Merge pull request #884 from frannerin/rbfe-raw-report

'raw' gather report should output all PU repeats

openfecli/commands/gather.py

@@ -131,10 +131,11 @@ def _generate_bad_legs_error_message(set_vals, ligpair):
 def _parse_raw_units(results: dict) -> list[tuple]:
     # grab individual unit results from master results dict
     # returns list of (estimate, uncertainty) tuples
-    list_of_pur = list(results['protocol_result']['data'].values())[0]
+    list_of_pur = list(results['protocol_result']['data'].values())
 
-    return [(pu['outputs']['unit_estimate'],
-             pu['outputs']['unit_estimate_error'])
+    # could add to each tuple pu[0]["source_key"] for repeat ID
+    return [(pu[0]['outputs']['unit_estimate'],
+             pu[0]['outputs']['unit_estimate_error'])
             for pu in list_of_pur]
 
 
@@ -192,18 +193,18 @@ def _write_ddg(legs, writer, allow_partial):
 
 
 def _write_raw(legs, writer, allow_partial=True):
-    writer.writerow(["leg", "ligand_i", "ligand_j", "DG(i->j) (kcal/mol)",
-                     "MBAR uncertainty (kcal/mol)"])
+    writer.writerow(["leg", "repeat", "ligand_i", "ligand_j",
+                     "DG(i->j) (kcal/mol)", "MBAR uncertainty (kcal/mol)"])
 
     for ligpair, vals in sorted(legs.items()):
         for simtype, repeats in sorted(vals.items()):
-            for m, u in repeats:
+            for rep, (m, u) in enumerate(repeats):
                 if m is None:
                     m, u = 'NaN', 'NaN'
                 else:
                     m, u = format_estimate_uncertainty(m.m, u.m)
 
-                writer.writerow([simtype, *ligpair, m, u])
+                writer.writerow([simtype, rep, *ligpair, m, u])
 
 
 def _write_dg_raw(legs, writer, allow_partial):  # pragma: no-cover

openfecli/tests/commands/test_gather.py

@@ -87,25 +87,61 @@ def results_dir(tmpdir):
 
