nerdd-module 0.3.33__tar.gz → 0.3.35__tar.gz

{nerdd_module-0.3.33 → nerdd_module-0.3.35}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.33
+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-0.3.33 → nerdd_module-0.3.35}/nerdd_module/cli.py

@@ -27,7 +27,7 @@ Note that input formats shouldn't be mixed.
 
 def infer_click_type(param: JobParameter) -> click.ParamType:
     if param.choices is not None:
-        choices = [c.value for c in param.choices]
+        choices = [str(c.value) for c in param.choices]
         return click.Choice(choices)
 
     type_map = {

{nerdd_module-0.3.33 → nerdd_module-0.3.35}/nerdd_module/config/models.py

@@ -46,8 +46,8 @@ class ColorPalette(BaseModel):
     unknown: Optional[str] = None
 
 
-class JobParameterChoice(BaseModel):
-    value: str
+class Choice(BaseModel):
+    value: Union[str, int, float, bool]
     label: Optional[str] = None
 
 
@@ -58,7 +58,7 @@ class JobParameter(BaseModel):
     help_text: Optional[str] = None
     default: Any = None
     required: bool = False
-    choices: Optional[List[JobParameterChoice]] = None
+    choices: Optional[List[Choice]] = None
 
 
 Task = Literal[
@@ -85,6 +85,7 @@ class ResultProperty(BaseModel):
     sortable: bool = False
     group: Optional[str] = None
     level: Level = "molecule"
+    choices: Optional[List[Choice]] = None
     formats: Union[FormatSpec, IncludeExcludeFormatSpec, None] = None
     representation: Optional[str] = None
     from_property: Optional[str] = None

{nerdd_module-0.3.33 → 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-0.3.33 → nerdd_module-0.3.35}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.33
+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-0.3.33 → nerdd_module-0.3.35}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.33"
+version = "0.3.35"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = { file = "LICENSE" }