Merge pull request #88 from molssi-seamm/dev

Added support for charge in chemical formulae

HISTORY.rst

@@ -1,6 +1,9 @@
 =======
 History
 =======
+2024.11.27.1 -- Added support for charge in chemical formulae
+    * Added support for charge in chemical formulae, e.g. [H2 O]+.
+
 2024.11.27 -- Bugfix: error with charge and multiplicity
     * The charge and multiplicity of the system were not correctly set when creating a
       system from a SMILES string using RDKit. More generally, the charge and

molsystem/configuration.py

@@ -354,6 +354,22 @@ def formula(self):
             else:
                 formula.append(element)
 
+        formula = " ".join(formula)
+
+        # Handle any charge
+        if self.charge == -1:
+            formula = f"[{formula}]-"
+            counts.append(1)
+        elif self.charge == 1:
+            formula = f"[{formula}]+"
+            counts.append(1)
+        elif self.charge < 0:
+            formula = f"[{formula}]-{-self.charge}"
+            counts.append(-self.charge)
+        elif self.charge > 0:
+            formula = f"[{formula}]+{self.charge}"
+            counts.append(self.charge)
+
         # And the empirical formula
         Z = reduce(math.gcd, counts)
         empirical_formula_list = []
@@ -367,7 +383,20 @@ def formula(self):
             else:
                 empirical_formula.append(element)
 
-        return " ".join(formula), " ".join(empirical_formula), Z
+        empirical_formula = " ".join(empirical_formula)
+
+        # Handle any charge
+        charge = self.charge / Z
+        if charge == -1:
+            empirical_formula = f"[{empirical_formula}]-"
+        elif charge == 1:
+            empirical_formula = f"[{empirical_formula}]+"
+        elif charge < 0:
+            empirical_formula = f"[{empirical_formula}]-{-charge}"
+        elif charge > 0:
+            empirical_formula = f"[{empirical_formula}]+{charge}"
+
+        return formula, empirical_formula, Z
 
     @property
     def group(self):

tests/test_formula.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""Tests for `bonds` in the `molsystem` package."""
+
+import pytest  # noqa: F401
+
+
+def test_simple(AceticAcid):
+    """Simple test for acetic acid"""
+    assert AceticAcid.formula == ("C2 H4 O2", "C H2 O", 2)
+
+
+def test_periodic(copper):
+    """Test for copper crystal"""
+    assert copper.formula == ("Cu4", "Cu", 4)
+
+
+def test_charged(configuration):
+    """Test for charged configuration"""
+    configuration.from_smiles("[NH4+]")
+    assert configuration.formula == ("[H4 N]+", "[H4 N]+", 1)
+
+
+def test_doubly_charged(configuration):
+    """Test for charged configuration"""
+    configuration.from_smiles("[NH4+].[NH4+]")
+    assert configuration.formula == ("[H8 N2]+2", "[H4 N]+", 2)