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postprocessing.rst

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.. module:: alchemlyb.postprocessors

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 :ref:`metadata <metadata>` is stored as :attr:`pandas.DataFrame.attrs`. The unit of the data can be converted to kT, kJ/mol or kcal/mol via the functions :func:`~alchemlyb.postprocessors.units.to_kT`, :func:`~alchemlyb.postprocessors.units.to_kJmol`, :func:`~alchemlyb.postprocessors.units.to_kcalmol`.

Unit Conversion Functions

.. currentmodule:: alchemlyb.postprocessors


.. autosummary::
    :toctree: postprocessors

    units

Constants and auxiliary functions

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

Scientific constants

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

.. currentmodule:: alchemlyb.postprocessors.units


.. autodata:: kJ2kcal

.. autodata:: R_kJmol

Unit conversion developer information

The function :func:`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 :attr:`pandas.DataFrame.attrs` as described under :ref:`note-on-units`.

When implementing code then ensure that the :ref:`metadata are maintained <metadata>` by using :func:`alchemlyb.concat` in place of :func:`pandas.concat` and use the :func:`alchemlyb.pass_attrs` decorator to copy metadata from an input dataframe to an output dataframe.