reformatted with black

MDAnalysis · May 23, 2024 · 56c792e · 56c792e
1 parent e569863
commit 56c792e
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Showing 5 changed files with 175 additions and 114 deletions.
diff --git a/mdgeom/distances.py b/mdgeom/distances.py
@@ -59,6 +59,7 @@ def minimage_distance(a, b):
     d = calc_bonds(a, b, box=a.dimensions)
     return d
 
+
 def minimage_difference_vector(a, b):
     r"""Calculate the minimum image difference vector r_a - r_b
 
@@ -120,9 +121,7 @@ def _check_groups(a, b):
     if a.dimensions is None and b.dimensions is None:
         # it's ok when both AtomGroups have no unitcell
         pass
-    elif (a.dimensions is None) != (b.dimensions is None): # xor
+    elif (a.dimensions is None) != (b.dimensions is None):  # xor
         raise ValueError("One AtomGroup does not have unit cell information")
     elif not np.allclose(a.dimensions, b.dimensions):
         raise ValueError("Unit cell dimensions differ between groups.")
-
-
diff --git a/mdgeom/info.py b/mdgeom/info.py
@@ -24,28 +24,49 @@ def summary(*universes, labels=None):
         There needs to be one element on `labels` for each universe.
 
     """
-    data_column_keys  = ["n_atoms", "Lx", "Ly", "Lz", "alpha", "beta", "gamma",
-                         "n_frames", "totaltime", "dt"]
-    data_column_names = ["n_atoms", "Lx/Å", "Ly/Å", "Lz/Å", "alpha", "beta", "gamma",
-                         "n_frames", "totaltime/ns", "dt/ps"]
+    data_column_keys = [
+        "n_atoms",
+        "Lx",
+        "Ly",
+        "Lz",
+        "alpha",
+        "beta",
+        "gamma",
+        "n_frames",
+        "totaltime",
+        "dt",
+    ]
+    data_column_names = [
+        "n_atoms",
+        "Lx/Å",
+        "Ly/Å",
+        "Lz/Å",
+        "alpha",
+        "beta",
+        "gamma",
+        "n_frames",
+        "totaltime/ns",
+        "dt/ps",
+    ]
 
     if len(labels) != len(universes):
-        raise ValueError(f"labels {labels} must contain one "
-                         f"label per universe {universes}")
+        raise ValueError(
+            f"labels {labels} must contain one "
+            f"label per universe {universes}"
+        )
 
     if labels is None:
         labels = len(universes) * [None]
         column_names = data_column_names
     else:
         column_names = ["simulation"] + data_column_names
 
-
     table = prettytable.PrettyTable()
     table.field_names = column_names
 
     for u, label in zip(universes, labels):
         data = extract(u)
-        data['totaltime'] /= 1000 # convert ps to ns
+        data["totaltime"] /= 1000  # convert ps to ns
         row = [data[key] for key in data_column_keys]
         if label is not None:
             row = [label] + row
@@ -82,17 +103,17 @@ def extract(u):
         Lx, Ly, Lz, alpha, beta, gamma = u.dimensions
     except TypeError:
         # universe without a regular box
-        Lx, Ly, Lz, alpha, beta, gamma = 0, 0, 0,  0, 0, 0
+        Lx, Ly, Lz, alpha, beta, gamma = 0, 0, 0, 0, 0, 0
     data = {
-        'n_atoms': u.atoms.n_atoms,
-        'Lx': Lx, 'Ly': Ly, 'Lz': Lz,
-        'alpha': alpha, 'beta': beta, 'gamma': gamma,
-        'n_frames': u.trajectory.n_frames,
-        'totaltime': u.trajectory.totaltime,
-        'dt': u.trajectory.dt,
+        "n_atoms": u.atoms.n_atoms,
+        "Lx": Lx,
+        "Ly": Ly,
+        "Lz": Lz,
+        "alpha": alpha,
+        "beta": beta,
+        "gamma": gamma,
+        "n_frames": u.trajectory.n_frames,
+        "totaltime": u.trajectory.totaltime,
+        "dt": u.trajectory.dt,
     }
     return data
-
-
-
-
diff --git a/mdgeom/tests/test_distances.py b/mdgeom/tests/test_distances.py
@@ -9,7 +9,8 @@
 fret_pairs = [
     ("resname ALA and resid 55", "resname VAL and resid 169"),
     ("resname ALA and resid 127", "resname ALA and resid 194"),
-    ("resname ILE and resid 52", "resname LYS* and resid 145")]
+    ("resname ILE and resid 52", "resname LYS* and resid 145"),
+]
 
 
 @pytest.fixture
@@ -30,6 +31,7 @@ def u_pbc():
 # Tests for distances.minimage_distance()
 #
 
+
 def _minimage_distance(u):
     # helper function
     a = sum(u.select_atoms(pair[0] + " and name CA") for pair in fret_pairs)
@@ -39,11 +41,13 @@ def _minimage_distance(u):
 
     return r
 
+
 def test_minimage_distance_nopbc(u_nopbc):
     reference = np.array([12.91501288, 30.57278011, 28.92306815])
     r = _minimage_distance(u_nopbc)
     assert_allclose(r, reference)
 
+
 def test_minimage_distance_pbc(u_pbc):
     reference = np.array([29.67992244, 38.36642607, 42.18877151])
     r = _minimage_difference_vector(u_pbc)
@@ -54,6 +58,7 @@ def test_minimage_distance_pbc(u_pbc):
 # Tests for distances.minimage_difference_vector()
 #
 
+
 def _minimage_difference_vector(u):
     # helper function
     a = sum(u.select_atoms(pair[0] + " and name CA") for pair in fret_pairs)
@@ -66,18 +71,23 @@ def _minimage_difference_vector(u):
 
 def test_minimage_difference_vector_nopbc(u_nopbc):
     reference = np.array(
-        [[ -6.7521524,  -7.5131125,  -8.047306 ],
-         [-21.687479 , -15.805498 , -14.646992 ],
-         [ 16.235527 , -19.996527 ,  13.156384 ]])
+        [
+            [-6.7521524, -7.5131125, -8.047306],
+            [-21.687479, -15.805498, -14.646992],
+            [16.235527, -19.996527, 13.156384],
+        ]
+    )
     r = _minimage_difference_vector(u_nopbc)
     assert_allclose(r, reference)
 
 
 def test_minimage_difference_vector_pbc(u_pbc):
     reference = np.array(
-        [[-11.659996 ,   8.610001 ,  25.900003 ],
-         [ -9.439999 ,  37.177002 ,   0.8600006],
-         [-31.1585   ,  21.841507 , -18.220566 ]])
+        [
+            [-11.659996, 8.610001, 25.900003],
+            [-9.439999, 37.177002, 0.8600006],
+            [-31.1585, 21.841507, -18.220566],
+        ]
+    )
     r = _minimage_difference_vector(u_pbc)
     assert_allclose(r, reference)
-