Add tests for ligand class

hjkgrp · Nov 11, 2023 · 5cc7c87 · 5cc7c87
1 parent 252eb1b
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diff --git a/tests/test_ligand_class.py b/tests/test_ligand_class.py
@@ -0,0 +1,26 @@
+from molSimplify.Classes.ligand import ligand
+
+
+def test_ligand_class(resource_path_root):
+    mol2_file = str(
+        resource_path_root / "inputs" / "ligand_class" / "fe_acac.mol2"
+    )
+    lig = ligand(
+        master_mol=None,
+        index_list=None,
+        dent=None,
+        read_lig=mol2_file,
+    )
+    assert lig.dent == 2
+    assert lig.master_mol.make_formula(latex=False) == "Fe1O2C5H7"
+
+    lig_graph_det, mol2_str = lig.get_lig_mol2()
+    assert lig_graph_det == '-2.023585127e+17'
+
+    with open(resource_path_root / "inputs" / "ligand_class" / "acac_ref.mol2") as fin:
+        ref_str = fin.read()
+    # Remove last new line (because of our autoformatting)
+    assert mol2_str[:-1] == ref_str
+
+    buried_vol = lig.percent_buried_vol()
+    assert abs(buried_vol - 30.034) < 1e-3
diff --git a/tests/testresources/inputs/ligand_class/acac_ref.mol2 b/tests/testresources/inputs/ligand_class/acac_ref.mol2
@@ -0,0 +1,42 @@
+@<TRIPOS>MOLECULE
+ligand
+15	15	1
+SMALL
+PartialCharges
+****
+Generated from molSimplify
+
+@<TRIPOS>ATOM
+1 O1	3.1117  0.8158  -1.394 O.2	1 RES1 0.0
+2 C1	2.5035  0.2178  -0.5193 C.2	1 RES1 0.0
+3 C2	1.0119  0.1135  -0.5927 C.3	1 RES1 0.0
+4 C3	3.2352  -0.4172  0.6354 C.2	1 RES1 0.0
+5 C4	4.7377  -0.323  0.7389 C.2	1 RES1 0.0
+6 O2	5.3853  0.2682  -0.1114 O.2	1 RES1 0.0
+7 C5	5.4522  -0.9568  1.8929 C.3	1 RES1 0.0
+8 H1	0.6247  0.6297  -1.4972 H	1 RES1 0.0
+9 H2	0.5611  0.5821  0.307 H	1 RES1 0.0
+10 H3	0.7146  -0.9552  -0.636 H	1 RES1 0.0
+11 H4	4.7384  -1.4561  2.5816 H	1 RES1 0.0
+12 H5	6.007  -0.1796  2.459 H	1 RES1 0.0
+13 H6	6.1702  -1.7146  1.5151 H	1 RES1 0.0
+14 H7	2.7035  -0.9212  1.3622 H	1 RES1 0.0
+15 X1	0.0  0.0  0.0 X	1 RES1 0.0
+@<TRIPOS>BOND
+1 1 2 2
+1 1 15 1
+1 2 3 1
+1 2 4 1
+1 3 8 1
+1 3 9 1
+1 3 10 1
+1 4 5 2
+1 4 14 1
+1 5 6 1
+1 5 7 1
+1 6 15 1
+1 7 11 1
+1 7 12 1
+1 7 13 1
+@<TRIPOS>SUBSTRUCTURE
+1 RES1 15
diff --git a/tests/testresources/inputs/ligand_class/fe_acac.mol2 b/tests/testresources/inputs/ligand_class/fe_acac.mol2
@@ -0,0 +1,38 @@
+@<TRIPOS>MOLECULE
+*****
+ 15 15 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1 O           3.1117    0.8158   -1.3940 O.2     1  UNL1       -0.2958
+      2 C           2.5035    0.2178   -0.5193 C.2     1  UNL1        0.1238
+      3 C           1.0119    0.1135   -0.5927 C.3     1  UNL1       -0.0046
+      4 C           3.2352   -0.4172    0.6354 C.2     1  UNL1       -0.1413
+      5 C           4.7377   -0.3230    0.7389 C.2     1  UNL1       -0.1413
+      6 O           5.3853    0.2682   -0.1114 O.2     1  UNL1       -0.5072
+      7 C           5.4522   -0.9568    1.8929 C.3     1  UNL1       -0.1389
+      8 H           0.6247    0.6297   -1.4972 H       1  UNL1        0.0308
+      9 H           0.5611    0.5821    0.3070 H       1  UNL1        0.0308
+     10 H           0.7146   -0.9552   -0.6360 H       1  UNL1        0.0308
+     11 H           4.7384   -1.4561    2.5816 H       1  UNL1       -0.0057
+     12 H           6.0070   -0.1796    2.4590 H       1  UNL1       -0.0057
+     13 H           6.1702   -1.7146    1.5151 H       1  UNL1       -0.0057
+     14 H           2.7035   -0.9212    1.3622 H       1  UNL1        0.0298
+     15 Fe          0.0000    0.0000    0.0000 Fe      1  UNL1        0.0000
+@<TRIPOS>BOND
+     1     1     2    2
+     2     2     3    1
+     3     2     4    1
+     4     3     8    1
+     5     3     9    1
+     6     3    10    1
+     7     4     5    2
+     8     4    14    1
+     9     5     6    1
+    10     5     7    1
+    11     7    11    1
+    12     7    12    1
+    13     7    13    1
+    14     1    15    1
+    15     6    15    1