From 1e299c75b947aeb43b0fb2d565e2ff339e1df5d3 Mon Sep 17 00:00:00 2001
From: Corin Wagen <corin.wagen@gmail.com>
Date: Wed, 10 Jan 2024 09:48:44 -0500
Subject: [PATCH] modify smiles stuff

---
 cctk/molecule.py      | 9 ++++++---
 setup.py              | 4 ++--
 test/test_molecule.py | 6 ++++++
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/cctk/molecule.py b/cctk/molecule.py
index 0db733c..8e2df70 100644
--- a/cctk/molecule.py
+++ b/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():
diff --git a/setup.py b/setup.py
index 4ddb669..27c3ae4 100644
--- a/setup.py
+++ b/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="corin.wagen@gmail.com",
     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',
diff --git a/test/test_molecule.py b/test/test_molecule.py
index 2fcc104..5e7e49a 100644
--- a/test/test_molecule.py
+++ b/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)