Merge pull request #90 from molssi-seamm/dev

Bugfix: Properties in SDF files

HISTORY.rst

@@ -1,6 +1,11 @@
 =======
 History
 =======
+2024.12.11 -- Bugfix: Properties in SDF files
+    * Transferring properties to the Open Babel and RDKit molecules was incorrect after
+      recent changes to the handling of properties. This fixes the problem, and now SDF
+      files have the properties correctly.
+
 2024.12.7 -- Significant internal enhancement to property handling.
     * An internal change, allowing listing and getting properties with wildcards,
       working with multiple values at once. This is a significant change, but should

molsystem/openbabel.py

@@ -81,6 +81,7 @@ def to_OBMol(self, properties=None):
         if properties is not None:
             data = self.properties.get(properties, include_system_properties=True)
             for key, value in data.items():
+                value = value["value"]
                 pair.SetAttribute(key)
                 pair.SetValue(str(value))
                 ob_mol.CloneData(pair)

molsystem/rdkit_.py

@@ -103,6 +103,7 @@ def to_RDKMol(self, properties=None):
         if properties is not None:
             data = self.properties.get(properties, include_system_properties=True)
             for key, value in data.items():
+                value = value["value"]
                 if isinstance(value, int):
                     rdk_mol.SetIntProp(key, value)
                 elif isinstance(value, float):

tests/test_openbabel.py

@@ -501,12 +501,12 @@ def test_all_residue_search(configuration):
 def test_to_OBMol(Acetate):
     """Test creating an OBMol object from a structure."""
     correct = {
-        "float property": "{'sid': 1, 'cid': 1, 'value': 3.14}",
+        "float property": 3.14,
         "float property,units": "kcal/mol",
-        "int property": "{'sid': 1, 'cid': 1, 'value': 2}",
+        "int property": 2,
         "net charge": -1,
         "spin multiplicity": 1,
-        "str property": "{'sid': 1, 'cid': 1, 'value': 'Hi!'}",
+        "str property": "Hi!",
     }
 
     mol = Acetate.to_OBMol(properties="*")

tests/test_rdkit.py

@@ -20,12 +20,12 @@ def test_version():
 def test_to_RDKMol(Acetate):
     """Test creating a RDKMol object from a structure."""
     correct = {
-        "float property": "{'sid': 1, 'cid': 1, 'value': 3.14}",
+        "float property": 3.14,
         "float property,units": "kcal/mol",
-        "int property": "{'sid': 1, 'cid': 1, 'value': 2}",
+        "int property": 2,
         "net charge": -1,
         "spin multiplicity": 1,
-        "str property": "{'sid': 1, 'cid': 1, 'value': 'Hi!'}",
+        "str property": "Hi!",
     }
 
     mol = Acetate.to_RDKMol(properties="*")