Update entropy attribute name from delta_s to delta_sT

src/alchemlyb/estimators/base.py

@@ -1,14 +1,15 @@
 class _EstimatorMixOut:
-    """This class creates view for the d_delta_f_, delta_f_, states_ for the
-    estimator class to consume."""
+    """This class creates view for the attributes: states_, delta_f_, d_delta_f_,
+    delta_h_, d_delta_h_, delta_sT_, d_delta_sT_ for the estimator class to consume.
+    """
 
     _d_delta_f_ = None
     _delta_f_ = None
     _states_ = None
     _d_delta_h_ = None
     _delta_h_ = None
-    _d_delta_s_ = None
-    _delta_s_ = None
+    _d_delta_sT_ = None
+    _delta_sT_ = None
 
     @property
     def d_delta_f_(self):
@@ -27,12 +28,12 @@ def delta_h_(self):
         return self._delta_h_
 
     @property
-    def d_delta_s_(self):
-        return self._d_delta_s_
+    def d_delta_sT_(self):
+        return self._d_delta_sT_
 
     @property
-    def delta_s_(self):
-        return self._delta_s_
+    def delta_sT_(self):
+        return self._delta_sT_
 
     @property
     def states_(self):

src/alchemlyb/estimators/mbar_.py

@@ -64,10 +64,10 @@ class MBAR(BaseEstimator, _EstimatorMixOut):
         The estimated statistical uncertainty (one standard deviation) in
         dimensionless enthalpy differences.
 
-    delta_s_ : DataFrame, optional
+    delta_sT_ : DataFrame, optional
         The estimated dimensionless entropy difference between each state.
 
-    d_delta_s_ : DataFrame
+    d_delta_sT_ : DataFrame
         The estimated statistical uncertainty (one standard deviation) in
         dimensionless entropy differences.
 
@@ -218,10 +218,10 @@ def fit(self, u_nk, compute_entropy_enthalpy=False):
             self._d_delta_h_ = pd.DataFrame(
                 out["dDelta_u"], columns=self._states_, index=self._states_
             )
-            self._delta_s_ = pd.DataFrame(
+            self._delta_sT_ = pd.DataFrame(
                 out["Delta_s"], columns=self._states_, index=self._states_
             )
-            self._d_delta_s_ = pd.DataFrame(
+            self._d_delta_sT_ = pd.DataFrame(
                 out["dDelta_s"], columns=self._states_, index=self._states_
             )
 
@@ -230,8 +230,8 @@ def fit(self, u_nk, compute_entropy_enthalpy=False):
         if compute_entropy_enthalpy:
             self._delta_h_.attrs = u_nk.attrs
             self._d_delta_h_.attrs = u_nk.attrs
-            self._delta_s_.attrs = u_nk.attrs
-            self._d_delta_s_.attrs = u_nk.attrs
+            self._delta_sT_.attrs = u_nk.attrs
+            self._d_delta_sT_.attrs = u_nk.attrs
 
         return self
 

src/alchemlyb/postprocessors/units.py

@@ -18,7 +18,7 @@ def to_kT(df, T=None):
 
     Note that if entropy values are passed it is assumed that they are
     multiplied by the temperature, S * T.
-    
+
     If temperature `T` is not provided, the DataFrame need to have attribute
     `temperature` and `energy_unit`. Otherwise, the temperature of the output
     dateframe will be set accordingly.
@@ -68,7 +68,7 @@ def to_kcalmol(df, T=None):
 
     Note that if entropy values are passed, the result is S * T in units
     of kcal/mol.
-    
+
     If temperature `T` is not provided, the DataFrame need to have attribute
     `temperature` and `energy_unit`. Otherwise, the temperature of the output
     dateframe will be set accordingly.
@@ -96,7 +96,7 @@ def to_kJmol(df, T=None):
 
     Note that if entropy values are passed, the result is S * T in units
     of kJ/mol.
-    
+
     If temperature `T` is not provided, the DataFrame need to have attribute
     `temperature` and `energy_unit`. Otherwise, the temperature of the output
     dateframe will be set accordingly.

src/alchemlyb/tests/test_fep_estimators.py

@@ -209,7 +209,7 @@ def test_enthalpy_entropy_mbar(gmx_benzene_Coulomb_u_nk):
     assert mbar.delta_h_.iloc[0, :].to_numpy() == pytest.approx(
         np.array([0.0, 1.241970, 1.695000, 1.706555, 1.388906]), abs=1e-6
     )
-    assert mbar.delta_s_.iloc[0, :].to_numpy() == pytest.approx(
+    assert mbar.delta_sT_.iloc[0, :].to_numpy() == pytest.approx(
         np.array([0.0, -0.377099, -0.862990, -1.279746, -1.652250]), abs=1e-6
     )
     assert mbar.d_delta_f_.iloc[0, :].to_numpy() == pytest.approx(
@@ -218,7 +218,7 @@ def test_enthalpy_entropy_mbar(gmx_benzene_Coulomb_u_nk):
     assert mbar.d_delta_h_.iloc[0, :].to_numpy() == pytest.approx(
         np.array([0.0, 0.011598, 0.016538, 0.018077, 0.018940]), abs=1e-6
     )
-    assert mbar.d_delta_s_.iloc[0, :].to_numpy() == pytest.approx(
+    assert mbar.d_delta_sT_.iloc[0, :].to_numpy() == pytest.approx(
         np.array([0.0, 0.012242, 0.019519, 0.023606, 0.026107]), abs=1e-6
     )