alchemlyb: the simple alchemistry library
Abstract
alchemlyb is an open-source Python software package for the analysis of alchemical free energy
calculations, an important method in computational chemistry and biology, most notably in
the field of drug discovery (Merz et al., 2010). Its functionality contains individual composable
building blocks for all aspects of a full typical free energy analysis workflow, starting with the
extraction of raw data from the output of diverse molecular simulation packages, moving on to
data preprocessing tasks such as decorrelation of time series, using various estimators to derive
free energy estimates from simulation samples, and finally providing quality analysis tools for
data convergence checking and visualization. alchemlyb also contains high-level end-to-end
workflows that combine multiple building blocks into a user-friendly analysis pipeline from the
initial data input stage to the final results. This workflow functionality enhances accessibility
by enabling researchers from diverse scientific backgrounds, and not solely computational
chemistry specialists, to use alchemlyb effectively.
Domains
Chemical Sciences| Origin | Publisher files allowed on an open archive |
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