Merge pull request #624 from openforcefield/conformer-energies-single…

…-mol

Update conformer energy notebook and CLI to work for single conf molecule

examples/conformer_energies/conformer_energies.ipynb

@@ -58,6 +58,12 @@
     "# Load in the molecule and its conformers.\n",
     "# Note that all conformers of the same molecule are loaded as separate Molecule objects\n",
     "loaded_molecules = Molecule.from_file('ruxolitinib_conformers.sdf', toolkit_registry=rdktkw)\n",
+    "\n",
+    "# The logic below only works for lists of molecules, so if a\n",
+    "# single molecule was loaded, cast it to list\n",
+    "if type(loaded_molecules) is not list:\n",
+    "    loaded_molecules = [loaded_molecules]\n",
+    "\n",
     "# Collatate all conformers of the same molecule\n",
     "# NOTE: This isn't necessary if you have already loaded or created multi-conformer molecules;\n",
     "# it is just needed because our SDF reader does not automatically collapse conformers.\n",

examples/conformer_energies/conformer_energies.py

@@ -12,6 +12,10 @@ def compute_conformer_energies_from_file(filename):
     # different behavior in some cases. So, here we force loading through RDKit to ensure the correct behavior
     rdktkw = RDKitToolkitWrapper()
     loaded_molecules = Molecule.from_file(filename, toolkit_registry=rdktkw)
+    # The logic below only works for lists of molecules, so if a
+    # single molecule was loaded, cast it to list
+    if type(loaded_molecules) is not list:
+        loaded_molecules = [loaded_molecules]
     # Collatate all conformers of the same molecule
     # NOTE: This isn't necessary if you have already loaded or created multi-conformer molecules;
     # it is just needed because our SDF reader does not automatically collapse conformers.