nerdd-module 0.3.34__tar.gz → 0.3.36__tar.gz

{nerdd_module-0.3.34 → nerdd_module-0.3.36}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.34
+Version: 0.3.36
 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-0.3.34 → nerdd_module-0.3.36}/nerdd_module/model/simple_model.py

@@ -64,7 +64,7 @@ class SimpleModel(Model):
         return [
             EnforceSchemaStep(self.config, output_format),
             ConvertRepresentationsStep(self.config, output_format, **kwargs),
-            WriteOutputStep(output_format, **kwargs),
+            WriteOutputStep(output_format, config=self.config, **kwargs),
         ]
 
     def _preprocess(self, mol: Mol) -> Tuple[Optional[Mol], List[Problem]]:

{nerdd_module-0.3.34 → nerdd_module-0.3.36}/nerdd_module/model/write_output_step.py

@@ -1,5 +1,6 @@
 from typing import Any, Iterator
 
+from ..config import Module
 from ..output import Writer
 from ..steps import OutputStep
 
@@ -7,16 +8,17 @@ __all__ = ["WriteOutputStep"]
 
 
 class WriteOutputStep(OutputStep):
-    def __init__(self, output_format: str, **kwargs: Any) -> None:
+    def __init__(self, output_format: str, config: Module, **kwargs: Any) -> None:
         super().__init__()
         self._output_format = output_format
-        self._kawrgs = kwargs
+        self._config = config
+        self._kwargs = kwargs
 
     def _get_result(self, source: Iterator[dict]) -> Any:
         # get the correct output writer
-        writer = Writer.get_writer(self._output_format, **self._kawrgs)
+        writer = Writer.get_writer(self._output_format, config=self._config, **self._kwargs)
         result = writer.write(source)
         return result
 
     def __repr__(self) -> str:
-        return f"WriteOutputStep(output_format={self._output_format}, kwargs={self._kawrgs})"
+        return f"WriteOutputStep(output_format={self._output_format}, kwargs={self._kwargs})"

{nerdd_module-0.3.34 → nerdd_module-0.3.36}/nerdd_module/output/sdf_writer.py

@@ -1,6 +1,6 @@
 from typing import IO, Any, Dict, Iterable
 
-from rdkit.Chem import Mol, SDWriter
+from rdkit.Chem import Mol, SanitizeMol, SDWriter
 
 from .file_writer import FileLike, FileWriter
 from .writer_config import WriterConfig
@@ -19,6 +19,12 @@ class SdfWriter(FileWriter):
                 # assume that there is a mol object
                 mol = entry["input_mol"]
 
+                # sanitize molecule to avoid basic writing errors (e.g. AtomKekulizeException)
+                try:
+                    SanitizeMol(mol)
+                except:  # noqa: E722
+                    mol = None
+
                 # if the molecule is erroneous, use an empty molecule
                 if mol is None:
                     mol = Mol()
@@ -38,7 +44,16 @@ class SdfWriter(FileWriter):
                     mol.SetProp(key, value_as_str)
 
                 # write molecule
-                writer.write(mol)
+                try:
+                    writer.write(mol)
+                except:  # noqa: E722
+                    # if the molecule can't be written, try to use an empty molecule
+                    empty_mol = Mol()
+                    # copy all properties from the original molecule
+                    for key, value in mol.GetPropsAsDict().items():
+                        empty_mol.SetProp(key, value)
+                    # write the empty molecule
+                    writer.write(mol)
         finally:
             writer.close()
 

{nerdd_module-0.3.34 → nerdd_module-0.3.36}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.34
+Version: 0.3.36
 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-0.3.34 → nerdd_module-0.3.36}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.34"
+version = "0.3.36"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = { file = "LICENSE" }