Didn't quite fix that completely in last commit

mpcat/apprehend/jaguar_output.py

@@ -6,7 +6,7 @@
 
 from monty.json import MSONable, jsanitize
 
-from pymatgen.core.periodic_table import DummySpecies
+from pymatgen.core.periodic_table import DummySpecie
 
 from schrodinger.application.jaguar.output import JaguarOutput
 from schrodinger.application.jaguar.results import JaguarResults
@@ -255,10 +255,10 @@ def __init__(self, filename: str, allow_failure: Optional[bool] = False,
                     base_dir / self.data["output"]["output_file"])
                 self.data["output"]["molecule"] = self.data["molecule_trajectory"][-1]
 
-                self.data["input"]["molecule"].remove_species([DummySpecies("")])
+                self.data["input"]["molecule"].remove_species([DummySpecie("")])
                 for m in self.data["molecule_trajectory"]:
-                    m.remove_species([DummySpecies("")])
-                self.data["output"]["molecule"].remove_species([DummySpecies("")])
+                    m.remove_species([DummySpecie("")])
+                self.data["output"]["molecule"].remove_species([DummySpecie("")])
 
             else:
                 self.data["input"]["molecule"] = None

mpcat/automate/atomate/drones.py

@@ -32,6 +32,9 @@
 
 logger = get_logger(__name__)
 
+#TODO: Parse charge properly
+# Also as an int (rather than float)
+
 
 class GSMDrone(AbstractDrone):
     """
@@ -86,6 +89,7 @@ def assimilate(self, path, molecule_file="input.xyz", template_file="qin",
         logger.info("Getting task doc for base dir :{}".format(path))
 
         all_files = os.listdir(path)
+        all_scratch_files = list()
         if "scratch" in all_files:
             all_scratch_files = os.listdir(os.path.join(path, "scratch"))