture.base_organism.adaptations.Tadaptations module NutMEG.culture.base_organism.base_organism module NutMEG.culture.base_organism.base_organism_dbhelper module NutMEG.culture.base_organism.CHNOPSexchanger module NutMEG.culture.base_organism.maintainer module NutMEG.culture.base_organism.respirator module NutMEG.culture.base_organism.synthesis module NutMEG.culture.base_organism.synthesis.BioMolecule module NutMEG.culture.base_organism.synthesis.cell_synthesis module NutMEG.culture.base_organism.synthesis.importers module NutMEG.culture.colony module NutMEG.culture.colony.colony module NutMEG.culture.colony.colony_output module NutMEG.culture.culture module NutMEG.culture.culture_output module

NutMEG.culture.horde module NutMEG.culture.horde.horde module NutMEG.culture.horde.horde_output module NutMEG.culture.organism module NutMEG.culture.organism.organism module NutMEG.culture.saved_organisms module NutMEG.culture.saved_organisms.TypicalOptimalMethanogen module NutMEG.ecosystem module NutMEG.ecosystem_dbhelper module NutMEG.environment module NutMEG.environment.environment module NutMEG.plotter module NutMEG.plotter.growthparams module NutMEG.plotter.habitabilitymap module NutMEG.plotter.plotter_setup module NutMEG.reaction module NutMEG.reaction.reaction module NutMEG.reaction.reagent module NutMEG.reaction.special module NutMEG.reaction.special.plotter module NutMEG.reaction.special.solutions module NutMEG.reaction.special.Tdep module NutMEG.reaction.thermo module NutMEG.reaction.thermo.reaction_thermo module NutMEG.reaction.thermo.reagent_thermo module NutMEG.reactor module NutMEG.reactor.reactor module NutMEG.reactor.reactor_dbhelper module NutMEG.reactor.saved_systems module NutMEG.reactor.saved_systems.Enceladus module NutMEG.reactor.saved_systems.VenusDrop module NutMEmatcher (class in NutMEG.applications.NutMEmatcher) nutrients (NutMEG.culture.base_organism.CHNOPSexchanger.CHNOPSexchanger attribute)

O

ocean_pH (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) oceanvals (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) org (NutMEG.applications.theory_estimates.theory_estimates attribute) organism (class in NutMEG.culture.organism.organism) OrgIDs (NutMEG.ecosystem_dbhelper.db_helper attribute)

OrgNames (NutMEG.ecosystem_dbhelper.db_helper attribute) OrgNums (NutMEG.ecosystem_dbhelper.db_helper attribute) output (NutMEG.culture.colony.colony.colony attribute) (NutMEG.culture.culture.culture attribute) output_step_data() (NutMEG.ecosystem.ecosystem method)

P

P (NutMEG.environment.environment.environment attribute) P_growth (NutMEG.culture.base_organism.base_organism.base_organism attribute) P_loss (NutMEG.culture.base_organism.maintainer.maintainer attribute) P_RTP (NutMEG.environment.environment.environment attribute) P_s (NutMEG.culture.base_organism.base_organism.base_organism attribute) params (NutMEG.culture.colony.colony_output.colony_output attribute) (NutMEG.culture.culture_output.culture_output attribute) (NutMEG.culture.horde.horde_output.horde_output attribute), [1] paramtypelst() (NutMEG.culture.colony.colony_output.colony_output method) (NutMEG.culture.culture_output.culture_output method) (NutMEG.culture.horde.horde_output.horde_output method) Pconc (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute), [1] perform_reaction() (NutMEG.reactor.reactor.reactor method) PermH (NutMEG.culture.base_organism.base_organism.base_organism attribute) PermOH (NutMEG.culture.base_organism.base_organism.base_organism attribute) pH (NutMEG.reactor.reactor.reactor attribute) (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute), [1] pH_interior (NutMEG.culture.base_organism.base_organism.base_organism attribute)

