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])
plotFluxPathways(statetype='macro', mode='net_flux', fraction=1.0, plot=True, save=None, results=False)#

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

  • results (bool) – Set to True to return fluxes, paths and path_fluxes

plotMarkovModel(plot=True, save=None)#

Plot graph of transition probabilities

Parameters
  • 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