From 0395c8ced79b3671a658958e0a3d92700fe57040 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Fri, 8 Sep 2023 10:09:55 -0700 Subject: [PATCH 1/2] Update cli_tutorial.md for new gather options --- rbfe_tutorial/cli_tutorial.md | 47 ++++++++++++++++------------------- 1 file changed, 22 insertions(+), 25 deletions(-) diff --git a/rbfe_tutorial/cli_tutorial.md b/rbfe_tutorial/cli_tutorial.md index e888de9..e183b48 100644 --- a/rbfe_tutorial/cli_tutorial.md +++ b/rbfe_tutorial/cli_tutorial.md @@ -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 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 resulting file looks something like this: ```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 ``` From 75cffab50b0c56cb6ee85e01c54e0dcbe7a8e276 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Fri, 8 Sep 2023 10:26:18 -0700 Subject: [PATCH 2/2] added comments from code review --- rbfe_tutorial/cli_tutorial.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/rbfe_tutorial/cli_tutorial.md b/rbfe_tutorial/cli_tutorial.md index e183b48..26324a0 100644 --- a/rbfe_tutorial/cli_tutorial.md +++ b/rbfe_tutorial/cli_tutorial.md @@ -222,10 +222,10 @@ 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 uncertainty in - that. + 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 + 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.