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Add experimental mean ΔG back to calculated and experimental ΔGs when plotting #42

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jchodera opened this issue Feb 25, 2022 · 1 comment
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enhancement New feature or request

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@jchodera
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Right now, we subtract the mean calculated ΔG and mean experimental ΔG and plot, making for a ridiculous plot that include ΔG >= 0 (Kd > 1 Molar), which is totally nonsensical for an absolute ΔG.

image

We should instead add back the experimental mean ΔG if there are no calculated ΔG values so the overall absolute ΔG are in fact absolute ΔG.

@jchodera jchodera self-assigned this Feb 25, 2022
@jchodera
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It turns out this is easy to do by just specifying the experimental mean, as in

# Absolute plot, with experimental data shifted to correct mean
experimental_mean_dg = np.asarray([node[1]["exp_DG"] for node in fe.graph.nodes(data=True)]).mean()
plotting.plot_DGs(fe.graph,
                  target_name=f'{target}',
                  title=f'Absolute binding energies - {target}',
                  figsize=5,
                  filename='./plot_absolute.png',
                  shift=experimental_mean_dg,
                  )

We might make it easier to do this automatically as a best practice for analyzing relative free energy calculations.

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