htmd.kinetics module

class htmd.kinetics.Kinetics(model, temperature, concentration=1, source=None, sink=None)

Bases: object

Constructor for the Kinetics class

Parameters

  • 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

Parameters

  • source (int, optional) – The state index to use as source

  • sink (int, optional) – The state index to use as sink

  • states (['macro','micro'], optional) – The state type of the states given before

Returns

rates – A Rates object containing the rates

Return type

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=True, save=None)

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.

Parameters

  • 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

plotRates(rates='mfptoff', 'mfpton', 'g0eq')

Plot the MFPT on, off and DG of all the macrostates to the sink state

Parameters

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()
class htmd.kinetics.Rates(mfpton=None, mfptoff=None, kon=None, koff=None, kdeq=None, g0eq=None)

Bases: object

A class containing a set of rates

mfpton

The mean first passage time of going from source to sink

Type

float

mfptoff

The mean first passage time of going from sink to source

Type

float

kon

The Kon rate (association constant) from source to sink

Type

float

koff

The Koff rate (dissociation constant) from sink to source

Type

float

kdeq

The Kd, calculated from the equilibrium probability

Type

float

g0eq

The free energy between source and sink, calculated from the equilibrium probability

Type

float