Add regression test analysis (#69)

SimonBoothroyd · Jan 16, 2024 · 7cdd5c8 · 7cdd5c8
1 parent ff1c8ba
commit 7cdd5c8
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Showing 7 changed files with 861 additions and 3,743 deletions.
diff --git a/absolv/config.py b/absolv/config.py
@@ -1,5 +1,4 @@
 """Configure free energy calculations."""
-import math
 import typing
 
 import femto.md.config
@@ -355,28 +354,3 @@ class Result(pydantic.BaseModel):
     dg_std_solvent_b: OpenMMQuantity[KCAL_MOL] = pydantic.Field(
         description="The standard error in ``dg_solvent_b``."
     )
-
-    @property
-    def dg(self) -> openmm.unit.Quantity:
-        """The change in free energy of transferring the solute from *solvent-a* to
-        *solvent-b* in units of kT."""
-        return self.dg_solvent_b - self.dg_solvent_a
-
-    @property
-    def dg_std(self) -> openmm.unit.Quantity:
-        """The standard error in ``ddg``."""
-
-        std = math.sqrt(
-            self.dg_std_solvent_a.value_in_unit(KCAL_MOL) ** 2
-            + self.dg_std_solvent_b.value_in_unit(KCAL_MOL) ** 2
-        )
-        return std * KCAL_MOL
-
-    def __str__(self):
-        return (
-            f"ΔG a->b={self.dg.value_in_unit(KCAL_MOL):.3f} kcal/mol "
-            f"ΔG a->b std={self.dg_std.value_in_unit(KCAL_MOL):.3f} kcal/mol"
-        )
-
-    def __repr__(self):
-        return f"{self.__repr_name__()}({self.__str__()})"
diff --git a/absolv/setup.py b/absolv/setup.py
@@ -118,9 +118,6 @@ def setup_system(
         tolerance: The minimum spacing between molecules during packing in units
              compatible with angstroms.
 
-    Raises:
-        * PACKMOLRuntimeError
-
     Returns:
         A topology containing the molecules the coordinates were generated for and
         a unit [A] wrapped numpy array of coordinates with shape=(n_atoms, 3).

diff --git a/absolv/tests/test_config.py b/absolv/tests/test_config.py
@@ -1,10 +1,7 @@
-import math
-
-import openmm.unit
 import pydantic
 import pytest
 
-from absolv.config import EquilibriumProtocol, Result, System
+from absolv.config import EquilibriumProtocol, System
 
 
 class TestSystem:
@@ -80,26 +77,3 @@ def test_validate_lambda_lengths(self, lambda_sterics, lambda_electrostatics):
                 lambda_sterics=lambda_sterics,
                 lambda_electrostatics=lambda_electrostatics,
             )
-
-
-class TestResult:
-    @pytest.fixture
-    def mock_result(self):
-        return Result(
-            dg_solvent_a=1.0 * openmm.unit.kilocalorie_per_mole,
-            dg_std_solvent_a=0.2 * openmm.unit.kilocalorie_per_mole,
-            dg_solvent_b=3.0 * openmm.unit.kilocalorie_per_mole,
-            dg_std_solvent_b=0.4 * openmm.unit.kilocalorie_per_mole,
-        )
-
-    def test_dg(self, mock_result):
-        assert mock_result.dg == pytest.approx(2.0) * openmm.unit.kilocalorie_per_mole
-        assert (
-            mock_result.dg_std
-            == pytest.approx(math.sqrt(0.2**2 + 0.4**2))
-            * openmm.unit.kilocalorie_per_mole
-        )
-
-    def test_repr(self, mock_result):
-        assert repr(mock_result) is not None
-        assert str(mock_result) is not None