Featurizer tuneup (WIP)

matminer/featurizers/composition.py

@@ -16,6 +16,7 @@
 
 from matminer.featurizers.base import BaseFeaturizer
 from matminer.featurizers.utils.stats import PropertyStats
+from matminer.featurizers.utils.oxidation import has_oxidation_states
 from matminer.utils.data import DemlData, MagpieData, PymatgenData, \
     CohesiveEnergyData, MixingEnthalpy, MatscholarElementData, MEGNetElementData
 
@@ -25,24 +26,6 @@
 module_dir = os.path.dirname(os.path.abspath(__file__))
 data_dir = os.path.join(module_dir, "..", "utils", "data_files")
 
-
-# Utility operations
-def has_oxidation_states(comp):
-    """Check if a composition object has oxidation states for each element
-
-    TODO: Does this make sense to add to pymatgen? -wardlt
-
-    Args:
-        comp (Composition): Composition to check
-    Returns:
-        (boolean) Whether this composition object contains oxidation states
-    """
-    for el in comp.elements:
-        if not hasattr(el, "oxi_state") or el.oxi_state is None:
-            return False
-    return True
-
-
 def is_ionic(comp):
     """Determines whether a compound is an ionic compound.
 
@@ -1186,6 +1169,7 @@ def citations(self):
             "url = {http://linkinghub.elsevier.com/retrieve/pii/S0927025614007113}, "
             "volume = {97}, year = {2015} } "]
 
+
 class Miedema(BaseFeaturizer):
     """
     Formation enthalpies of intermetallic compounds, from Miedema et al.

matminer/featurizers/site.py

@@ -2488,6 +2488,27 @@ def __init__(
         self.soap = None
         self.n_elements = None
 
+
+    @classmethod
+    def from_preset(cls, preset):
+        """
+        Create a SOAP featurizer object from sensible or published presets.
+
+        Args:
+            preset (str): Choose from:
+                "formation energy": Preset used for formation energy prediction
+                    in the original Dscribe paper.
+
+        Returns:
+
+        """
+        valid_presets = ["formation_energy"]
+        if preset == "formation_energy":
+            return cls(6, 8, 8, 0.4, True, "gto", True)
+        else:
+            raise ValueError(f"'{preset}' is not a valid preset. Choose from {valid_presets}")
+
+
     def _check_fitted(self):
         if not self.soap:
             raise NotFittedError("Please fit SOAP before featurizing.")