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 and the results are the maximum

likelihood estimate of its absolute free, and the uncertainty in

that.

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

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

* ‘dg-raw’ reports the raw results, giving the leg (vacuum, solvent, or

complex), ligand_i, ligand_j, the raw DG(i->j) associated with it.

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 ‘dg-raw’ gives the raw result of the deltaG for a leg.

Default:

dg

Options:

dg | ddg | dg-raw

-o <output>

Arguments

ROOTDIR

Required argument