 
 _EXPECTED_RAW = b"""\
-leg	ligand_i	ligand_j	DG(i->j) (kcal/mol)	MBAR uncertainty (kcal/mol)
-complex\tlig_ejm_31\tlig_ejm_42\t-14.9\t0.8
-solvent\tlig_ejm_31\tlig_ejm_42\t-15.7\t0.8
-complex\tlig_ejm_31\tlig_ejm_46\t-40.7\t0.8
-solvent\tlig_ejm_31\tlig_ejm_46\t-39.8\t0.8
-complex\tlig_ejm_31\tlig_ejm_47\t-27.8\t0.8
-solvent\tlig_ejm_31\tlig_ejm_47\t-27.8\t0.8
-complex\tlig_ejm_31\tlig_ejm_48\t-16.2\t0.8
-solvent\tlig_ejm_31\tlig_ejm_48\t-16.8\t0.8
-complex\tlig_ejm_31\tlig_ejm_50\t-57.3\t0.8
-solvent\tlig_ejm_31\tlig_ejm_50\t-58.3\t0.8
-complex\tlig_ejm_42\tlig_ejm_43\t-19.0\t0.8
-solvent\tlig_ejm_42\tlig_ejm_43\t-20.3\t0.8
-complex\tlig_ejm_46\tlig_jmc_23\t17.3\t0.8
-solvent\tlig_ejm_46\tlig_jmc_23\t17.2\t0.8
-complex\tlig_ejm_46\tlig_jmc_27\t15.9\t0.8
-solvent\tlig_ejm_46\tlig_jmc_27\t16.0\t0.8
-complex\tlig_ejm_46\tlig_jmc_28\t23.1\t0.8
-solvent\tlig_ejm_46\tlig_jmc_28\t23.5\t0.8
+leg	repeat	ligand_i	ligand_j	DG(i->j) (kcal/mol)	MBAR uncertainty (kcal/mol)
+complex	0	lig_ejm_31	lig_ejm_42	-14.9	0.8
+complex	1	lig_ejm_31	lig_ejm_42	-14.8	0.8
+complex	2	lig_ejm_31	lig_ejm_42	-15.1	0.8
+solvent	0	lig_ejm_31	lig_ejm_42	-15.7	0.8
+solvent	1	lig_ejm_31	lig_ejm_42	-15.7	0.8
+solvent	2	lig_ejm_31	lig_ejm_42	-15.7	0.8
+complex	0	lig_ejm_31	lig_ejm_46	-40.7	0.8
+complex	1	lig_ejm_31	lig_ejm_46	-40.7	0.8
+complex	2	lig_ejm_31	lig_ejm_46	-40.8	0.8
+solvent	0	lig_ejm_31	lig_ejm_46	-39.8	0.8
+solvent	1	lig_ejm_31	lig_ejm_46	-39.9	0.8
+solvent	2	lig_ejm_31	lig_ejm_46	-39.8	0.8
+complex	0	lig_ejm_31	lig_ejm_47	-27.8	0.8
+complex	1	lig_ejm_31	lig_ejm_47	-28.0	0.8
+complex	2	lig_ejm_31	lig_ejm_47	-27.7	0.8
+solvent	0	lig_ejm_31	lig_ejm_47	-27.8	0.8
+solvent	1	lig_ejm_31	lig_ejm_47	-27.8	0.8
+solvent	2	lig_ejm_31	lig_ejm_47	-27.9	0.8
+complex	0	lig_ejm_31	lig_ejm_48	-16.2	0.8
+complex	1	lig_ejm_31	lig_ejm_48	-16.2	0.8
+complex	2	lig_ejm_31	lig_ejm_48	-16.0	0.8
+solvent	0	lig_ejm_31	lig_ejm_48	-16.8	0.8
+solvent	1	lig_ejm_31	lig_ejm_48	-16.7	0.8
+solvent	2	lig_ejm_31	lig_ejm_48	-16.8	0.8
+complex	0	lig_ejm_31	lig_ejm_50	-57.3	0.8
+complex	1	lig_ejm_31	lig_ejm_50	-57.3	0.8
+complex	2	lig_ejm_31	lig_ejm_50	-57.4	0.8
+solvent	0	lig_ejm_31	lig_ejm_50	-58.3	0.8
+solvent	1	lig_ejm_31	lig_ejm_50	-58.4	0.8
+solvent	2	lig_ejm_31	lig_ejm_50	-58.3	0.8
+complex	0	lig_ejm_42	lig_ejm_43	-19.0	0.8
+complex	1	lig_ejm_42	lig_ejm_43	-18.7	0.8
+complex	2	lig_ejm_42	lig_ejm_43	-19.0	0.8
+solvent	0	lig_ejm_42	lig_ejm_43	-20.3	0.8
+solvent	1	lig_ejm_42	lig_ejm_43	-20.3	0.8
+solvent	2	lig_ejm_42	lig_ejm_43	-20.3	0.8
+complex	0	lig_ejm_46	lig_jmc_23	17.3	0.8
+complex	1	lig_ejm_46	lig_jmc_23	17.4	0.8
+complex	2	lig_ejm_46	lig_jmc_23	17.5	0.8
+solvent	0	lig_ejm_46	lig_jmc_23	17.2	0.8
+solvent	1	lig_ejm_46	lig_jmc_23	17.1	0.8
+solvent	2	lig_ejm_46	lig_jmc_23	17.1	0.8
+complex	0	lig_ejm_46	lig_jmc_27	15.9	0.8
+complex	1	lig_ejm_46	lig_jmc_27	15.8	0.8
+complex	2	lig_ejm_46	lig_jmc_27	15.7	0.8
+solvent	0	lig_ejm_46	lig_jmc_27	16.0	0.8
+solvent	1	lig_ejm_46	lig_jmc_27	15.9	0.8
+solvent	2	lig_ejm_46	lig_jmc_27	15.9	0.8
+complex	0	lig_ejm_46	lig_jmc_28	23.1	0.8
+complex	1	lig_ejm_46	lig_jmc_28	23.2	0.8
+complex	2	lig_ejm_46	lig_jmc_28	23.1	0.8
+solvent	0	lig_ejm_46	lig_jmc_28	23.5	0.8
+solvent	1	lig_ejm_46	lig_jmc_28	23.3	0.8
+solvent	2	lig_ejm_46	lig_jmc_28	23.4	0.8
 """