gather command

openfe gather

Gather simulation result jsons of relative calculations to a tsv file

This walks ROOTDIR recursively and finds all result JSON files from the quickrun command (these files must end in .json). Each of these contains the results of a separate leg from a relative free energy thermodynamic cycle.

The results reported depend on --report flag:

* ‘dg’ (default) reports the ligand, its absolute free energy, and

the associated uncertainty as the maximum likelihood estimate obtained

from DDG replica averages and standard deviations. These MLE estimates

are centred around 0.0, and when plotted can be shifted to match

experimental values.

* ‘ddg’ reports pairs of ligand_i and ligand_j, the calculated

relative free energy DDG(i->j) = DG(j) - DG(i) and its uncertainty.

* ‘raw’ reports the raw results, which each repeat simulation given

separately (i.e. no combining of redundant simulations is performed)

The output is a table of tab separated values. By default, this outputs to stdout, use the -o option to choose an output file.

openfe gather [OPTIONS] ROOTDIR

Options

--report <report>

What data to report. ‘dg’ gives maximum-likelihood estimate of absolute deltaG, ‘ddg’ gives delta-delta-G, and ‘raw’ gives the raw result of the deltaG for a leg.

Default:

dg

Options:

dg | ddg | raw

-o <output>

--allow-partial

Do not raise errors is results are missing parts for some edges. (Skip those edges and issue warning instead.)

Arguments

ROOTDIR

Required argument