pHadaptations (class in NutMEG.culture.base_organism.adaptations.pHadaptations) phase (NutMEG.reaction.reagent.reagent attribute) phase_ss (NutMEG.reaction.reagent.reagent attribute) pHdef (NutMEG.culture.base_organism.maintainer.maintainer attribute) phi (NutMEG.reaction.special.solutions.neutralsol attribute) predict_growth() (NutMEG.ecosystem.ecosystem method) print_composition() (NutMEG.reactor.reactor.reactor method) print_major_tables() (NutMEG.ecosystem_dbhelper.db_helper static method) print_nutrients() (NutMEG.culture.base_organism.CHNOPSexchanger.CHNOPSexchanger method) print_reactions() (NutMEG.reactor.reactor.reactor method) print_table() (NutMEG.culture.base_organism.base_organism_dbhelper.bodb_helper method) (NutMEG.ecosystem_dbhelper.db_helper static method) (NutMEG.reactor.reactor_dbhelper.rdb_helper method) print_theory_estimates() (NutMEG.applications.NutMEmatcher.NutMEmatcher method) printcheck() (NutMEG.plotter.plotter_setup.nutfig static method) probrange (NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule attribute) products (NutMEG.reaction.reaction.reaction attribute) proteinfraction (NutMEG.culture.base_organism.base_organism.base_organism attribute) ProteinSynthCost() (NutMEG.culture.base_organism.synthesis.cell_synthesis.cell_synthesis static method)

Q

quotient (NutMEG.reaction.reaction.reaction attribute)

quotient_calculator() (NutMEG.reaction.reaction.reaction method)

R

r (NutMEG.ecosystem.ecosystem attribute), [1] r_from_db() (NutMEG.reactor.reactor.reactor class method) radius (NutMEG.reaction.reagent.reagent attribute) rate (NutMEG.culture.base_organism.respirator.respirator attribute) rate_constant_env (NutMEG.reaction.reaction.reaction attribute) rate_constant_RTP (NutMEG.reaction.reaction.reaction attribute) rdb_helper (class in NutMEG.reactor.reactor_dbhelper) react() (NutMEG.reaction.reaction.reaction method) (NutMEG.reaction.special.solutions.redox method) reactants (NutMEG.reaction.reaction.reaction attribute) ReactIDs (NutMEG.reactor.reactor.reactor attribute) reaction (class in NutMEG.reaction.reaction) reaction_db_sqlparams() (NutMEG.reactor.reactor_dbhelper.rdb_helper static method) reaction_thermo (class in NutMEG.reaction.thermo.reaction_thermo) reactionlist (NutMEG.reactor.reactor.reactor attribute) reactor (class in NutMEG.reactor.reactor) reagent (class in NutMEG.reaction.reagent)

reagent_thermo (class in NutMEG.reaction.thermo.reagent_thermo) reagents_name() (NutMEG.reaction.reaction.reaction method) redefine() (NutMEG.reaction.reagent.reagent method) redox (class in NutMEG.reaction.special.solutions) redox_half (class in NutMEG.reaction.special.solutions) refresh_output() (NutMEG.culture.culture.culture method) refreshparams() (NutMEG.culture.colony.colony_output.colony_output method) (NutMEG.culture.culture_output.culture_output method) (NutMEG.culture.horde.horde_output.horde_output method) removesimdata() (NutMEG.ecosystem_dbhelper.db_helper static method) reproduce() (NutMEG.culture.base_organism.base_organism.base_organism method) (NutMEG.culture.horde.horde.horde method) reset_from_db_dict() (NutMEG.culture.base_organism.base_organism.base_organism method) respirator (class in NutMEG.culture.base_organism.respirator) reverse (NutMEG.reaction.special.solutions.redox attribute) rlist_from_ReactIDs() (NutMEG.reactor.reactor.reactor method) rto_current_env() (NutMEG.reaction.reaction.reaction method) rto_reagents() (NutMEG.reaction.reaction.reaction method)

