From f3834087fb427d52f5213afad1002050c0a8105d Mon Sep 17 00:00:00 2001
From: tom <tom.young.316@gmail.com>
Date: Sat, 12 Nov 2022 11:16:16 +0000
Subject: [PATCH 1/3] Add checking for incompatible charge/mult

---
 autode/__init__.py         |  2 +-
 autode/species/molecule.py | 22 ++++++++++++++++++++++
 doc/changelog.rst          | 12 ++++++++++++
 setup.py                   |  2 +-
 tests/test_molecule.py     | 15 +++++++++++++++
 5 files changed, 51 insertions(+), 2 deletions(-)

diff --git a/autode/__init__.py b/autode/__init__.py
index af21c8a59..eff4ba3b0 100644
--- a/autode/__init__.py
+++ b/autode/__init__.py
@@ -38,7 +38,7 @@
   - Merge when tests pass
 """
 
-__version__ = "1.3.2"
+__version__ = "1.3.3"
 
 
 __all__ = [
diff --git a/autode/species/molecule.py b/autode/species/molecule.py
index e2983506d..964f650ea 100644
--- a/autode/species/molecule.py
+++ b/autode/species/molecule.py
@@ -87,6 +87,7 @@ def _init_smiles(self, smiles: str):
             smiles (str):
         """
         at_strings = re.findall(r"\[.*?]", smiles)
+        init_charge, init_mult = self._charge, self._mult
 
         if any(metal in string for metal in metals for string in at_strings):
             init_smiles(self, smiles)
@@ -94,6 +95,19 @@ def _init_smiles(self, smiles: str):
         else:
             init_organic_smiles(self, smiles)
 
+        if not _is_default_mult(init_mult) and init_mult != self._mult:
+            logger.warning(
+                "Specified multiplicity did not match SMILES "
+                "calculated value - using the former"
+            )
+            self._mult = init_mult
+
+        if not _is_default_charge(init_charge) and init_charge != self._charge:
+            raise ValueError(
+                "SMILES charge was not the same as the "
+                f"defined value. {self._charge} ≠ {init_charge}"
+            )
+
         logger.info(
             f"Initialisation with SMILES successful. "
             f"Charge={self.charge}, Multiplicity={self.mult}, "
@@ -242,3 +256,11 @@ class Reactant(Molecule):
 
 class Product(Molecule):
     """Product molecule"""
+
+
+def _is_default_mult(value) -> bool:
+    return value == 1
+
+
+def _is_default_charge(value) -> bool:
+    return value == 0
diff --git a/doc/changelog.rst b/doc/changelog.rst
index 8818deed9..1f215ddc8 100644
--- a/doc/changelog.rst
+++ b/doc/changelog.rst
@@ -1,6 +1,18 @@
 Changelog
 =========
 
+1.3.3
+--------
+----------
+
+Bugfix release.
+
+
+Bug Fixes
+*********
+- Adds checking of SMILES-defined charge and multiplicity against user-specified values
+
+
 1.3.2
 --------
 ----------
diff --git a/setup.py b/setup.py
index 9822fe342..b8206c6dd 100644
--- a/setup.py
+++ b/setup.py
@@ -24,7 +24,7 @@
 
 setup(
     name="autode",
-    version="1.3.2",
+    version="1.3.3",
     python_requires=">3.7",
     packages=[
         "autode",
diff --git a/tests/test_molecule.py b/tests/test_molecule.py
index 4372605af..10c9e4302 100644
--- a/tests/test_molecule.py
+++ b/tests/test_molecule.py
@@ -271,3 +271,18 @@ def test_atom_class_defined_for_organic():
 
     mol = Molecule(smiles="[Br-:1]")
     assert mol.atoms[0].atom_class is not None
+
+
+def test_smiles_and_user_defined_charge_raises_exception():
+
+    with pytest.raises(Exception):
+        _ = Molecule(smiles="[Cl-]", charge=1)
+
+
+def test_user_defined_charge_overrides_smiles_mult():
+
+    ch2 = Molecule(smiles="[H][C][H]")
+    default_mult = ch2.mult
+
+    ch2_alt = Molecule(smiles="[H][C][H]", mult=3 if default_mult == 1 else 1)
+    assert ch2_alt.mult != default_mult

From b8ce7afa6b5025fabf188936b40139a9037bfa5e Mon Sep 17 00:00:00 2001
From: tom <tom.young.316@gmail.com>
Date: Tue, 15 Nov 2022 18:53:44 +0000
Subject: [PATCH 2/3] Remove non-required warning

---
 autode/species/molecule.py | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/autode/species/molecule.py b/autode/species/molecule.py
index 964f650ea..59964e739 100644
--- a/autode/species/molecule.py
+++ b/autode/species/molecule.py
@@ -87,7 +87,7 @@ def _init_smiles(self, smiles: str):
             smiles (str):
         """
         at_strings = re.findall(r"\[.*?]", smiles)
-        init_charge, init_mult = self._charge, self._mult
+        init_charge = self._charge
 
         if any(metal in string for metal in metals for string in at_strings):
             init_smiles(self, smiles)
@@ -95,13 +95,6 @@ def _init_smiles(self, smiles: str):
         else:
             init_organic_smiles(self, smiles)
 
-        if not _is_default_mult(init_mult) and init_mult != self._mult:
-            logger.warning(
-                "Specified multiplicity did not match SMILES "
-                "calculated value - using the former"
-            )
-            self._mult = init_mult
-
         if not _is_default_charge(init_charge) and init_charge != self._charge:
             raise ValueError(
                 "SMILES charge was not the same as the "

From 80d96748e86776df4393a28dbc6f510a926c38e3 Mon Sep 17 00:00:00 2001
From: tom <tom.young.316@gmail.com>
Date: Tue, 15 Nov 2022 19:55:25 +0000
Subject: [PATCH 3/3] Remove unused function

---
 autode/species/molecule.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/autode/species/molecule.py b/autode/species/molecule.py
index 59964e739..f59ce0a80 100644
--- a/autode/species/molecule.py
+++ b/autode/species/molecule.py
@@ -251,9 +251,5 @@ class Product(Molecule):
     """Product molecule"""
 
 
-def _is_default_mult(value) -> bool:
-    return value == 1
-
-
 def _is_default_charge(value) -> bool:
     return value == 0