Issue 382 (#401)

* issue #339: implemented instance-specific logging formatting

* NegativeLonePairsError exception;  JazzyError exception handler for API; migrated utils.py into exception.py

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "jazzy"
-version = "0.0.12"
+version = "0.0.13"
 description = "Jazzy"
 authors = ["Gian Marco Ghiandoni <[email protected]>", "Eike Caldeweyher <[email protected]>"]
 license = "Apache-2.0"

src/jazzy/__main__.py

@@ -6,7 +6,7 @@
 from jazzy.api import atomic_strength_vis_from_smiles
 from jazzy.api import molecular_vector_from_smiles
 from jazzy.config import Config
-from jazzy.utils import JazzyError
+from jazzy.exception import JazzyError
 
 pass_config = click.make_pass_decorator(Config, ensure=True)
 

src/jazzy/api.py

@@ -13,10 +13,11 @@
 from jazzy.core import get_covalent_atom_idxs
 from jazzy.core import kallisto_molecule_from_rdkit_molecule
 from jazzy.core import rdkit_molecule_from_smiles
+from jazzy.exception import exception_handling
+from jazzy.exception import JazzyError
 from jazzy.helpers import condense_atomic_map
 from jazzy.helpers import convert_map_to_tuples
 from jazzy.helpers import sum_atomic_map
-from jazzy.utils import JazzyError
 from jazzy.visualisation import depict_strengths
 
 
@@ -37,6 +38,7 @@ def __smiles_to_molecule_objects(smiles, minimisation_method=MINIMISATION_METHOD
     return rdkit_mol, kallisto_mol
 
 
+@exception_handling
 def molecular_vector_from_smiles(
     smiles: str, minimisation_method=MINIMISATION_METHOD, only_strengths=False
 ):
@@ -92,6 +94,7 @@ def molecular_vector_from_smiles(
     return mol_vector
 
 
+@exception_handling
 def deltag_from_smiles(smiles: str, minimisation_method=MINIMISATION_METHOD):
     """API route to calculate molecular free energy scalar.
 
@@ -134,6 +137,7 @@ def deltag_from_smiles(smiles: str, minimisation_method=MINIMISATION_METHOD):
     return round(sum(dg.values()), ROUNDING_DIGITS)
 
 
+@exception_handling
 def atomic_tuples_from_smiles(smiles: str, minimisation_method=MINIMISATION_METHOD):
     """API route to generate a tuple representation on the atomic map.
 
@@ -160,6 +164,7 @@ def atomic_tuples_from_smiles(smiles: str, minimisation_method=MINIMISATION_METH
     return convert_map_to_tuples(atomic_map)
 
 
+@exception_handling
 def atomic_map_from_smiles(smiles: str, minimisation_method=MINIMISATION_METHOD):
     """API route to generate a condensed representation on the atomic map.
 
@@ -186,6 +191,7 @@ def atomic_map_from_smiles(smiles: str, minimisation_method=MINIMISATION_METHOD)
     return condense_atomic_map(atomic_map)
 
 
+@exception_handling
 def atomic_strength_vis_from_smiles(
     smiles: str,
     minimisation_method=MINIMISATION_METHOD,

src/jazzy/core.py

@@ -14,8 +14,9 @@
 from rdkit.Chem import rdMolDescriptors
 
 from jazzy.config import ROUNDING_DIGITS
+from jazzy.exception import KallistoError
+from jazzy.exception import NegativeLonePairsError
 from jazzy.logging import logger
-from jazzy.utils import KallistoError
 
 
 def rdkit_molecule_from_smiles(smiles: str, minimisation_method=None):
@@ -494,8 +495,13 @@ def calculate_delta_polar(
             sdi = sdi / nh
 
