Merge pull request #209 from shuyana/fix-zero-division

fix zero division error in conformers

Author: hadim

datamol/conformers/_conformers.py

@@ -91,7 +91,8 @@ def generate(
             ["ETDG", "ETKDG", "ETKDGv2", "ETKDGv3"]. If None, "ETKDGv3" is used.
         forcefield: molecular forcefield to use, one of ['UFF','MMFF94s','MMFF94s_noEstat']
         ewindow: maximum energy above minimum energy conformer to output
-        eratio: max delta-energy divided by rotatable bonds for conformers
+        eratio: max delta-energy divided by rotatable bonds for conformers.
+            Ignored if the molecule has no rotatable bonds.
         energy_iterations: Maximum number of iterations during the energy minimization procedure.
             It corresponds to the `maxIters` argument in RDKit.
         warning_not_converged: Wether to log a warning when the number of not converged conformers
@@ -211,7 +212,8 @@ def generate(
         ordered_conformers = [
             conf
             for E, conf in sorted(zip(energies, mol_clone.GetConformers()), key=lambda x: x[0])
-            if E - minE <= ewindow and (E - minE) / rotatable_bonds <= eratio
+            if E - minE <= ewindow
+            and (rotatable_bonds == 0 or (E - minE) / rotatable_bonds <= eratio)
         ]
         mol.RemoveAllConformers()
         [mol.AddConformer(conf, assignId=True) for conf in ordered_conformers]

tests/test_conformers.py

@@ -325,3 +325,18 @@ def test_conformer_energy():
     e3 = mol3.GetConformer(3).GetPropsAsDict()
     assert np.isclose(e3["rdkit_MMFF94s_noEstat_energy"], 38.217380, atol=1)
     assert np.isclose(e3["rdkit_MMFF94s_noEstat_delta_energy"], 0.0, atol=0.1)
+
+
+def test_conformer_no_rotatable_bonds():
+    mol = dm.to_mol("c1ccccc1")
+
+    random.seed(42)
+    np.random.seed(42)
+    mol1 = dm.conformers.generate(mol, minimize_energy=True)
+
+    random.seed(42)
+    np.random.seed(42)
+    mol2 = dm.conformers.generate(mol, minimize_energy=True, eratio=3)
+
+    # `eratio` should be ignored for this molecule as it has no rotatable bonds
+    assert mol1.GetNumConformers() == mol2.GetNumConformers()

tests/test_predictors.py

@@ -34,9 +34,9 @@ def test_esol_from_data():
     # series
     v = dm.predictors.esol_from_data(data.iloc[0])
     v = float(v)
-    assert type(v) == float
+    assert isinstance(v, float)
 
     # dict
     v = dm.predictors.esol_from_data(data.iloc[0].to_dict())
     v = float(v)
-    assert type(v) == float
+    assert isinstance(v, float)