ChemEnvSiteFingerprint.from_preset() removal of not-implemented CEs (#…

…948) * Removed ces that are not implemented in chemenv, added tests that previously would have failed (issue #945). * Fix linting errors.
hackingmaterials · Oct 11, 2024 · dcbaf06 · dcbaf06
1 parent ee5747d
commit dcbaf06
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Showing 2 changed files with 6 additions and 7 deletions.
diff --git a/matminer/featurizers/site/fingerprint.py b/matminer/featurizers/site/fingerprint.py
@@ -771,23 +771,18 @@ def from_preset(preset):
             "PA:10",
             "SBSA:10",
             "MI:10",
-            "S:10",
-            "H:10",
             "BS_1:10",
             "BS_2:10",
             "TBSA:10",
             "PCPA:11",
             "H:11",
-            "SH:11",
-            "CO:11",
             "DI:11",
             "I:12",
             "PBP:12",
             "TT:12",
             "C:12",
             "AC:12",
             "SC:12",
-            "S:12",
             "HP:12",
             "HA:12",
             "SH:13",

diff --git a/matminer/featurizers/site/tests/test_fingerprint.py b/matminer/featurizers/site/tests/test_fingerprint.py
@@ -277,9 +277,11 @@ def test_crystal_nn_fingerprint(self):
 
     def test_chemenv_site_fingerprint(self):
         cefp = ChemEnvSiteFingerprint.from_preset("multi_weights")
+        implemented_cetypes = {gg.ce_symbol for gg in cefp.lgf.allcg.get_implemented_geometries()}
+        assert set(cefp.cetypes).difference(implemented_cetypes) == set()  # Added after issue #945
         l = cefp.feature_labels()
         cevals = cefp.featurize(self.sc, 0)
-        self.assertEqual(len(cevals), 66)
+        self.assertEqual(len(cevals), 61)
         self.assertAlmostEqual(cevals[l.index("O:6")], 1, places=7)
         self.assertAlmostEqual(cevals[l.index("C:8")], 0, places=7)
         cevals = cefp.featurize(self.cscl, 0)
@@ -288,12 +290,14 @@ def test_chemenv_site_fingerprint(self):
         cefp = ChemEnvSiteFingerprint.from_preset("simple")
         l = cefp.feature_labels()
         cevals = cefp.featurize(self.sc, 0)
-        self.assertEqual(len(cevals), 66)
+        self.assertEqual(len(cevals), 61)
         self.assertAlmostEqual(cevals[l.index("O:6")], 1, places=7)
         self.assertAlmostEqual(cevals[l.index("C:8")], 0, places=7)
         cevals = cefp.featurize(self.cscl, 0)
         self.assertAlmostEqual(cevals[l.index("C:8")], 0.9953721, places=7)
         self.assertAlmostEqual(cevals[l.index("O:6")], 0, places=7)
+        cevals = cefp.featurize(self.ni3al, 0)  # Added after issue #945
+        self.assertAlmostEqual(cevals[l.index("I:12")], 0.3401699, places=7)
 
     def test_voronoifingerprint(self):
         df_sc = pd.DataFrame({"struct": [self.sc], "site": [0]})