Allow square brackets in composition. Fixes #3583.

Author: Shyue Ping Ong

pymatgen/core/composition.py

@@ -544,6 +544,8 @@ def _parse_formula(self, formula: str, strict: bool = True) -> dict[str, float]:
             raise ValueError(f"Invalid {formula=}")
         # for Metallofullerene like "Y3N@C80"
         formula = formula.replace("@", "")
+        formula = formula.replace("[", "(")
+        formula = formula.replace("]", ")")
 
         def get_sym_dict(form: str, factor: float) -> dict[str, float]:
             sym_dict: dict[str, float] = collections.defaultdict(float)
@@ -1009,7 +1011,9 @@ def _get_oxi_state_guesses(self, all_oxi_states, max_sites, oxi_states_override,
                 *(
                     (y, x)
                     for (z, y, x) in sorted(
-                        zip(all_scores, all_sols, all_oxid_combo), key=lambda pair: pair[0], reverse=True
+                        zip(all_scores, all_sols, all_oxid_combo),
+                        key=lambda pair: pair[0],
+                        reverse=True,
                     )
                 )
             )

tests/core/test_composition.py

@@ -143,9 +143,15 @@ def test_init(self):
 
     def test_str_and_repr(self):
         test_cases = [
-            ({"Li+": 2, "Mn3+": 2, "O2-": 4}, {"str": "Li+2 Mn3+2 O2-4", "repr": "Composition('Li+:2 Mn3+:2 O2-:4')"}),
+            (
+                {"Li+": 2, "Mn3+": 2, "O2-": 4},
+                {"str": "Li+2 Mn3+2 O2-4", "repr": "Composition('Li+:2 Mn3+:2 O2-:4')"},
+            ),
             ("H2O", {"str": "H2 O1", "repr": "Composition('H2 O1')"}),
-            ({"Fe3+": 2, "O2-": 3}, {"str": "Fe3+2 O2-3", "repr": "Composition('Fe3+:2 O2-:3')"}),
+            (
+                {"Fe3+": 2, "O2-": 3},
+                {"str": "Fe3+2 O2-3", "repr": "Composition('Fe3+:2 O2-:3')"},
+            ),
             ("C6H6", {"str": "C6 H6", "repr": "Composition('C6 H6')"}),
         ]
 
@@ -154,7 +160,16 @@ def test_str_and_repr(self):
             assert repr(Composition(comp)) == expected["repr"]
 
     def test_average_electroneg(self):
-        electro_negs = (2.7224999999999997, 2.4160000000000004, 2.5485714285714285, 2.21, 2.718, 3.08, 1.21, 2.43)
+        electro_negs = (
+            2.7224999999999997,
+            2.4160000000000004,
+            2.5485714285714285,
+            2.21,
+            2.718,
+            3.08,
+            1.21,
+            2.43,
+        )
         for elem, val in zip(self.comps, electro_negs):
             assert elem.average_electroneg == approx(val)
 
@@ -197,7 +212,10 @@ def test_formula(self):
         assert Composition("(C)((C)0.9(B)0.1)") == Composition("C1.9 B0.1")
 
         assert Composition("NaN").reduced_formula == "NaN"
-        with pytest.raises(ValueError, match=r"float\('NaN'\) is not a valid Composition, did you mean str\('NaN'\)\?"):
+        with pytest.raises(
+            ValueError,
+            match=r"float\('NaN'\) is not a valid Composition, did you mean str\('NaN'\)\?",
+        ):
             Composition(float("NaN"))
 
         # test bad formulas raise ValueError
@@ -313,7 +331,10 @@ def test_integer_formula(self):
         ]
         all_formulas = [c.get_integer_formula_and_factor()[0] for c in self.comps]
         assert all_formulas == correct_reduced_formulas
-        assert Composition("Li0.5O0.25").get_integer_formula_and_factor() == ("Li2O", 0.25)
+        assert Composition("Li0.5O0.25").get_integer_formula_and_factor() == (
+            "Li2O",
+            0.25,
+        )
         assert Composition("O0.25").get_integer_formula_and_factor() == ("O2", 0.125)
         formula, factor = Composition("Li0.16666667B1.0H1.0").get_integer_formula_and_factor()
         assert formula == "Li(BH)6"
@@ -365,7 +386,12 @@ def test_anonymized_formula(self):
             assert comp.anonymized_formula == expected_formulas[idx]
 
     def test_get_wt_fraction(self):
-        correct_wt_frac = {"Li": 0.0498841610868, "Fe": 0.267567687258, "P": 0.222604831158, "O": 0.459943320496}
+        correct_wt_frac = {
+            "Li": 0.0498841610868,
+            "Fe": 0.267567687258,
+            "P": 0.222604831158,
+            "O": 0.459943320496,
+        }
         for el in correct_wt_frac:
             assert correct_wt_frac[el] == approx(self.comps[0].get_wt_fraction(el)), "Wrong computed weight fraction"
         assert self.comps[0].get_wt_fraction(Element("S")) == 0, "Wrong computed weight fractions"
@@ -378,7 +404,11 @@ def test_from_dict(self):
         assert comp == comp2
 
     def test_from_weight_dict(self):
-        weight_dict_list = [{"Ti": 90, "V": 6, "Al": 4}, {"Ni": 60, "Ti": 40}, {"H": 0.1119, "O": 0.8881}]
+        weight_dict_list = [
+            {"Ti": 90, "V": 6, "Al": 4},
+            {"Ni": 60, "Ti": 40},
+            {"H": 0.1119, "O": 0.8881},
+        ]
         formula_list = ["Ti87.6 V5.5 Al6.9", "Ti44.98 Ni55.02", "H2O"]
 
         for weight_dict, formula in zip(weight_dict_list, formula_list):
@@ -492,7 +522,10 @@ def test_comparisons(self):
         Fe = Element("Fe")
         assert c1 != Fe, NotImplemented
         assert c1 != Fe
-        with pytest.raises(TypeError, match="'<' not supported between instances of 'Composition' and 'Element'"):
+        with pytest.raises(
+            TypeError,
+            match="'<' not supported between instances of 'Composition' and 'Element'",
+        ):
             c1 < Fe  # noqa: B015
 
     def test_almost_equals(self):
@@ -615,7 +648,10 @@ def test_oxi_state_guesses(self):
         # to under the abs(max_sites) number of sites. Will also timeout if
         # incorrect.
         assert Composition("Sb10000O10000F10000").oxi_state_guesses(max_sites=-3)[0] == {"Sb": 3, "O": -2, "F": -1}
-        with pytest.raises(ValueError, match="Composition Li1 O1 F1 cannot accommodate max_sites setting"):
+        with pytest.raises(
+            ValueError,
+            match="Composition Li1 O1 F1 cannot accommodate max_sites setting",
+        ):
             Composition("LiOF").oxi_state_guesses(max_sites=-2)
 
         with pytest.raises(ValueError, match="Composition V2 O3 cannot accommodate max_sites setting"):
@@ -800,3 +836,7 @@ def test_math(self):
         assert pots_x2 - pots == pots
         assert fe_pot + o_pot == pots
         assert fe_pot - o_pot == pots - o_pot - o_pot
+
+    def test_square_brackets(self):
+        c = Composition("(NH4)2[FeCl5(H2O)]")
+        assert str(c) == "N2 H10 Fe1 Cl5 O1"