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.
* ‘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 ‘dg-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