Skip molecules with zero count in Packmol wrapper

openff/interchange/_tests/unit_tests/components/test_packmol.py

@@ -447,3 +447,16 @@ def test_save_error_on_convergence_failure(self, use_local_path):
             assert "STOP 173" in open("packmol_error.log").read()
         else:
             assert not pathlib.Path("packmol_error.log").is_file()
+
+    def test_trim_zero_molecules(self, caffeine, water, ligand, ethanol):
+        """
+        Test that pack_box trims molecules from inputs when the count is zero.
+        See Issue #1267: https://github.com/openforcefield/openff-interchange/issues/1267
+        """
+        topology = pack_box(
+            molecules=[caffeine, ligand, water, ethanol],
+            number_of_copies=[1, 0, 10, 0],
+            box_vectors=Quantity(3 * numpy.eye(3), "nanometer"),
+        )
+
+        assert topology.n_molecules == 11

openff/interchange/components/_packmol.py

@@ -458,9 +458,9 @@ def _build_input_file(
     Parameters
     ----------
     molecule_file_names: list of str
-        The paths to the molecule pdb files.
+        The paths to the molecule pdb files. No file will be produced for molecules where corresponding count is zero.
     molecule_counts: list of int
-        The number of each molecule to add.
+        The number of each molecule to add. No file will be produced for molecules where corresponding count is zero.
     structure_to_solvate: str, optional
         The path to the structure to solvate.
     box_size: openff.units.Quantity
@@ -504,6 +504,9 @@ def _build_input_file(
 
     # Add a section for each type of molecule to add.
     for file_name, count in zip(molecule_file_names, molecule_counts):
+        if count == 0:
+            continue
+
         input_lines.extend(
             [
                 f"structure {file_name}",
@@ -578,7 +581,8 @@ def pack_box(
         The molecules in the system.
     number_of_copies : list of int
         A list of the number of copies of each molecule type, of length
-        equal to the length of ``molecules``.
+        equal to the length of ``molecules``. If any element is zero, the
+        corresponding molecule is not added.
     solute: Topology, optional
         An OpenFF :py:class:`Topology <openff.toolkit.Topology>` to
         include in the box. If ``box_vectors`` and ``target_density`` are not