perses.bias.MinimizedPotentialBias

class perses.bias.MinimizedPotentialBias(smiles_list, implicit_solvent=OBC2, constraints=HBonds)

This class calculates the bias potential for expanded ensemble simulations, using a minimized potential energy as the bias.

Methods

g_k(molecule_smiles)	Retrieve or compute the g_k for the given molecule
precompute_gk()	A utility function to compute all the g_ks and return them as a {smiles : g_k} dict

__init__(smiles_list, implicit_solvent=OBC2, constraints=HBonds)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(smiles_list[, implicit_solvent, …])	Initialize self.
g_k(molecule_smiles)	Retrieve or compute the g_k for the given molecule
precompute_gk()	A utility function to compute all the g_ks and return them as a {smiles : g_k} dict

g_k(molecule_smiles)

Retrieve or compute the g_k for the given molecule

Returns:

g_k : float

Bias weight

precompute_gk()

A utility function to compute all the g_ks and return them as a {smiles : g_k} dict

gks : dict of type {string : float}

dict of {smiles : g_k}