Merge pull request #48 from shirte/main

Make SdfWriter handle mol=None

nerdd_module/converters/__init__.py

@@ -1,6 +1,6 @@
+from .basic_type_converter import *
 from .converter import *
 from .converter_config import *
-from .identity_converter import *
 from .mol_converter import *
 from .mol_to_image_converter import *
 from .problem_list_converter import *

nerdd_module/converters/identity_converter.py → nerdd_module/converters/basic_type_converter.py

@@ -3,21 +3,21 @@
 from .converter import Converter
 from .converter_config import ALL, ConverterConfig
 
-__all__ = ["IdentityConverter", "primitive_data_types"]
+__all__ = ["BasicTypeConverter", "basic_data_types"]
 
-primitive_data_types = [
+basic_data_types = [
     "int",
     "float",
     "string",
     "bool",
 ]
 
 
-class IdentityConverter(Converter):
+class BasicTypeConverter(Converter):
     def _convert(self, input: Any, context: dict) -> Any:
         return input
 
     config = ConverterConfig(
-        data_types=primitive_data_types,
+        data_types=basic_data_types,
         output_formats=ALL,
     )

nerdd_module/output/sdf_writer.py

@@ -1,6 +1,6 @@
 from typing import IO, Any, Dict, Iterable
 
-from rdkit.Chem import SDWriter
+from rdkit.Chem import Mol, SDWriter
 
 from .file_writer import FileLike, FileWriter
 
@@ -18,13 +18,22 @@ def _write(self, output: IO[Any], entries: Iterable[Dict]) -> None:
                 # assume that there is a mol object
                 mol = entry["input_mol"]
 
+                # if the molecule is erroneous, use an empty molecule
+                if mol is None:
+                    mol = Mol()
+
                 # write (almost) all properties to the mol object
                 for key, value in entry.items():
-                    value_as_str = str(value)
-                    if "\n" in value_as_str:
-                        # SDF can't write multi-line strings
+                    # skip "input_mol" key, because we use it as the main molecule
+                    if key == "input_mol":
                         continue
 
+                    value_as_str = str(value)
+
+                    # SDF can't write multi-line strings
+                    # -> replace newline with space
+                    value_as_str = value_as_str.replace("\n", " ")
+
                     mol.SetProp(key, value_as_str)
 
                 # write molecule

tests/basic/converters/test_converters.py

@@ -1,11 +1,7 @@
 from nerdd_module import Problem
 from nerdd_module.config import ResultProperty
-from nerdd_module.converters import (
-    Converter,
-    IdentityConverter,
-    ProblemListConverter,
-    VoidConverter,
-)
+from nerdd_module.converters import (BasicTypeConverter, Converter,
+                                     ProblemListConverter, VoidConverter)
 
 primitive_data_types = [
     "int",
@@ -23,7 +19,7 @@ def test_basic_data_types():
             result_property = ResultProperty(name="test", type=primitive_data_type)
             converter = Converter.get_converter(result_property, output_format)
             assert converter is not None
-            assert isinstance(converter, IdentityConverter)
+            assert isinstance(converter, BasicTypeConverter)
 
 
 def test_non_existing_data_type():