Fix geometry -> InChI generation

src/autochem/rate/data.py

@@ -648,7 +648,10 @@ def fit(
         if not validate or bad_fit == "fill":
             try:
                 with np.errstate(all="raise"):
-                    obj(T=T)
+                    vals = obj(T=T)
+                    if not np.all(np.isfinite(vals)):
+                        msg = "Fitted rate gives non-finite values over the input temperature range."
+                        raise FloatingPointError(msg)
             except FloatingPointError as e:
                 if A_fill is not None:
                     return cls(order=order, A=A_fill, b=0, E=0)
@@ -917,22 +920,25 @@ def fit(  # noqa: PLR0913
             (Options: "fill", replace with the fill value, or numpy.seterr options)
         :return: Rate fit
         """
-        bad_fits = [
-            "fill" if np.any(np.isclose(p, bad_fit_fill_pressures)) else bad_fit
-            for p in Ps
-        ]
-        k_data_fits = [
-            ArrheniusRateFit.fit(
+        k_fits = []
+        for k_data, P in zip(np.transpose(k_data), Ps, strict=True):
+            if validate:
+                print(f"Fitting Arrhenius rate for {P = }")
+
+            bad_fit = (
+                "fill" if np.any(np.isclose(P, bad_fit_fill_pressures)) else bad_fit
+            )
+            k_fit = ArrheniusRateFit.fit(
                 Ts=Ts,
-                ks=ks,
+                ks=k_data,
                 A_fill=A_fill,
-                bad_fit=f,  # pyright: ignore[reportArgumentType]
+                bad_fit=bad_fit,
                 validate=validate,
                 order=order,
                 units=units,
             )
-            for ks, f in zip(np.transpose(k_data), bad_fits, strict=True)
-        ]
+            k_fits.append(k_fit)
+
         k_high_fit = None
         if k_high is not None:
             k_high_fit = ArrheniusRateFit.fit(
@@ -943,9 +949,9 @@ def fit(  # noqa: PLR0913
 
         return cls(
             order=order,
-            As=[f.A for f in k_data_fits],
-            bs=[f.b for f in k_data_fits],
-            Es=[f.E for f in k_data_fits],
+            As=[f.A for f in k_fits],
+            bs=[f.b for f in k_fits],
+            Es=[f.E for f in k_fits],
             Ps=Ps,  # pyright: ignore[reportArgumentType]
         )
 

src/autochem/tests/test__therm.py

@@ -81,10 +81,8 @@ def test__from_chemkin_string(name, spc_str0):
     # Plot
     therm.display(spc)
     therm.display(
-        spc,
-        label="original",
-        others=[spc_times_2, spc_divided_by_2],
-        others_labels=["doubled", "halved"],
+        [spc, spc_times_2, spc_divided_by_2],
+        label=["original","doubled", "halved"]
     )
 
 
@@ -105,7 +103,7 @@ def test__fit(name, spc_str0):
         units={"energy": "kcal"},
     )
     spc_fit = therm.fit(spc)
-    therm.display(spc, label="data", others=[spc_fit], others_labels=["fit"])
+    therm.display([spc, spc_fit], label=["data", "fit"])
 
 
 if __name__ == "__main__":

src/autochem/therm/_species.py

@@ -1,8 +1,9 @@
 """Thermodynamic data."""
 
 import datetime
+import re
 from collections.abc import Sequence
-from typing import ClassVar, Literal
+from typing import ClassVar, Literal, Self
 
 import altair as alt
 import numpy as np
@@ -23,6 +24,17 @@ class Species(Scalable):
     name: str
     therm: Therm_
 
+    def racemize(
+        self, enant_suffixes: tuple[str, str] = ("0", "1"), rac_suffix: str = "R"
+    ) -> Self:
+        """Racemize the thermodynamic functions for a chiral species."""
+        suffix0, suffix1 = enant_suffixes
+        pattern = re.compile(rf"(?:{re.escape(suffix0)}|{re.escape(suffix1)})$")
+        if pattern.search(self.name):
+            self.name = pattern.sub(rac_suffix, self.name)
+            self.therm = self.therm.racemize()
+        return self
+
     # Private attributes
     _scalers: ClassVar[Scalers] = {"therm": (lambda c, x: c * x)}
 
@@ -259,16 +271,17 @@ def fit(
 
 # Display
 def display(  # noqa: PLR0913
-    spc: Species,
+    spc: Species | Sequence[Species],
     *,
     props: Sequence[Literal["Cv", "Cp", "S", "H", "dH"]] = ("Cp", "S", "H"),
-    others: Sequence[Species] = (),
-    others_labels: Sequence[str] = (),
     T_range: tuple[float, float] = (200, 3000),  # noqa: N803
     units: UnitsData | None = None,
-    label: str = "This work",
-    x_label: str = "𝑇",  # noqa: RUF001
+    label: str | Sequence[str] | None = None,
+    color: str | Sequence[str] | None = None,
+    x_label: str = "temperature",
     y_labels: Sequence[str | None] | None = None,
+    x_unit: str | None = "K",
+    y_unit: str | Sequence[str | None] | None = None,
     horizontal: bool = False,
 ) -> alt.Chart:
     """Display as an Arrhenius plot, optionally comparing to other rates.
@@ -284,15 +297,19 @@ def display(  # noqa: PLR0913
     :param y_label: Y-axis label
     :return: Chart
     """
-    return spc.therm.display(
+    spcs = [spc] if isinstance(spc, Species) else spc
+    therms = [s.therm for s in spcs]
+    return data.display(
+        therm_=therms,
         props=props,
-        others=[o.therm for o in others],
-        others_labels=others_labels,
         T_range=T_range,
         units=units,
         label=label,
+        color=color,
         x_label=x_label,
         y_labels=y_labels,
+        x_unit=x_unit,
+        y_unit=y_unit,
         horizontal=horizontal,
     )