SMILES naming fix and associated tests

chai_lab/data/sources/rdkit.py

@@ -3,6 +3,7 @@
 # See the LICENSE file for details.
 
 import logging
+from collections import defaultdict
 from pathlib import Path
 
 import antipickle
@@ -157,8 +158,13 @@ def generate(self, smiles: str) -> ConformerData:
 
         AllChem.EmbedMultipleConfs(mol_with_hs, numConfs=1, params=params)
         AllChem.RemoveHs(mol_with_hs)
+
+        element_counter: dict = defaultdict(int)
         for atom in mol_with_hs.GetAtoms():
-            atom.SetProp("name", atom.GetSymbol())
+            elem = atom.GetSymbol()
+            element_counter[elem] += 1  # Start each counter at 1
+            atom.SetProp("name", elem + str(element_counter[elem]))
+
         retval = self._load_ref_conformer_from_rdkit(mol_with_hs)
         retval.atom_names = [a.upper() for a in retval.atom_names]
         return retval

tests/test_parsing.py

@@ -68,3 +68,12 @@ def test_fasta_parsing():
     assert records[0].sequence == "RKDES"
     assert records[1].header == "bar"
     assert records[1].sequence == "KEDESRRR"
+
+
+def test_smiles_parsing():
+    smiles = ">smiles\nCc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C"
+    with TemporaryDirectory() as tmpdir:
+        fa_file = Path(tmpdir) / "test.fasta"
+        fa_file.write_text(smiles)
+        records = read_fasta(fa_file)
+    assert len(records) == 1

tests/test_rdkit.py

@@ -0,0 +1,24 @@
+# Copyright (c) 2024 Chai Discovery, Inc.
+# Licensed under the Apache License, Version 2.0.
+# See the LICENSE file for details.
+
+from chai_lab.data.sources.rdkit import RefConformerGenerator
+
+
+def test_ref_conformer_from_smiles():
+    """Test ref conformer generation from SMILES."""
+    smiles = "Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C"
+    rcg = RefConformerGenerator()
+
+    conformer = rcg.generate(smiles)
+
+    assert len(set(conformer.atom_names)) == conformer.num_atoms
+
+
+def test_ref_conformer_glycan_ccd():
+    """Ref conformer from CCD code for a sugar ring."""
+    rcg = RefConformerGenerator()
+    conformer = rcg.get("MAN")
+    assert conformer is not None
+
+    assert len(set(conformer.atom_names)) == conformer.num_atoms