Linted files with black

paprika/analysis/analysis.py

@@ -1272,11 +1272,11 @@ def compute_free_energy(self, phases=["attach", "pull", "release"], seed=None):
                         phase
                     ][method]["fraction_fe_matrix"][fraction][0, -1]
 
-                    self.results[phase][method]["fraction_sem"][
-                        fraction
-                    ] = self.results[phase][method]["fraction_sem_matrix"][fraction][
-                        0, -1
-                    ]
+                    self.results[phase][method]["fraction_sem"][fraction] = (
+                        self.results[phase][method]["fraction_sem_matrix"][fraction][
+                            0, -1
+                        ]
+                    )
 
                 # Set these higher level (total) values, which will be slightly
                 # easier to access
@@ -1298,23 +1298,23 @@ def compute_free_energy(self, phases=["attach", "pull", "release"], seed=None):
                     # Store convergence values, which are helpful for running
                     # simulations
                     windows = len(self.results[phase][method]["sem_matrix"])
-                    self.results[phase][method][
-                        "largest_neighbor"
-                    ] = openff_unit.Quantity(
-                        np.ones([windows], np.float64) * -1.0,
-                        units=self.energy_unit,
+                    self.results[phase][method]["largest_neighbor"] = (
+                        openff_unit.Quantity(
+                            np.ones([windows], np.float64) * -1.0,
+                            units=self.energy_unit,
+                        )
                     )
                     logger.info(f"{phase}: computing largest_neighbor for {method}...")
 
                     for i in range(windows):
                         if i == 0:
-                            self.results[phase][method]["largest_neighbor"][
-                                i
-                            ] = self.results[phase][method]["sem_matrix"][i][i + 1]
+                            self.results[phase][method]["largest_neighbor"][i] = (
+                                self.results[phase][method]["sem_matrix"][i][i + 1]
+                            )
                         elif i == windows - 1:
-                            self.results[phase][method]["largest_neighbor"][
-                                i
-                            ] = self.results[phase][method]["sem_matrix"][i][i - 1]
+                            self.results[phase][method]["largest_neighbor"][i] = (
+                                self.results[phase][method]["sem_matrix"][i][i - 1]
+                            )
                         else:
                             left = self.results[phase][method]["sem_matrix"][i][i - 1]
                             right = self.results[phase][method]["sem_matrix"][i][i + 1]

paprika/restraints/openmm.py

@@ -1,4 +1,5 @@
 """A module aimed at applying restraints directly to OpenMM systems."""
+
 import logging
 
 import numpy as np
@@ -67,11 +68,7 @@ def apply_positional_restraints(
             # But then we can't access atom indices. Using `atom.xx` works for
             # coordinates, but is unitless.
             if isinstance(k_pos, float):
-                k = (
-                    k_pos
-                    * openmm_unit.kilocalories_per_mole
-                    / openmm_unit.angstroms**2
-                )
+                k = k_pos * openmm_unit.kilocalories_per_mole / openmm_unit.angstroms**2
             elif isinstance(k_pos, openmm_unit.Quantity):
                 k = k_pos
             elif isinstance(k_pos, openff_unit.Quantity):

paprika/restraints/restraints.py

@@ -612,9 +612,9 @@ def initialize(self):
                 if phase[key] is not None:
                     phase[key] = check_unit(
                         phase[key],
-                        base_unit=target_unit
-                        if key == "target"
-                        else force_constant_unit,
+                        base_unit=(
+                            target_unit if key == "target" else force_constant_unit
+                        ),
                     )
 
         # Check pull units
@@ -637,9 +637,11 @@ def initialize(self):
                 if key in self._custom_restraint_values:
                     self._custom_restraint_values[key] = check_unit(
                         self._custom_restraint_values[key],
-                        base_unit=force_constant_unit
-                        if key in ["rk2", "rk3"]
-                        else target_unit,
+                        base_unit=(
+                            force_constant_unit
+                            if key in ["rk2", "rk3"]
+                            else target_unit
+                        ),
                     )
                 else:
                     self._custom_restraint_values[key] = None

paprika/tests/test_evaluator.py

@@ -1,6 +1,7 @@
 """
 Tests evaluator modules.
 """
+
 import logging
 import os
 import shutil

paprika/tests/test_io.py

@@ -1,6 +1,7 @@
 """
 Test that we can save and load restraints as JSON.
 """
+
 import os
 import shutil
 

paprika/tests/test_restraints.py

@@ -1,6 +1,7 @@
 """
 Tests the restraints utilities.
 """
+
 import logging
 import os
 
