applied black

MDANSE/Src/MDANSE/Chemistry/ChemicalEntity.py

@@ -182,7 +182,10 @@ def center_of_mass(self, configuration: _Configuration) -> NDArray[np.float64]:
         :rtype: numpy.ndarray
         """
         coords = configuration["coordinates"]
-        masses = [ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight") for at in self.atom_list]
+        masses = [
+            ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight")
+            for at in self.atom_list
+        ]
 
         return center_of_mass(coords, masses)
 
@@ -198,7 +201,10 @@ def mass(self) -> float:
     @property
     def masses(self) -> list[float]:
         """A list of masses of all non-ghost atoms within this chemical entity."""
-        return [ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight") for at in self.atom_list]
+        return [
+            ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight")
+            for at in self.atom_list
+        ]
 
     def find_transformation_as_quaternion(
         self, conf1: _Configuration, conf2: Union[_Configuration, None] = None

MDANSE/Src/MDANSE/Framework/Configurators/AtomSelectionConfigurator.py

@@ -85,7 +85,10 @@ def configure(self, value):
         self["elements"] = [[at.symbol] for at in selectedAtoms]
         self["names"] = [at.symbol for at in selectedAtoms]
         self["unique_names"] = sorted(set(self["names"]))
-        self["masses"] = [[ATOMS_DATABASE.get_atom_property(n, "atomic_weight")] for n in self["names"]]
+        self["masses"] = [
+            [ATOMS_DATABASE.get_atom_property(n, "atomic_weight")]
+            for n in self["names"]
+        ]
         self.error_status = "OK"
 
     def get_natoms(self):

MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py

@@ -120,7 +120,8 @@ def transmutate(self, selection, element):
 
         atomSelConfigurator["unique_names"] = sorted(set(atomSelConfigurator["names"]))
         atomSelConfigurator["masses"] = [
-            [ATOMS_DATABASE.get_atom_property(n, "atomic_weight")] for n in atomSelConfigurator["names"]
+            [ATOMS_DATABASE.get_atom_property(n, "atomic_weight")]
+            for n in atomSelConfigurator["names"]
         ]
         self.error_status = "OK"
 

MDANSE/Src/MDANSE/Framework/Jobs/Density.py

@@ -114,7 +114,12 @@ def run_step(self, index):
         atomic_density = self._n_atoms / cell_volume
 
         mass_density = (
-            sum([ATOMS_DATABASE.get_atom_property(s, "atomic_weight") for s in self._symbols])
+            sum(
+                [
+                    ATOMS_DATABASE.get_atom_property(s, "atomic_weight")
+                    for s in self._symbols
+                ]
+            )
             / NAVOGADRO
             / cell_volume
         )

MDANSE/Src/MDANSE/Framework/Jobs/Eccentricity.py

@@ -196,7 +196,9 @@ def run_step(self, index):
             atomsCoordinates = series[idxs, :]
             difference = atomsCoordinates - com
 
-            w = ATOMS_DATABASE.get_atom_property(name, self.configuration["weights"]["property"])
+            w = ATOMS_DATABASE.get_atom_property(
+                name, self.configuration["weights"]["property"]
+            )
 
             xx += np.add.reduce(
                 w

MDANSE/Src/MDANSE/Framework/Jobs/SolventAccessibleSurface.py

@@ -102,7 +102,10 @@ def initialize(self):
         # A mapping between the atom indexes and covalent_radius radius for the whole universe.
         self.vdwRadii = dict(
             [
-                (at.index, ATOMS_DATABASE.get_atom_property(at.symbol, "covalent_radius"))
+                (
+                    at.index,
+                    ATOMS_DATABASE.get_atom_property(at.symbol, "covalent_radius"),
+                )
                 for at in self.configuration["trajectory"][
                     "instance"
                 ].chemical_system.atom_list

MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py

@@ -25,15 +25,15 @@
 def atomic_scattering_factor(element, qvalues):
     a = np.empty((4,), dtype=np.float64)
     a[0] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_a1")
-    a[1] = ATOMS_DATABASE.get_atom_property(element ,"xray_asf_a2")
-    a[2] = ATOMS_DATABASE.get_atom_property(element ,"xray_asf_a3")
-    a[3] = ATOMS_DATABASE.get_atom_property(element ,"xray_asf_a4")
+    a[1] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_a2")
+    a[2] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_a3")
+    a[3] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_a4")
 
     b = np.empty((4,), dtype=np.float64)
-    b[0] = ATOMS_DATABASE.get_atom_property(element ,"xray_asf_b1")
-    b[1] = ATOMS_DATABASE.get_atom_property(element ,"xray_asf_b2")
-    b[2] = ATOMS_DATABASE.get_atom_property(element ,"xray_asf_b3")
-    b[3] = ATOMS_DATABASE.get_atom_property(element ,"xray_asf_b4")
+    b[0] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_b1")
+    b[1] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_b2")
+    b[2] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_b3")
+    b[3] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_b4")
 
     c = ATOMS_DATABASE.get_atom_property(element, "xray_asf_c")
 

MDANSE/Src/MDANSE/MolecularDynamics/MockTrajectory.py

@@ -351,7 +351,12 @@ def read_com_trajectory(
             last = len(self)
 
         indexes = [at.index for at in atoms]
-        masses = np.array([ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight") for at in atoms])
+        masses = np.array(
+            [
+                ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight")
+                for at in atoms
+            ]
+        )
 
         frames = np.array([self.coordinates(fnum) for fnum in range(first, last, step)])
         coords = frames[:, indexes, :].astype(np.float64)

MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py

@@ -229,7 +229,12 @@ def read_com_trajectory(
             last = len(self)
 
         indexes = [at.index for at in atoms]
-        masses = np.array([ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight") for at in atoms])
+        masses = np.array(
+            [
+                ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight")
+                for at in atoms
+            ]
+        )
         grp = self._h5_file["/configuration"]
 
         coords = grp["coordinates"][first:last:step, :, :].astype(np.float64)
@@ -613,7 +618,9 @@ def __init__(
 
         atoms = chemical_entity.atom_list
 
-        masses = [ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight") for at in atoms]
+        masses = [
+            ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight") for at in atoms
+        ]
 
         mass = sum(masses)
 

MDANSE/Src/MDANSE/MolecularDynamics/TrajectoryUtils.py

@@ -240,7 +240,9 @@ def build_connectivity(
         coords = conf.to_real_coordinates()[indexes, :]
         cov_radii = np.zeros((n_atoms,), dtype=np.float64)
         for i, at in enumerate(atoms):
-            cov_radii[i] = ATOMS_DATABASE.get_atom_property(at.symbol.capitalize(), "covalent_radius")
+            cov_radii[i] = ATOMS_DATABASE.get_atom_property(
+                at.symbol.capitalize(), "covalent_radius"
+            )
 
         bonds = fast_calculation.cpt_cluster_connectivity_nopbc(
             coords, cov_radii, tolerance

MDANSE_GUI/Src/MDANSE_GUI/MolecularViewer/MolecularViewer.py

@@ -141,9 +141,7 @@ def setDataModel(self, datamodel: TrajectoryAtomData):
         self._datamodel = datamodel
 
     def _new_trajectory_object(self, fname: str, data: HDFTrajectoryInputData):
-        reader = hdf5wrapper.HDF5Wrapper(
-            fname, data.trajectory, data.chemical_system
-        )
+        reader = hdf5wrapper.HDF5Wrapper(fname, data.trajectory, data.chemical_system)
         self.set_reader(reader)
 
     @Slot(str)
@@ -577,9 +575,12 @@ def set_coordinates(self, frame: int, tolerance=0.04):
 
         # update the atoms
         coords = self._reader.read_frame(self._current_frame)
-        cov_radii = np.array([
-            CHEMICAL_ELEMENTS.get_atom_property(at, "covalent_radius") for at in self._reader.atom_types
-        ])
+        cov_radii = np.array(
+            [
+                CHEMICAL_ELEMENTS.get_atom_property(at, "covalent_radius")
+                for at in self._reader.atom_types
+            ]
+        )
 
         atoms = vtk.vtkPoints()
         atoms.SetNumberOfPoints(self._n_atoms)
@@ -598,7 +599,7 @@ def set_coordinates(self, frame: int, tolerance=0.04):
                 continue
             diff = coords[i] - coords[idxs]
             dist = np.sum(diff * diff, axis=1)
-            sum_radii = (cov_radii[i] + cov_radii[idxs] + tolerance)**2
+            sum_radii = (cov_radii[i] + cov_radii[idxs] + tolerance) ** 2
             js = np.array(idxs)[(0 < dist) & (dist < sum_radii)]
             for j in js[i < js]:
                 line = vtk.vtkLine()
@@ -621,7 +622,20 @@ def set_coordinates(self, frame: int, tolerance=0.04):
         self._uc_polydata.SetPoints(uc_points)
 
         uc_lines = vtk.vtkCellArray()
-        for i, j in [(0, 1), (0, 2), (0, 3), (1, 4), (1, 5), (4, 7), (2, 4), (2, 6), (5, 7), (3, 5), (3, 6), (6, 7)]:
+        for i, j in [
+            (0, 1),
+            (0, 2),
+            (0, 3),
+            (1, 4),
+            (1, 5),
+            (4, 7),
+            (2, 4),
+            (2, 6),
+            (5, 7),
+            (3, 5),
+            (3, 6),
+            (6, 7),
+        ]:
             line = vtk.vtkLine()
             line.GetPointIds().SetId(0, i)
             line.GetPointIds().SetId(1, j)
@@ -664,7 +678,10 @@ def set_reader(self, reader, frame=0):
         # this returs a list of indices, mapping colours to atoms
 
         self._atom_scales = np.array(
-            [CHEMICAL_ELEMENTS.get_atom_property(at, "vdw_radius") for at in self._atoms]
+            [
+                CHEMICAL_ELEMENTS.get_atom_property(at, "vdw_radius")
+                for at in self._atoms
+            ]
         ).astype(np.float32)
 
         scalars = ndarray_to_vtkarray(

MDANSE_GUI/Src/MDANSE_GUI/Tabs/JobTab.py

@@ -69,7 +69,9 @@ def set_current_trajectory(self, new_name: str) -> None:
         )
         # The combobox was changed we need to update the action
         # widgets with the new trajectory
-        self.action.set_trajectory(path=None, trajectory=traj_model._nodes[node_number][0])
+        self.action.set_trajectory(
+            path=None, trajectory=traj_model._nodes[node_number][0]
+        )
         current_item = self._core.current_item()
         if current_item is not None:
             # we only update the widget if a job is selected from the