acelleralivehtmd.kinetics.Kinetics(model, temperature, concentration=1, source=None, sink=None)¶Bases: object
Constructor for the Kinetics class
model (Model) – The model from which this class will calculate the kinetics
concentration (float, optional) – If a ligand is contained in the simulation, give the concentration of the ligand.
temperature (float, optional) – The simulation temperature
source (int, optional) – The source macrostate. Default it will be detected as the most disassociated state or the most extended conformation.
sink (int, optional) – The sink macrostate. Default it will be calculated as the macrostate with the highest equilibrium population.
Examples
>>> kin = Kinetics(model, temperature=300, concentration=0.015)
Methods
Attributes
getRates(source=None, sink=None, states='macro', _logger=True)¶Get the rates between two (sets of) states
rates – A Rates object containing the rates
Rates object
Example
>>> kin = Kinetics(model, temperature=300, concentration=0.015)
>>> r = kin.getRates()
>>> print(r)
>>> dg = r.g0eq
>>> r = kin.getRates(source=4, sink=[0,1,2,3])
mfptGraph()¶Not yet implemented
plotFluxPathways(statetype='macro', mode='net_flux', fraction=1.0)¶Plot flux pathways between source and sink state.
The flux is in units of transition events per lag time used to construct the Markov model.
statetype ({'macro','coarse','micro'}) – What type of states to plot
mode ({'net_flux', 'gross_flux'}) – Type of fluxes to plot
fraction (float) – Fraction of fluxes for which to report pathways. Doesn’t change the plot, only the text output.
plotRates(rates=('mfptoff', 'mfpton', 'g0eq'))¶Plot the MFPT on, off and DG of all the macrostates to the sink state
rates (tuple) – Specify which rates you want to plot. Options are (‘mfptoff’,’mfpton’,’g0eq’,’kdeq’,’kon’,’koff’)
Examples
>>> kin = Kinetics(model, temperature=300, concentration=0.015)
>>> kin.plotRates()