'raw' gather report should output all PU repeats

[frannerin]

Function _parse_raw_units in openfecli/commands/gather.py only processed first ProtocolUnit repeat and then _write_raw did not distinguish between repeats if there were any. _write_dg_raw is left unchanged because it seems to be unused.

Example output (openfe gather --report raw ) before fix for a RBFE protocol with 3 PU repeats for the solvent legs, and 1 repeat for the complex legs:

leg	ligand_i	ligand_j	DG(i->j) (kcal/mol)	MBAR uncertainty (kcal/mol)
complex	lig_ejm_31	lig_ejm_42	-14.47	0.04
solvent	lig_ejm_31	lig_ejm_42	-14.89	0.03
complex	lig_ejm_31	lig_ejm_46	-33.90	0.05
solvent	lig_ejm_31	lig_ejm_46	-32.75	0.04
complex	lig_ejm_31	lig_ejm_47	-20.77	0.07
solvent	lig_ejm_31	lig_ejm_47	-20.72	0.05
complex	lig_ejm_31	lig_ejm_48	-14.19	0.07
solvent	lig_ejm_31	lig_ejm_48	-14.48	0.06
complex	lig_ejm_31	lig_ejm_50	-49.55	0.04
solvent	lig_ejm_31	lig_ejm_50	-50.07	0.04
complex	lig_ejm_42	lig_ejm_43	-11.47	0.05
solvent	lig_ejm_42	lig_ejm_43	-12.95	0.03
complex	lig_ejm_46	lig_jmc_23	8.96	0.02
solvent	lig_ejm_46	lig_jmc_23	9.37	0.02
complex	lig_ejm_46	lig_jmc_27	10.54	0.03
solvent	lig_ejm_46	lig_jmc_27	11.03	0.03
complex	lig_ejm_46	lig_jmc_28	16.03	0.03
solvent	lig_ejm_46	lig_jmc_28	16.16	0.03

Example output after fix:

leg	repeat	ligand_i	ligand_j	DG(i->j) (kcal/mol)	MBAR uncertainty (kcal/mol)
complex	1	lig_ejm_31	lig_ejm_42	-14.47	0.04
solvent	1	lig_ejm_31	lig_ejm_42	-14.89	0.03
solvent	2	lig_ejm_31	lig_ejm_42	-14.91	0.03
solvent	3	lig_ejm_31	lig_ejm_42	-14.90	0.03
complex	1	lig_ejm_31	lig_ejm_46	-33.90	0.05
solvent	1	lig_ejm_31	lig_ejm_46	-32.75	0.04
solvent	2	lig_ejm_31	lig_ejm_46	-32.75	0.05
solvent	3	lig_ejm_31	lig_ejm_46	-32.78	0.04
complex	1	lig_ejm_31	lig_ejm_47	-20.77	0.07
solvent	1	lig_ejm_31	lig_ejm_47	-20.72	0.05
solvent	2	lig_ejm_31	lig_ejm_47	-20.78	0.05
solvent	3	lig_ejm_31	lig_ejm_47	-20.75	0.05
complex	1	lig_ejm_31	lig_ejm_48	-14.19	0.07
solvent	1	lig_ejm_31	lig_ejm_48	-14.48	0.06
solvent	2	lig_ejm_31	lig_ejm_48	-14.51	0.06
solvent	3	lig_ejm_31	lig_ejm_48	-14.50	0.06
complex	1	lig_ejm_31	lig_ejm_50	-49.55	0.04
solvent	1	lig_ejm_31	lig_ejm_50	-50.07	0.04
solvent	2	lig_ejm_31	lig_ejm_50	-49.97	0.04
solvent	3	lig_ejm_31	lig_ejm_50	-50.08	0.04
complex	1	lig_ejm_42	lig_ejm_43	-11.47	0.05
solvent	1	lig_ejm_42	lig_ejm_43	-12.95	0.03
solvent	2	lig_ejm_42	lig_ejm_43	-13.03	0.03
solvent	3	lig_ejm_42	lig_ejm_43	-13.01	0.03
complex	1	lig_ejm_46	lig_jmc_23	8.96	0.02
solvent	1	lig_ejm_46	lig_jmc_23	9.37	0.02
solvent	2	lig_ejm_46	lig_jmc_23	9.35	0.02
solvent	3	lig_ejm_46	lig_jmc_23	9.37	0.02
complex	1	lig_ejm_46	lig_jmc_27	10.54	0.03
solvent	1	lig_ejm_46	lig_jmc_27	11.03	0.03
solvent	2	lig_ejm_46	lig_jmc_27	11.09	0.03
solvent	3	lig_ejm_46	lig_jmc_27	11.08	0.03
complex	1	lig_ejm_46	lig_jmc_28	16.03	0.03
solvent	1	lig_ejm_46	lig_jmc_28	16.16	0.03
solvent	2	lig_ejm_46	lig_jmc_28	16.17	0.04
solvent	3	lig_ejm_46	lig_jmc_28	16.20	0.03

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[IAlibay]

Thanks @frannerin - just a couple of things.

I think there's that one test that will fail and will require manually adding in the repeats to the stored table string.

[frannerin]

I did the zero-indexed repeats thing and updated the test_gather.py. I ran pytest -k test_gather and got: 23 passed, 3 skipped, 840 deselected, 1 xfailed, 2 xpassed, 25 warnings

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[atravitz]

lgtm! @frannerin would you like to be added to our list of contributors?

[frannerin]

Super glad that this was useful!!!

lgtm! @frannerin would you like to be added to our list of contributors?

That would be great, thank you so much