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richardjgowers merged 2 commits into from
Dec 8, 2023
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Update cli_tutorial.md for new gather options #85

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Update cli_tutorial.md for new gather options
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47 changes: 22 additions & 25 deletions rbfe_tutorial/cli_tutorial.md
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Expand Up @@ -215,37 +215,34 @@ To gather all the $\Delta G$ estimates into a single file, use the `openfe
gather` command from within the working directory used above:

```bash
openfe gather ./results/ -o final_results.tsv
openfe gather results/ --report dg -o final_results.tsv
```

This will write out a tab-separated table of results, including both the
$\Delta G$ for each leg and the $\Delta\Delta G$ computed from pairs of legs.
The first column is a description of the data, e.g., `DGcomplex(ligandB,
ligandA)` for the $\Delta G$ of the transformation of ligand
A into ligand B complexed to a protein, or `DDGbind(ligandB, ligandA)` for the binding
$\Delta\Delta G$ going from ligand A to ligand B. The second column tells the type of
the result, either `RBFE` for a relative result or `solvent`/`complex` for an
individual leg. The next two columns are the labels of the ligands, and then
the computed result and its uncertainty.
This will write out a tab-separated table of results where the results
reported are controlled by the `--report` option:

* `dg` (default) reports the ligand and the results are the maximum
likelihood estimate of its absolute free, and the associated
uncertainty 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.
* `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 resulting file looks something like this:

<!-- take top lines from `cat final_results.tsv` -->

```text
measurement type ligand_i ligand_j estimate (kcal/mol) uncertainty (kcal/mol)
DDGbind(lig_ejm_48, lig_ejm_31) RBFE lig_ejm_31 lig_ejm_48 0.45 0.17
DDGbind(lig_jmc_28, lig_ejm_46) RBFE lig_ejm_46 lig_jmc_28 -0.12 0.044
DDGbind(lig_ejm_46, lig_ejm_31) RBFE lig_ejm_31 lig_ejm_46 -0.73 0.097
DDGbind(lig_ejm_50, lig_ejm_31) RBFE lig_ejm_31 lig_ejm_50 0.94 0.072
DDGbind(lig_ejm_42, lig_ejm_31) RBFE lig_ejm_31 lig_ejm_42 0.49 0.09
DDGbind(lig_jmc_23, lig_ejm_46) RBFE lig_ejm_46 lig_jmc_23 -0.39 0.046
DDGbind(lig_ejm_43, lig_ejm_42) RBFE lig_ejm_42 lig_ejm_43 1.2 0.14
DDGbind(lig_jmc_27, lig_ejm_46) RBFE lig_ejm_46 lig_jmc_27 -0.65 0.1
DDGbind(lig_ejm_47, lig_ejm_31) RBFE lig_ejm_31 lig_ejm_47 0.016 0.15
DGsolvent(lig_ejm_31, lig_ejm_48) solvent lig_ejm_31 lig_ejm_48 -20.0 0.043
DGcomplex(lig_ejm_31, lig_ejm_48) complex lig_ejm_31 lig_ejm_48 -19.0 0.17
DGsolvent(lig_ejm_46, lig_jmc_28) solvent lig_ejm_46 lig_jmc_28 14.0 0.043
DGcomplex(lig_ejm_46, lig_jmc_28) complex lig_ejm_46 lig_jmc_28 14.0 0.0069
[continues]
lig_ejm_31 -0.21 0.06
lig_ejm_42 0.63 0.08
lig_ejm_46 -0.80 0.07
lig_ejm_47 -0.1 0.2
lig_ejm_48 0.6 0.3
lig_ejm_50 1.0 0.1
lig_ejm_43 1.9 0.1
lig_jmc_23 -0.94 0.09
lig_jmc_27 -0.91 0.09
lig_jmc_28 -1.2 0.1
```