update gather tests

openfecli/tests/commands/test_gather.py

@@ -27,73 +27,82 @@ def test_get_column(val, col):
 @pytest.fixture
 def results_dir(tmpdir):
     with tmpdir.as_cwd():
-        with resources.path('openfecli.tests.data', 'results.tar.gz') as f:
+        with resources.path('openfecli.tests.data', 'rbfe_results.tar.gz') as f:
             t = tarfile.open(f, mode='r')
             t.extractall('.')
 
         yield
 
+_EXPECTED_DG = b"""
+ligand	DG(MLE) (kcal/mol)	uncertainty (kcal/mol)
+lig_ejm_31	-0.09	0.05
+lig_ejm_42	0.7	0.1
+lig_ejm_46	-0.98	0.05
+lig_ejm_47	-0.1	0.1
+lig_ejm_48	0.53	0.09
+lig_ejm_50	0.91	0.06
+lig_ejm_43	2.0	0.2
+lig_jmc_23	-0.68	0.09
+lig_jmc_27	-1.1	0.1
+lig_jmc_28	-1.25	0.08
+"""
 
-@pytest.fixture
-def ref_gather():
-    return b"""\
-measurement\ttype\tligand_i\tligand_j\testimate (kcal/mol)\tuncertainty (kcal/mol)
-DDGhyd(lig_15, lig_12)\tRHFE\tlig_12\tlig_15\t-1.1\t0.055
-DDGhyd(lig_16, lig_15)\tRHFE\tlig_15\tlig_16\t-5.7\t0.043
-DDGhyd(lig_15, lig_11)\tRHFE\tlig_11\tlig_15\t5.4\t0.045
-DDGhyd(lig_3, lig_14)\tRHFE\tlig_14\tlig_3\t1.3\t0.12
-DDGhyd(lig_6, lig_1)\tRHFE\tlig_1\tlig_6\t-3.5\t0.038
-DDGhyd(lig_8, lig_6)\tRHFE\tlig_6\tlig_8\t4.1\t0.074
-DDGhyd(lig_3, lig_2)\tRHFE\tlig_2\tlig_3\t0.23\t0.044
-DDGhyd(lig_5, lig_10)\tRHFE\tlig_10\tlig_5\t-8.8\t0.099
-DDGhyd(lig_15, lig_10)\tRHFE\tlig_10\tlig_15\t1.4\t0.047
-DDGhyd(lig_6, lig_14)\tRHFE\tlig_14\tlig_6\t-2.1\t0.034
-DDGhyd(lig_15, lig_14)\tRHFE\tlig_14\tlig_15\t3.3\t0.056
-DDGhyd(lig_9, lig_6)\tRHFE\tlig_6\tlig_9\t-0.079\t0.021
-DDGhyd(lig_7, lig_3)\tRHFE\tlig_3\tlig_7\t73.0\t2.0
-DDGhyd(lig_7, lig_4)\tRHFE\tlig_4\tlig_7\t2.7\t0.16
-DDGhyd(lig_14, lig_13)\tRHFE\tlig_13\tlig_14\t0.49\t0.038
-DGsolvent(lig_12, lig_15)\tsolvent\tlig_12\tlig_15\t-5.1\t0.055
-DGvacuum(lig_12, lig_15)\tvacuum\tlig_12\tlig_15\t-4.0\t0.0014
-DGsolvent(lig_15, lig_16)\tsolvent\tlig_15\tlig_16\t-17.0\t0.043
-DGvacuum(lig_15, lig_16)\tvacuum\tlig_15\tlig_16\t-11.0\t0.0064
-DGsolvent(lig_11, lig_15)\tsolvent\tlig_11\tlig_15\t4.1\t0.041
-DGvacuum(lig_11, lig_15)\tvacuum\tlig_11\tlig_15\t-1.3\t0.019
-DGvacuum(lig_14, lig_3)\tvacuum\tlig_14\tlig_3\t-29.0\t0.051
-DGsolvent(lig_14, lig_3)\tsolvent\tlig_14\tlig_3\t-28.0\t0.11
-DGvacuum(lig_1, lig_6)\tvacuum\tlig_1\tlig_6\t20.0\t0.022
-DGsolvent(lig_1, lig_6)\tsolvent\tlig_1\tlig_6\t17.0\t0.032
-DGsolvent(lig_6, lig_8)\tsolvent\tlig_6\tlig_8\t-6.1\t0.069
-DGvacuum(lig_6, lig_8)\tvacuum\tlig_6\tlig_8\t-10.0\t0.027
-DGsolvent(lig_2, lig_3)\tsolvent\tlig_2\tlig_3\t15.0\t0.03
-DGvacuum(lig_2, lig_3)\tvacuum\tlig_2\tlig_3\t15.0\t0.032
-DGvacuum(lig_10, lig_5)\tvacuum\tlig_10\tlig_5\t19.0\t0.046
-DGsolvent(lig_10, lig_5)\tsolvent\tlig_10\tlig_5\t11.0\t0.087
-DGvacuum(lig_10, lig_15)\tvacuum\tlig_10\tlig_15\t2.3\t0.01
-DGsolvent(lig_10, lig_15)\tsolvent\tlig_10\tlig_15\t3.7\t0.046
-DGvacuum(lig_14, lig_6)\tvacuum\tlig_14\tlig_6\t16.0\t0.011
-DGsolvent(lig_14, lig_6)\tsolvent\tlig_14\tlig_6\t14.0\t0.032
-DGsolvent(lig_14, lig_15)\tsolvent\tlig_14\tlig_15\t10.0\t0.056
-DGvacuum(lig_14, lig_15)\tvacuum\tlig_14\tlig_15\t6.9\t0.0028
-DGvacuum(lig_6, lig_9)\tvacuum\tlig_6\tlig_9\t-5.0\t0.00056
-DGsolvent(lig_6, lig_9)\tsolvent\tlig_6\tlig_9\t-5.1\t0.021
-DGvacuum(lig_3, lig_7)\tvacuum\tlig_3\tlig_7\t-28.0\t0.91
-DGsolvent(lig_3, lig_7)\tsolvent\tlig_3\tlig_7\t45.0\t1.8
-DGsolvent(lig_4, lig_7)\tsolvent\tlig_4\tlig_7\t-3.3\t0.15
-DGvacuum(lig_4, lig_7)\tvacuum\tlig_4\tlig_7\t-6.1\t0.048
-DGsolvent(lig_13, lig_14)\tsolvent\tlig_13\tlig_14\t15.0\t0.037
-DGvacuum(lig_13, lig_14)\tvacuum\tlig_13\tlig_14\t15.0\t0.0057
+_EXPECTED_DDG = b"""
+ligand_i	ligand_j	DDG(i->j) (kcal/mol)	uncertainty (kcal/mol)
+lig_ejm_31	lig_ejm_42	0.8	0.1
+lig_ejm_31	lig_ejm_46	-0.89	0.06
+lig_ejm_31	lig_ejm_47	0.0	0.1
+lig_ejm_31	lig_ejm_48	0.61	0.09
+lig_ejm_31	lig_ejm_50	1.00	0.04
+lig_ejm_42	lig_ejm_43	1.4	0.2
+lig_ejm_46	lig_jmc_23	0.29	0.09
+lig_ejm_46	lig_jmc_27	-0.1	0.1
+lig_ejm_46	lig_jmc_28	-0.27	0.06
 """
 