@@ -134,9 +135,7 @@ def test_DAT_restraint():
     rest2.initialize()
 
     target_units = openff_unit.degrees
-    force_constant_units = (
-        openff_unit.kcal / openff_unit.mole / openff_unit.radians**2
-    )
+    force_constant_units = openff_unit.kcal / openff_unit.mole / openff_unit.radians**2
     assert rest2.restraint_type == RestraintType.Angle
     assert rest2.index1 == [13, 31, 49, 67, 85, 103]
     assert rest2.index2 == [119]
@@ -205,9 +204,7 @@ def test_DAT_restraint():
     rest3.initialize()
 
     target_units = openff_unit.degrees
-    force_constant_units = (
-        openff_unit.kcal / openff_unit.mole / openff_unit.radians**2
-    )
+    force_constant_units = openff_unit.kcal / openff_unit.mole / openff_unit.radians**2
     assert rest3.restraint_type == RestraintType.Torsion
     assert rest3.index1 == [31]
     assert rest3.index2 == [13]
@@ -278,9 +275,7 @@ def test_DAT_restraint():
     rest4.initialize()
 
     target_units = openff_unit.degrees
-    force_constant_units = (
-        openff_unit.kcal / openff_unit.mole / openff_unit.radians**2
-    )
+    force_constant_units = openff_unit.kcal / openff_unit.mole / openff_unit.radians**2
     assert rest4.index1 == [31]
     assert rest4.index2 == [13]
     assert rest4.index3 == [119]
@@ -348,9 +343,7 @@ def test_DAT_restraint():
     rest5.initialize()
 
     target_units = openff_unit.angstrom
-    force_constant_units = (
-        openff_unit.kcal / openff_unit.mole / openff_unit.angstrom**2
-    )
+    force_constant_units = openff_unit.kcal / openff_unit.mole / openff_unit.angstrom**2
     assert rest5.index1 == [13, 31, 49, 67, 85, 103]
     assert rest5.index2 == [109, 113, 115, 119]
     assert rest5.index3 is None
@@ -417,9 +410,7 @@ def test_DAT_restraint():
     rest6.initialize()
 
     target_units = openff_unit.angstrom
-    force_constant_units = (
-        openff_unit.kcal / openff_unit.mole / openff_unit.angstrom**2
-    )
+    force_constant_units = openff_unit.kcal / openff_unit.mole / openff_unit.angstrom**2
     assert rest6.index1 == [13, 31, 49, 67, 85, 103]
     assert rest6.index2 == [109, 113, 115, 119]
     assert rest6.index3 is None
@@ -484,9 +475,7 @@ def test_DAT_restraint():
     rest7.initialize()
 
     target_units = openff_unit.angstrom
-    force_constant_units = (
-        openff_unit.kcal / openff_unit.mole / openff_unit.angstrom**2
-    )
+    force_constant_units = openff_unit.kcal / openff_unit.mole / openff_unit.angstrom**2
     assert rest7.index1 == [13, 14, 111]
     assert rest7.index2 == [3]
     assert rest7.index3 is None
@@ -547,9 +536,7 @@ def test_DAT_restraint():
     rest8.initialize()
 
     target_units = openff_unit.angstrom
-    force_constant_units = (
-        openff_unit.kcal / openff_unit.mole / openff_unit.angstrom**2
-    )
+    force_constant_units = openff_unit.kcal / openff_unit.mole / openff_unit.angstrom**2
     assert rest8.index1 == [13]
     assert rest8.index2 == [119]
     assert rest8.index3 is None
@@ -587,9 +574,7 @@ def test_DAT_restraint():
     rest9.initialize()
 
     target_units = openff_unit.angstrom
-    force_constant_units = (
-        openff_unit.kcal / openff_unit.mole / openff_unit.angstrom**2
-    )
+    force_constant_units = openff_unit.kcal / openff_unit.mole / openff_unit.angstrom**2
     assert rest9.index1 == [13]
     assert rest9.index2 == [119]
     assert rest9.index3 is None
@@ -627,9 +612,7 @@ def test_DAT_restraint():
     rest10.initialize()
 
     target_units = openff_unit.angstrom
-    force_constant_units = (
-        openff_unit.kcal / openff_unit.mole / openff_unit.angstrom**2
-    )
+    force_constant_units = openff_unit.kcal / openff_unit.mole / openff_unit.angstrom**2
     assert rest10.index1 == [13]
     assert rest10.index2 == [119]
     assert rest10.index3 is None

paprika/tests/test_tleap.py

@@ -1,6 +1,7 @@
 """
 Tests tleap tools.
 """
+
 import logging
 import os
 import random as random