Energy ratio bug (#30)

* Catch divide-by-zero error in `energy_ratio.py` (#29) * Update version --------- Co-authored-by: Alex Morehead <[email protected]>
maabuu · Mar 15, 2024 · 58e7581 · 58e7581
1 parent b363659
commit 58e7581
Show file tree

Hide file tree

Showing 5 changed files with 36 additions and 1 deletion.
diff --git a/posebusters/__init__.py b/posebusters/__init__.py
@@ -24,4 +24,4 @@
     "check_volume_overlap",
 ]
 
-__version__ = "0.2.10"
+__version__ = "0.2.11"
diff --git a/posebusters/modules/energy_ratio.py b/posebusters/modules/energy_ratio.py
@@ -1,4 +1,5 @@
 """Module to check energy of ligand conformations."""
+
 from __future__ import annotations
 
 import logging
@@ -80,6 +81,10 @@ def check_energy_ratio(
         logger.warning("Failed to calculate ensemble conformation energy for %s: %s", inchi, e)
         avg_energy = np.nan
 
+    if avg_energy == 0:
+        logger.warning("Average energy of molecule is 0 for %s", inchi)
+        avg_energy = np.nan
+
     pred_factor = conf_energy / avg_energy
     ratio_passes = pred_factor <= threshold_energy_ratio
 

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -180,3 +180,8 @@ def mol_lig_7ztl_bcn():
 @pytest.fixture
 def mol_cond_7ztl_bcn():
     return MolFromPDBFile("tests/conftest/7ZTL_BCN/7ZTL_BCN_protein.pdb", sanitize=False, proximityBonding=False)
+
+
+@pytest.fixture
+def mol_disconnnected_atoms():
+    return MolFromMolFile("tests/conftest/mol_disconnected_atoms.sdf", sanitize=True)
diff --git a/tests/conftest/mol_disconnected_atoms.sdf b/tests/conftest/mol_disconnected_atoms.sdf
@@ -0,0 +1,20 @@
+
+     RDKit          3D
+
+ 12  0  0  0  0  0  0  0  0  0999 V2000
+   -3.8457   60.3869   20.5367 K   0  0  0  0  0 15  0  0  0  0  0  0
+  -17.1252   54.3726   26.7594 K   0  0  0  0  0 15  0  0  0  0  0  0
+   29.1964   53.9284   36.4555 Cl  0  0  0  0  0 15  0  0  0  0  0  0
+    6.9173   57.0285    8.5658 K   0  0  0  0  0 15  0  0  0  0  0  0
+    4.3879   73.7718   35.3121 K   0  0  0  0  0 15  0  0  0  0  0  0
+  -16.8898   53.9997   26.2540 K   0  0  0  0  0 15  0  0  0  0  0  0
+  -16.2661   85.6351   15.9899 Cl  0  0  0  0  0 15  0  0  0  0  0  0
+   24.5865   61.8500   43.6942 K   0  0  0  0  0 15  0  0  0  0  0  0
+   17.5242   55.2461   23.6907 K   0  0  0  0  0 15  0  0  0  0  0  0
+  -21.4907   82.5627   19.9609 Cl  0  0  0  0  0 15  0  0  0  0  0  0
+   -5.6100   66.1723   26.3135 K   0  0  0  0  0 15  0  0  0  0  0  0
+  -16.4761   49.1911   30.6890 K   0  0  0  0  0 15  0  0  0  0  0  0
+M  CHG  8   1   1   2   1   3  -1   4   1   5   1   6   1   7  -1   8   1
+M  CHG  4   9   1  10  -1  11   1  12   1
+M  END
+$$$$
diff --git a/tests/test_modules/test_energy_ratio.py b/tests/test_modules/test_energy_ratio.py
@@ -16,3 +16,8 @@ def test_check_energy_ratio_approximate_consistency(mol_1a30_clash_2, mol_1a30_c
 
     # check numbers are approximately equal
     assert np.isclose(energy_2, energy_3)
+
+
+def test_check_energy_ratio_disconnected_atoms(mol_disconnnected_atoms):
+    out = check_energy_ratio(mol_disconnnected_atoms)
+    assert out["results"]["energy_ratio_passes"] is False