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
acelleralive>>> kin = Kinetics(model, temperature=300, concentration=0.015)
Methods
Attributes
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])
Not yet implemented
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.
plot (bool) – If set it False the plot will not show up in a figure
save (str) – If a path is passed to save, the plot will be saved to the specified file
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()