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htmd.kinetics module#

class htmd.kinetics.Kinetics(model: Model, temperature: float, concentration: float = 1, source: int | None = None, sink: int | None = None)#

Bases: object

Constructor for the Kinetics class

Parameters:

  • model (Model) – The model from which this class will calculate the kinetics.

  • temperature (float) – The simulation temperature in Kelvin.

  • concentration (float, optional) – If a ligand is contained in the simulation, give the concentration of the ligand in Molar.

  • source (int, optional) – The source macrostate. If None it will be detected as the most disassociated state or the most extended conformation.

  • sink (int, optional) – The sink macrostate. If None 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: int | list | None = None, sink: int | list | None = None, states: str = 'macro', _logger: bool = True) → Rates#

Get the rates between two (sets of) states.

Parameters:

  • source (int or list, optional) – The state index (or list of indices) to use as source. If None, uses the source detected at construction time.

  • sink (int or list, optional) – The state index (or list of indices) to use as sink. If None, uses the sink detected at construction time.

  • states (str, optional) – The state type of the states given. Either 'macro' or 'micro'.

Returns:

rates – A Rates object containing the computed rates.

Return type:

Rates

Examples

>>> 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: str = 'macro', mode: str = 'net_flux', fraction: float = 1.0, plot: bool = True, save: str | None = None, results: bool = 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 (str, optional) – What type of states to plot. One of 'macro', 'coarse', or 'micro'.

  • mode (str, optional) – Type of fluxes to plot. Either 'net_flux' or 'gross_flux'.

  • fraction (float, optional) – Fraction of fluxes for which to report pathways. Does not change the plot, only the text output.

  • plot (bool, optional) – If set to False the plot will not show up in a figure.

  • save (str, optional) – If a path is passed, the plot will be saved to the specified file.

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

plotMarkovModel(plot: bool = True, save: str | None = None)#

Plot graph of transition probabilities.

Parameters:

  • plot (bool, optional) – If set to False the plot will not show up in a figure.

  • save (str, optional) – If a path is passed, the plot will be saved to the specified file.

plotRates(rates: tuple = ('mfptoff', 'mfpton', 'g0eq'))#

Plot the MFPT on, off and free energy of all macrostates to the sink state.

Parameters:

rates (tuple, optional) – Specify which rates 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: float | None = None, mfptoff: float | None = None, kon: float | None = None, koff: float | None = None, kdeq: float | None = None, g0eq: float | None = None)#

Bases: object

A class containing a set of rates

Parameters:

  • mfpton (float) – The mean first passage time of going from source to sink

  • mfptoff (float) – The mean first passage time of going from sink to source

  • kon (float) – The Kon rate (association constant) from source to sink

  • koff (float) – The Koff rate (dissociation constant) from sink to source

  • kdeq (float) – The Kd, calculated from the equilibrium probability

  • g0eq (float) – The free energy between source and sink, calculated from the equilibrium probability

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