Merge pull request #82 from molssi-seamm/dev

Incorrect coordinates from PubChem

HISTORY.rst

@@ -1,6 +1,10 @@
 =======
 History
 =======
+2024.10.1 -- Bugfix: Incorrect coordinates from PubChem
+    * Fixed bug where the coordinates from PubChem were accidentally the 2-D rather than
+      3-D coordinates.
+
 2024.8.17 -- Bugfix: current configuration not updated properly
     * Existing instances of systems did not correctly update when the default
       configuration was changed. This is release fixes the problem.

molsystem/pubchem.py

@@ -115,7 +115,8 @@ def PC_from_identifier(self, identifier, namespace="detect", fallback=None):
 
         for namespace in namespaces:
             response = requests.get(
-                f"{pug_url}/compound/{namespace}/{url_quote(identifier)}/SDF"
+                f"{pug_url}/compound/{namespace}/{url_quote(identifier)}/"
+                "SDF?record_type=3d"
             )
             if response.status_code == 200:
                 self.from_sdf_text(response.text)

tests/test_pubchem.py

@@ -50,3 +50,37 @@ def test_from_name(configuration):
     if name != correct:
         print(name)
     assert name == correct
+
+
+def test_coordinates_from_name(configuration):
+    """Get the system from a name"""
+    correct = [
+        [0.0, 0.0, 0.0],
+        [-0.4417, 0.2906, 0.8711],
+        [0.7256, 0.6896, -0.1907],
+        [0.4875, -0.8701, 0.2089],
+    ]
+
+    configuration.PC_from_identifier("ammonia")
+
+    coordinates = configuration.coordinates
+    if coordinates != correct:
+        print(coordinates)
+    assert coordinates == correct
+
+
+def test_coordinates_from_smiles(configuration):
+    """Get the system from SMILES"""
+    correct = [
+        [0.0, 0.0, 0.0],
+        [-0.4417, 0.2906, 0.8711],
+        [0.7256, 0.6896, -0.1907],
+        [0.4875, -0.8701, 0.2089],
+    ]
+
+    configuration.PC_from_identifier("N", namespace="smiles")
+
+    coordinates = configuration.coordinates
+    if coordinates != correct:
+        print(coordinates)
+    assert coordinates == correct