Use openff-packmol

.github/workflows/ci.yaml

@@ -29,11 +29,9 @@ jobs:
           - py311amber
           - py311openeye
           - py311examples
-          - py311etc
           - py312amber
           - py312openeye
           - py312examples
-          - py312etc
           - py313openeye
           - py313examples
           - betas
@@ -50,6 +48,7 @@ jobs:
       with:
         pixi-version: v0.41.4
         environments: ${{ matrix.environment }}
+        frozen: true
 
     - name: Install and license OpenEye Toolkits
       if: ${{ !contains(matrix.environment, 'amber') }}

examples/ligand_in_water/ligand_in_water.ipynb

@@ -23,12 +23,12 @@
     "import openmm\n",
     "import openmm.app\n",
     "import openmm.unit\n",
+    "from openff.packmol import RHOMBIC_DODECAHEDRON, pack_box\n",
     "from openff.toolkit import ForceField, Molecule, unit\n",
     "from openff.toolkit.typing.engines.smirnoff.forcefield import get_available_force_fields\n",
     "from rich.pretty import pprint\n",
     "\n",
-    "from openff.interchange import Interchange\n",
-    "from openff.interchange.components._packmol import RHOMBIC_DODECAHEDRON, pack_box"
+    "from openff.interchange import Interchange"
    ]
   },
   {

examples/packed_box/packed_box.ipynb

@@ -18,11 +18,11 @@
    "outputs": [],
    "source": [
     "import nglview\n",
+    "from openff.packmol import UNIT_CUBE, pack_box\n",
     "from openff.toolkit import ForceField, Molecule\n",
     "from openff.units import unit\n",
     "\n",
     "from openff.interchange import Interchange\n",
-    "from openff.interchange.components._packmol import UNIT_CUBE, pack_box\n",
     "from openff.interchange.drivers import get_summary_data"
    ]
   },

examples/protein_ligand/protein_ligand.ipynb

@@ -27,11 +27,11 @@
     "\n",
     "import nglview\n",
     "import numpy as np\n",
+    "from openff.packmol import UNIT_CUBE, pack_box\n",
     "from openff.toolkit import ForceField, Molecule, Topology\n",
     "from openff.units import unit\n",
     "\n",
     "from openff.interchange import Interchange\n",
-    "from openff.interchange.components._packmol import UNIT_CUBE, pack_box\n",
     "from openff.interchange.drivers import get_openmm_energies\n",
     "from openff.interchange.drivers.all import get_summary_data"
    ]

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

@@ -1,11 +1,9 @@
 import pytest
+from openff.packmol import solvate_topology_nonwater
+from openff.packmol._packmol import _find_packmol
 from openff.toolkit import Quantity
 
 from openff.interchange._tests import MoleculeWithConformer
-from openff.interchange.components._packmol import (
-    _find_packmol,
-    solvate_topology_nonwater,
-)
 from openff.interchange.drivers import get_openmm_energies
 
 

openff/interchange/_tests/test_issues.py

@@ -5,12 +5,12 @@
 
 import numpy
 import pytest
+from openff.packmol import UNIT_CUBE, pack_box, solvate_topology
 from openff.toolkit import ForceField, Molecule, Quantity, Topology
 from openff.utilities import get_data_file_path, has_executable, skip_if_missing
 
 from openff.interchange import Interchange
 from openff.interchange._tests import MoleculeWithConformer, needs_gmx, shuffle_topology
-from openff.interchange.components._packmol import UNIT_CUBE, pack_box, solvate_topology
 from openff.interchange.drivers import get_amber_energies, get_gromacs_energies, get_openmm_energies
 from openff.interchange.exceptions import NonperiodicNoCutoffNotSupportedError
 from openff.interchange.warnings import PresetChargesAndVirtualSitesWarning