S

SAget() (in module NutMEG.culture.base_organism.base_organism) salts (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) select_timestep() (NutMEG.culture.colony.colony.colony method) (NutMEG.culture.horde.horde.horde method) set_activitycoefficient() (NutMEG.reaction.reagent.reagent method) set_concentration() (NutMEG.reaction.reagent.reagent method) set_from_netdictstr() (NutMEG.culture.base_organism.maintainer.maintainer method) set_molality() (NutMEG.reaction.reagent.reagent method) set_phase() (NutMEG.reaction.reagent.reagent method) set_products() (NutMEG.reaction.reaction.reaction method) set_reactants() (NutMEG.reaction.reaction.reaction method) setup_methanogenesis() (NutMEG.culture.saved_organisms.TypicalOptimalMethanogen.TypicalOptimalMethanogen method) setup_stoppingdict() (NutMEG.ecosystem.ecosystem method) SimID (NutMEG.ecosystem.ecosystem attribute) simulate_growth() (NutMEG.applications.NutMEmatcher.NutMEmatcher method) solubilityEQ() (NutMEG.reactor.saved_systems.VenusDrop.VenusDrop static method) solubilityEQparams() (NutMEG.reactor.saved_systems.VenusDrop.VenusDrop static method) solute_activity() (NutMEG.reaction.special.solutions.neutralsol method)

solvent_activity (NutMEG.reaction.special.solutions.neutralsol attribute) std_formation_enthalpy_env (NutMEG.reaction.reagent.reagent attribute) std_formation_enthalpy_RTP (NutMEG.reaction.reagent.reagent attribute) std_formation_entropy_env (NutMEG.reaction.reagent.reagent attribute) std_formation_entropy_RTP (NutMEG.reaction.reagent.reagent attribute) std_formation_gibbs (NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule attribute) std_formation_gibbs_env (NutMEG.reaction.reagent.reagent attribute) std_formation_gibbs_RTP (NutMEG.reaction.reagent.reagent attribute) std_formation_R (NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule attribute) std_molar_enthalpy (NutMEG.reaction.reaction.reaction attribute) std_molar_entropy (NutMEG.reaction.reaction.reaction attribute) std_molar_gibbs (NutMEG.reaction.reaction.reaction attribute) stdE (NutMEG.reaction.special.solutions.redox attribute) (NutMEG.reaction.special.solutions.redox_half attribute) stdE_RTP (NutMEG.reaction.special.solutions.redox attribute) (NutMEG.reaction.special.solutions.redox_half attribute) stoppingdict (NutMEG.ecosystem.ecosystem attribute) surfacearea (NutMEG.culture.base_organism.base_organism.base_organism attribute)

T

T (NutMEG.environment.environment.environment attribute) (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) T_RTP (NutMEG.environment.environment.environment attribute) Tadaptations (class in NutMEG.culture.base_organism.adaptations.Tadaptations) take_step() (NutMEG.culture.base_organism.base_organism.base_organism method) (NutMEG.culture.colony.colony.colony method) (NutMEG.culture.culture.culture method) (NutMEG.culture.horde.horde.horde method) take_step_lite() (NutMEG.culture.organism.organism.organism method) Tdef (NutMEG.culture.base_organism.maintainer.maintainer attribute) Tdep (class in NutMEG.reaction.special.Tdep) temperature_defenses() (NutMEG.applications.theory_estimates.theory_estimates method)

theory_estimates (class in NutMEG.applications.theory_estimates) thermo (NutMEG.culture.base_organism.synthesis.BioMolecule.BioMolecule attribute) (NutMEG.reaction.reagent.reagent attribute) thermo_finder() (NutMEG.reaction.reaction.reaction method) thermo_to_db() (NutMEG.reaction.thermo.reagent_thermo.reagent_thermo method) tigerstripeT (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) to_db() (NutMEG.culture.base_organism.base_organism_dbhelper.bodb_helper method) (NutMEG.reactor.reactor_dbhelper.rdb_helper method) total_molality (NutMEG.reaction.special.solutions.neutralsol attribute) TPcheck() (NutMEG.reaction.thermo.reaction_thermo.reaction_thermo method) (NutMEG.reaction.thermo.reagent_thermo.reagent_thermo method) TypicalOptimalMethanogen (class in NutMEG.culture.saved_organisms.TypicalOptimalMethanogen)