+_EXPECTED_DG_RAW = b"""
+leg	ligand_i	ligand_j	DG(i->j) (kcal/mol)	uncertainty (kcal/mol)
+complex	lig_ejm_31	lig_ejm_42	-15.0	0.1
+solvent	lig_ejm_31	lig_ejm_42	-15.71	0.03
+complex	lig_ejm_31	lig_ejm_46	-40.75	0.04
+solvent	lig_ejm_31	lig_ejm_46	-39.86	0.05
+complex	lig_ejm_31	lig_ejm_47	-27.8	0.1
+solvent	lig_ejm_31	lig_ejm_47	-27.83	0.06
+complex	lig_ejm_31	lig_ejm_48	-16.14	0.08
+solvent	lig_ejm_31	lig_ejm_48	-16.76	0.03
+complex	lig_ejm_31	lig_ejm_50	-57.33	0.04
+solvent	lig_ejm_31	lig_ejm_50	-58.33	0.02
+complex	lig_ejm_42	lig_ejm_43	-18.9	0.2
+solvent	lig_ejm_42	lig_ejm_43	-20.28	0.03
+complex	lig_ejm_46	lig_jmc_23	17.42	0.06
+solvent	lig_ejm_46	lig_jmc_23	17.12	0.06
+complex	lig_ejm_46	lig_jmc_27	15.81	0.09
+solvent	lig_ejm_46	lig_jmc_27	15.91	0.05
+complex	lig_ejm_46	lig_jmc_28	23.14	0.04
+solvent	lig_ejm_46	lig_jmc_28	23.41	0.05
+"""
 
-def test_gather(results_dir, ref_gather):
+
+@pytest.mark.parametrize('report', ["", "dg", "ddg", "dg-raw"])
+def test_gather(results_dir, report):
+    expected = {
+        "": _EXPECTED_DG,
+        "dg": _EXPECTED_DG,
+        "ddg": _EXPECTED_DDG,
+        "dg-raw": _EXPECTED_DG_RAW,
+    }[report]
     runner = CliRunner()
 
-    result = runner.invoke(gather, ['results', '-o', '-'])
+    if report:
+        args = ["--report", report]
+    else:
+        args = []
+
+    result = runner.invoke(gather, ['results'] + args + ['-o', '-'])
 
     assert result.exit_code == 0
 
     actual_lines = set(result.stdout_bytes.split(b'\n'))
 
-    assert set(ref_gather.split(b'\n')) == actual_lines
+    assert set(expected.split(b'\n')) == actual_lines