nerdd-module 0.3.34__tar.gz → 0.3.35__tar.gz

{nerdd_module-0.3.34 → nerdd_module-0.3.35}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.34
+Version: 0.3.35
 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-0.3.35}/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-0.3.35}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.34
+Version: 0.3.35
 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-0.3.35}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.34"
+version = "0.3.35"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = { file = "LICENSE" }