Reduce charge particle warnings; add static particle_charge method (#…

…1109)

* add better notes about unit conversions

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* adding a missing word

* fix a couple formatting issues

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* fix typos, clean up formatting

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* add static method for particle charge to reduce warnings

* fix return statement line

* add doc strings, add if statement to check for children

* change == to is

* fix docstyle

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Co Quach <[email protected]>
Co-authored-by: Co Quach <[email protected]>

mbuild/compound.py

@@ -275,9 +275,10 @@ def _n_particles(self, include_ports=False):
         return sum(1 for _ in self._particles(include_ports))
 
     def _contains_only_ports(self):
-        for part in self.children:
-            if not part.port_particle:
-                return False
+        if self.children:
+            for part in self.children:
+                if not part.port_particle:
+                    return False
         return True
 
     def print_hierarchy(self, print_full=False, index=None, show_tree=True):
@@ -547,7 +548,17 @@ def mass(self, value):
 
     @property
     def charge(self):
-        """Get the charge of the Compound."""
+        """Return the total charge of a compound.
+
+        If the compound contains children compouds, the total charge of all
+        children compounds is returned.
+
+        If the charge of a particle has not been explicitly set
+        then the particle's charge is None, and are not used when
+        calculating the total charge.
+        """
+        if self._contains_only_ports():
+            return self._particle_charge(self)
         charges = [p._charge for p in self.particles()]
         if None in charges:
             warn(
@@ -557,6 +568,11 @@ def charge(self):
         filtered_charges = [charge for charge in charges if charge is not None]
         return sum(filtered_charges) if filtered_charges else None
 
+    @staticmethod
+    def _particle_charge(particle):
+        """Return charge of a Compound with no children."""
+        return particle._charge
+
     @charge.setter
     def charge(self, value):
         if self._contains_only_ports():

mbuild/tests/test_compound.py

@@ -1702,16 +1702,15 @@ def test_charge_neutrality_warn(self, benzene):
 
     def test_none_charge(self):
         A = mb.Compound()
-        with pytest.warns(UserWarning):
-            A.charge
+        assert A.charge is None
 
         A.charge = 1
         B = mb.Compound()
         container = mb.Compound(subcompounds=[A, B])
+        assert A.charge == 1
+        assert B.charge is None
         with pytest.warns(UserWarning):
             container_charge = container.charge
-            assert A.charge == 1
-            assert B.charge == None
             assert container_charge == 1
 
     @pytest.mark.skipif(not has_openbabel, reason="Open Babel not installed")