API Documentation

Binding.Bind(self, **kwargs)

Applies an function to calculate the fraction of occupited receptors at equilibrium.

Parameters:

  • receptor_conc – Required (kwarg flt): concentration of receptor

  • lig_conc_range – Required (kwarg array): array of range of ligand concentration

  • pKd – Required (kwarg flt): pKd value of the ligand

Binding.ShowCurve(self)

Plots ligand-target binding curve

Binding.SubMaxConcentration(self)

Calculates the maximum bending point of a sigmoid-shaped curve according to the mathod of Sebaugh et al., 2003.

Parameters:

  • drug_receptor – Required (int): concentration of the receptor

  • lig_conc_range – Required (array): array of a range of ligand concentration

Returns:

instance .submax_concentration (flt)

Note

The minimization uses the Nelder-Mead method.

Utils.CalcOccupancy(receptor_conc, agonist_conc, antagonist_conc, pkd_agonist, pkd_antagonist)

This function calculates the fraction of occupited receptors at equilibrium.

Parameters:

  • receptor_conc – Required (int): concentration of the receptor

  • agonists_conc – Required (int): concentration of the agonist

  • antagonists_conc – Required (int): concentration of the antagonists (0 if antagonist shoul not be considered)

  • pkd_agonist – Required (int): pKd of agonist

  • pkd_antagonist – Required (int): pKd of antagonists (if antagonist shoul not be considered)

Return int:

fraction of occupied receptors in the equilibrium

Utils.GetGProtein(uniprotID)

This function query the SSBtoolkit internal database to extract the G protein associated to GPCR.

Warning

it just works for Human GPCRS!

Parameters:

uniprotID – Required (str)

Returns:

(str)

Utils.KineticTempScale(kon, koff, T1, T2, Tu='K', *kwargs)

This function rescales the kinetics constants to a specific temperature.

Parameters:

  • kon – Required (flt): foward kinetic constant

  • koff – Required (flt): reverse kinetic constant

  • T1 – Required (flt): Initial temperature

  • T2 – Required (flt): Final temperature

Paramter Tu:

Optional (kwarg str): Temperature Units (kelvin=’K’, celsius=’C’)

Returns:

(flt, flt)

Utils.MicrogramsToNanomolar(uniprotID, concentration)

This function converts micrograms of protein in nanomolar.

Parameters:

  • uniprotID – Required (str)

  • concentration – Required (int): concentration od protein in micrograms

Returns:

(flt) concentration of protein in nM

Note

This function will obtain the sequence of the protein from UNIPROT and calculate automatically its molecular mass

Utils.PrintProgressBar(iteration, total, prefix='', suffix='', decimals=1, length=100, fill='█', printEnd='\r')

Call in a loop to create terminal progress bar

Parameters:

  • iteration:Required – current iteration (Int)

  • total – Required: total iterations (Int)

  • prefix – Optional: prefix string (Str)

  • suffix – Optional: suffix string (Str)

  • decimals – Optional: positive number of decimals in percent complete (Int)

  • length – Optional: character length of bar (Int)

  • fill – Optional: bar fill character (Str)

  • printEnd – Optional: end character (Str)

class Utils.tauRAMD

Implementation of the tRAMD method by Kokh et al., 2018.

PlotRTDistribuitons(save=False, filename=None)

Plots the residence time distributions

Parameters:

  • save – Optional (kwarg boolean): default False

  • filename – Optional (kwarg str)

PlotRTStats(save=False, filename=None)

Plots the residence time statistics

Parameters:

  • save – Optional (kwarg boolean): default False

  • filename – Optional (kwarg str)

Run(**kwargs)

Calulates the residence time of a ligand from RAMD simualtions.

Parameters:

  • prefix – Required (kwarg str): directory path of .dat files

  • dt – Optional (kwarg flt): MD simulations time step in ns (defaul is 2E-6)

  • softwr – Optional (kwarg str): software used to perform RAMD simulations: NAMD, GROMACS (default)

Return (str):

residence time