nerdd-module 0.3.39__tar.gz → 0.3.40__tar.gz

{nerdd_module-0.3.39 → nerdd_module-0.3.40}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.39
+Version: 0.3.40
 Summary: Base package to create NERDD modules
 Author-email: Steffen Hirte <steffen.hirte@univie.ac.at>
 Maintainer-email: Steffen Hirte <steffen.hirte@univie.ac.at>

{nerdd_module-0.3.39 → nerdd_module-0.3.40}/nerdd_module/preprocessing/__init__.py

@@ -3,5 +3,6 @@ from .chembl_structure_pipeline import *
 from .filter_by_element import *
 from .filter_by_weight import *
 from .preprocessing_step import *
+from .remove_small_fragments import *
 from .remove_stereochemistry import *
 from .sanitize import *

{nerdd_module-0.3.39 → nerdd_module-0.3.40}/nerdd_module/preprocessing/filter_by_weight.py

@@ -6,12 +6,14 @@ from rdkit.Chem.rdMolDescriptors import CalcExactMolWt
 from ..problem import InvalidWeightProblem, Problem
 from .preprocessing_step import PreprocessingStep
 
+__all__ = ["FilterByWeight"]
+
 
 class FilterByWeight(PreprocessingStep):
     def __init__(
         self,
-        min_weight: float,
-        max_weight: float,
+        min_weight: float = 0,
+        max_weight: float = float("inf"),
         remove_invalid_molecules: bool = False,
     ) -> None:
         super().__init__()

nerdd_module-0.3.40/nerdd_module/preprocessing/remove_small_fragments.py

@@ -0,0 +1,26 @@
+from typing import List, Optional, Tuple
+
+from rdkit.Chem import GetMolFrags, Mol
+from rdkit.Chem.rdMolDescriptors import CalcExactMolWt
+
+from ..problem import Problem
+from .preprocessing_step import PreprocessingStep
+
+__all__ = ["RemoveSmallFragments"]
+
+
+class RemoveSmallFragments(PreprocessingStep):
+    def __init__(
+        self,
+    ) -> None:
+        super().__init__()
+
+    def _preprocess(self, mol: Mol) -> Tuple[Optional[Mol], List[Problem]]:
+        fragments = GetMolFrags(mol, asMols=True)
+        if len(fragments) > 1:
+            # select the largest fragment
+            largest_fragment = max(fragments, key=CalcExactMolWt)
+        else:
+            largest_fragment = mol
+
+        return largest_fragment, []

{nerdd_module-0.3.39 → nerdd_module-0.3.40}/nerdd_module/preprocessing/remove_stereochemistry.py

@@ -6,6 +6,8 @@ from rdkit.Chem import RemoveStereochemistry as remove_stereochemistry
 from ..problem import Problem
 from .preprocessing_step import PreprocessingStep
 
+__all__ = ["RemoveStereochemistry"]
+
 
 class RemoveStereochemistry(PreprocessingStep):
     def __init__(self) -> None:

nerdd_module-0.3.40/nerdd_module/preprocessing/sanitize.py

@@ -0,0 +1,31 @@
+import logging
+from typing import List, Optional, Tuple
+
+from rdkit.Chem import AtomKekulizeException, KekulizeException, Mol, SanitizeMol
+
+from ..problem import Problem
+from .preprocessing_step import PreprocessingStep
+
+__all__ = ["Sanitize"]
+
+
+logger = logging.getLogger(__name__)
+
+
+class Sanitize(PreprocessingStep):
+    def __init__(self) -> None:
+        super().__init__()
+
+    def _preprocess(self, mol: Mol) -> Tuple[Optional[Mol], List[Problem]]:
+        try:
+            SanitizeMol(mol)
+            return mol, []
+        except KekulizeException:
+            return None, [Problem("kekulization_error", "Failed kekulizing the molecule.")]
+        except AtomKekulizeException:
+            return None, [
+                Problem("atom_kekulization_error", "Failed kekulizing an atom in the molecule.")
+            ]
+        except Exception as e:
+            logger.exception(e)
+            return None, [Problem("sanitization_error", "Failed sanitizing the molecule.")]

{nerdd_module-0.3.39 → nerdd_module-0.3.40}/nerdd_module/tests/predictions.py

@@ -48,6 +48,12 @@ def predictions_atomic_mass_model(representations, version, multiplier):
         output_format="record_list",
     )
 
+@when(
+    "all results are considered",
+    target_fixture="subset",
+)
+def subset_without_none(predictions):
+    return predictions
 
 @when(
     "the subset of the result where the input was not None is considered",

{nerdd_module-0.3.39 → nerdd_module-0.3.40}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.39
+Version: 0.3.40
 Summary: Base package to create NERDD modules
 Author-email: Steffen Hirte <steffen.hirte@univie.ac.at>
 Maintainer-email: Steffen Hirte <steffen.hirte@univie.ac.at>

{nerdd_module-0.3.39 → nerdd_module-0.3.40}/nerdd_module.egg-info/SOURCES.txt

@@ -75,6 +75,7 @@ nerdd_module/preprocessing/chembl_structure_pipeline.py
 nerdd_module/preprocessing/filter_by_element.py
 nerdd_module/preprocessing/filter_by_weight.py
 nerdd_module/preprocessing/preprocessing_step.py
+nerdd_module/preprocessing/remove_small_fragments.py
 nerdd_module/preprocessing/remove_stereochemistry.py
 nerdd_module/preprocessing/sanitize.py
 nerdd_module/steps/__init__.py

{nerdd_module-0.3.39 → nerdd_module-0.3.40}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.39"
+version = "0.3.40"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = "BSD-3-Clause"

nerdd_module-0.3.39/nerdd_module/preprocessing/sanitize.py

@@ -1,21 +0,0 @@
-from typing import List, Optional, Tuple
-
-from rdkit.Chem import Mol, SanitizeMol
-
-from ..problem import Problem
-from .preprocessing_step import PreprocessingStep
-
-__all__ = ["Sanitize"]
-
-
-class Sanitize(PreprocessingStep):
-    def __init__(self) -> None:
-        super().__init__()
-
-    def _preprocess(self, mol: Mol) -> Tuple[Optional[Mol], List[Problem]]:
-        problems: List[Problem] = []
-
-        # sanitize molecule
-        SanitizeMol(mol)
-
-        return mol, problems