modify smiles stuff

cctk/molecule.py

@@ -1588,13 +1588,16 @@ def new_from_smiles(cls, smiles, max_num_atoms=None):
         try:
             status1 = Chem.EmbedMolecule(rdkm, maxAttempts=5000)
             assert status1 >= 0
-            status2 = Chem.MMFFOptimizeMolecule(rdkm, maxIters=200)
-            assert status2 >= 0
         except Exception:
             status1 = Chem.EmbedMolecule(rdkm, maxAttempts=5000, useRandomCoords=True)
-            assert status1 >= 0
+            if status1 < 0:
+                raise ValueError(f"Cannot embed molecule ``{smiles}``!")
+
+        try:
             status2 = Chem.MMFFOptimizeMolecule(rdkm, maxIters=200)
             assert status2 >= 0
+        except AssertionError:
+            pass
 
         nums = []
         for atom in rdkm.GetAtoms():

setup.py

@@ -11,13 +11,13 @@
     packages=["cctk", "cctk.data", "cctk.groups"],
 #    include_package_data=True,
     package_data={"cctk.data": ["*"], "cctk.groups": ["*"],},
-    version="v0.2.21",
+    version="v0.2.22",
     license="Apache 2.0",
     description="computational chemistry toolkit",
     author="Corin Wagen and Eugene Kwan",
     author_email="[email protected]",
     url="https://github.com/ekwan/cctk",
-    download_url="https://github.com/ekwan/cctk/archive/v0.2.21.tar.gz",
+    download_url="https://github.com/ekwan/cctk/archive/v0.2.22.tar.gz",
     install_requires=["numpy", "networkx", "importlib_resources", "scipy", "pyahocorasick", "basis_set_exchange", "pyyaml"],
     long_description=long_description,
     long_description_content_type='text/markdown',

test/test_molecule.py

@@ -159,6 +159,12 @@ def test_smiles_utils(self):
         mol = cctk.Molecule.new_from_smiles("[OH3+]")
         self.assertEqual(mol.charge, 1)
 
+        mol = cctk.Molecule.new_from_smiles("C1[Br+]C1(C)C")
+        self.assertEqual(mol.charge, 1)
+
+        mol = cctk.Molecule.new_from_smiles("C1[Hg+](Cl)C1(C)C")
+        self.assertEqual(mol.charge, 1)
+
     def test_renumber(self):
         mol = self.load_molecule()
         mol2 = mol.swap_atom_numbers(1, 2)