Tools for postprocessing

Tools are available for postprocessing the dataframes.

Unit Conversion

For all of the input and output dataframes (such as u_nk, dHdl, Estimator.delta_f_, Estimator.d_delta_f_), the metadata is stored as pandas.DataFrame.attrs. The unit of the data can be converted to \(kT\), kJ/mol or kcal/mol via the functions to_kT(), to_kJmol(), to_kcalmol().

Unit Conversion Functions

units

Unit conversion and constants

Constants and auxiliary functions

The postprocessing functions can make use of the following auxiliary functions, which in turn may use constants defined alchemlyb.postprocessors.units.

Scientific constants

Common scientific constants based on scipy.constants and are provided for use across alchemlyb.

alchemlyb.postprocessors.units.kJ2kcal = 0.2390057361376673

conversion factor from kJ to kcal, based on scipy.constants.calorie in scipy.constants

alchemlyb.postprocessors.units.R_kJmol = 0.008314462618

gas constant \(R\) in kJ/(mol K), based on scipy.constants.R in scipy.constants

Unit conversion developer information

The function alchemlyb.postprocessors.units.get_unit_converter() provides the relevant converter for unit conversion via a built-in dispatch table:

>>> from alchemlyb.postprocessors.units import get_unit_converter
>>> get_unit_converter('kT')
<function to_kT>
>>> get_unit_converter('kJ/mol')
<function to_kJmol>
>>> get_unit_converter('kcal/mol')
<function to_kcalmol>

For unit conversion to work, the dataframes must maintain the energy_unit and temperature metadata in pandas.DataFrame.attrs as described under A note on units.

When implementing code then ensure that the metadata are maintained by using alchemlyb.concat() in place of pandas.concat() and use the alchemlyb.pass_attrs() decorator to copy metadata from an input dataframe to an output dataframe.