U

unify_reaction() (NutMEG.reactor.reactor.reactor method) uniqueOrgs (NutMEG.ecosystem_dbhelper.db_helper attribute) uniqueReas (NutMEG.ecosystem_dbhelper.db_helper attribute) update_CompID() (NutMEG.reactor.reactor_dbhelper.rdb_helper method) update_composition() (NutMEG.reactor.reactor.reactor method) update_conditions() (NutMEG.reactor.saved_systems.VenusDrop.VenusDrop method) update_E() (NutMEG.reaction.special.solutions.redox method) (NutMEG.reaction.special.solutions.redox_half method) update_frac_dict() (NutMEG.culture.base_organism.maintainer.maintainer method) update_gammas() (NutMEG.reaction.special.solutions.electrolyte method) update_kappa() (NutMEG.reaction.special.solutions.electrolyte method) update_mean_gamma() (NutMEG.reaction.special.solutions.electrolyte method) update_metabolic_rate() (NutMEG.culture.base_organism.base_organism.base_organism method) update_molar_gibbs() (NutMEG.reaction.special.solutions.redox method) update_molar_gibbs_from_quotient() (NutMEG.reaction.reaction.reaction method) update_num() (NutMEG.culture.horde.horde.horde method) update_nutrient_yield() (NutMEG.culture.base_organism.CHNOPSexchanger.CHNOPSexchanger method) update_org_db() (NutMEG.culture.base_organism.base_organism_dbhelper.bodb_helper method)

update_P_loss() (NutMEG.culture.base_organism.maintainer.maintainer method) update_quotient() (NutMEG.reaction.reaction.reaction method) (NutMEG.reaction.special.solutions.redox method) update_ReactIDs() (NutMEG.reactor.reactor_dbhelper.rdb_helper method) update_reactor_db() (NutMEG.reactor.reactor_dbhelper.rdb_helper method) update_reagent() (NutMEG.reaction.reagent.reagent method) (NutMEG.reactor.saved_systems.VenusDrop.VenusDrop method) update_reagents() (NutMEG.reaction.reaction.reaction method) update_std_molar_enthalpy_of_reaction() (NutMEG.reaction.reaction.reaction method) update_std_molar_enthalpy_of_reaction_T() (NutMEG.reaction.special.Tdep.Tdep method) update_std_molar_entropy_of_reaction() (NutMEG.reaction.reaction.reaction method) update_std_molar_entropy_of_reaction_T() (NutMEG.reaction.special.Tdep.Tdep method) update_std_molar_gibbs() (NutMEG.reaction.special.solutions.redox_half method) update_std_molar_gibbs_from_quotient() (NutMEG.reaction.reaction.reaction method) update_std_molar_gibbs_G() (NutMEG.reaction.reaction.reaction method) update_std_molar_gibbs_HS() (NutMEG.reaction.reaction.reaction method) update_summary() (NutMEG.ecosystem_dbhelper.db_helper method) uptake_consts (NutMEG.culture.base_organism.CHNOPSexchanger.CHNOPSexchanger attribute), [1]

V

V (NutMEG.environment.environment.environment attribute) V_RTP (NutMEG.environment.environment.environment attribute) VenusDrop (class in NutMEG.reactor.saved_systems.VenusDrop)

volume (NutMEG.culture.base_organism.base_organism.base_organism attribute) (NutMEG.culture.horde.horde.horde attribute) (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute)

W

workoutID (NutMEG.reactor.saved_systems.Enceladus.Enceladus attribute) workoutID() (NutMEG.culture.base_organism.base_organism_dbhelper.bodb_helper method) (NutMEG.culture.horde.horde.horde method) (NutMEG.reactor.reactor_dbhelper.rdb_helper method)

X

xi (NutMEG.culture.base_organism.respirator.respirator attribute)