         # acceptor contribution
-        nlps = atom["num_lp"]
         sak = atom["sa"]
+        nlps = atom["num_lp"]
+        if nlps < 0:
+            raise NegativeLonePairsError(
+                "The input compound contains atoms with "
+                f"negative lone pairs (got {nlps} for atom at idx {idx})"
+            )
 
         don += sdi * (nh**expd)
         acc += sak * (nlps**expa)

src/jazzy/exception.py

@@ -0,0 +1,32 @@
+"""Anything about exceptions and their handling."""
+# src/jazzy/exception.py
+
+
+class JazzyError(Exception):
+    """Raised when Jazzy cannot calculate results."""
+
+    pass
+
+
+class KallistoError(Exception):
+    """Raised when something goes wrong inside kallisto."""
+
+    pass
+
+
+class NegativeLonePairsError(Exception):
+    """Raised when a molecule contains negative lone pairs."""
+
+    pass
+
+
+def exception_handling(func):
+    """Catches core exceptions and raises a JazzyError."""
+
+    def wrapper(*args, **kwargs):
+        try:
+            return func(*args, **kwargs)
+        except (NegativeLonePairsError, KallistoError) as e:
+            raise JazzyError(str(e))
+
+    return wrapper

tests/test_api.py

@@ -9,7 +9,7 @@
 from jazzy.api import molecular_vector_from_smiles
 from jazzy.config import Config
 from jazzy.config import ROUNDING_DIGITS
-from jazzy.utils import JazzyError
+from jazzy.exception import JazzyError
 
 # global jazzy config (parameter)
 config = Config()
@@ -68,6 +68,19 @@ def test_api_molecular_vector_from_smiles_fails_for_empty_smiles():
     assert error.value.args[0] == "An empty SMILES string was passed."
 
 
+def test_api_molecular_vector_from_smiles_complex_numbers():
+    """Exception for structure containing negative lone pairs."""
+    smiles = "C12C3C4C5C1[Fe]23456789C%10C6C7C8C9%10"
+    minimisation_method = "MMFF94"
+    only_strengths = False
+    with pytest.raises(JazzyError) as error:
+        molecular_vector_from_smiles(smiles, minimisation_method, only_strengths)
+    assert (
+        "The input compound contains atoms with negative lone pairs"
+        in error.value.args[0]
+    )
+
+
 def test_deltag_from_smiles():
     """Correcly calculates free energy scalar."""
     smiles = "CC"

tests/test_free_energy_contributions.py

@@ -1,5 +1,6 @@
 """Test cases for the free energy contributions."""
 import numpy as np
+import pytest
 
 from jazzy.core import any_hydrogen_neighbors
 from jazzy.core import calculate_delta_apolar
@@ -11,6 +12,7 @@
 from jazzy.core import interaction_strength
 from jazzy.core import kallisto_molecule_from_rdkit_molecule
 from jazzy.core import rdkit_molecule_from_smiles
+from jazzy.exception import NegativeLonePairsError
 
 
 def test_calculate_delta_apolar():
@@ -87,6 +89,35 @@ def test_calculate_delta_polar():
         assert np.isclose(got, want[idx], 3)
 
 
+def test_negative_lone_pairs_delta_polar():
+    """Exception calculating the polar free energy contribution."""
+    smiles = "C12C3C4C5C1[Fe]23456789C%10C6C7C8C9%10"
+    # mock parameters
+    parameter = [0, 0, 0, 0]
+    rdkit_molecule = rdkit_molecule_from_smiles(
+        smiles=smiles, minimisation_method="MMFF94"
+    )
+    kallisto_molecule = kallisto_molecule_from_rdkit_molecule(
+        rdkit_molecule=rdkit_molecule
+    )
+    eeq = get_charges_from_kallisto_molecule(kallisto_molecule, 0)
+    aan = get_covalent_atom_idxs(rdkit_molecule)
+    mol_map = calculate_polar_strength_map(rdkit_molecule, kallisto_molecule, aan, eeq)
+    with pytest.raises(NegativeLonePairsError) as error:
+        calculate_delta_polar(
+            mol_map=mol_map,
+            atoms_and_nbrs=aan,
+            gd=parameter[0],
+            ga=parameter[1],
+            expd=parameter[2],
+            expa=parameter[3],
+        )
+    assert (
+        "The input compound contains atoms with negative lone pairs"
+        in error.value.args[0]
+    )
+
+
 def test_correct_interaction_strength():
     """Correctly calculates interaction strength."""
     want = 4

tests/test_kallisto.py

@@ -9,7 +9,7 @@
 from jazzy.core import get_charges_from_kallisto_molecule
 from jazzy.core import kallisto_molecule_from_rdkit_molecule
 from jazzy.core import rdkit_molecule_from_smiles
-from jazzy.utils import KallistoError
+from jazzy.exception import KallistoError
 
 
 def test_kallisto_charges_are_correct_from_molecule():