diff --git a/MDANSE/Src/MDANSE/Chemistry/ChemicalEntity.py b/MDANSE/Src/MDANSE/Chemistry/ChemicalEntity.py index ef2f1e40b7..cf6db7df76 100644 --- a/MDANSE/Src/MDANSE/Chemistry/ChemicalEntity.py +++ b/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 diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/AtomSelectionConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/AtomSelectionConfigurator.py index 80336b5709..99a4509dc2 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/AtomSelectionConfigurator.py +++ b/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): diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py index 1aa5bd3fbc..11525dcaee 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py +++ b/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" diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/Density.py b/MDANSE/Src/MDANSE/Framework/Jobs/Density.py index 60ea566862..22df95e6b7 100644 --- a/MDANSE/Src/MDANSE/Framework/Jobs/Density.py +++ b/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 ) diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/Eccentricity.py b/MDANSE/Src/MDANSE/Framework/Jobs/Eccentricity.py index 75a78a300b..4cdfc7bee0 100644 --- a/MDANSE/Src/MDANSE/Framework/Jobs/Eccentricity.py +++ b/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 diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/SolventAccessibleSurface.py b/MDANSE/Src/MDANSE/Framework/Jobs/SolventAccessibleSurface.py index 06f1b93c47..46cf110393 100644 --- a/MDANSE/Src/MDANSE/Framework/Jobs/SolventAccessibleSurface.py +++ b/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 diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py b/MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py index 911ee829a9..3a6db723ff 100644 --- a/MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py +++ b/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") diff --git a/MDANSE/Src/MDANSE/MolecularDynamics/MockTrajectory.py b/MDANSE/Src/MDANSE/MolecularDynamics/MockTrajectory.py index e71bb450bb..edb966acf2 100644 --- a/MDANSE/Src/MDANSE/MolecularDynamics/MockTrajectory.py +++ b/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) diff --git a/MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py b/MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py index deda844373..e660f2f351 100644 --- a/MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py +++ b/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) diff --git a/MDANSE/Src/MDANSE/MolecularDynamics/TrajectoryUtils.py b/MDANSE/Src/MDANSE/MolecularDynamics/TrajectoryUtils.py index 5261b0243f..4e80587586 100644 --- a/MDANSE/Src/MDANSE/MolecularDynamics/TrajectoryUtils.py +++ b/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 diff --git a/MDANSE_GUI/Src/MDANSE_GUI/MolecularViewer/MolecularViewer.py b/MDANSE_GUI/Src/MDANSE_GUI/MolecularViewer/MolecularViewer.py index 12646619b4..e7a8107038 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/MolecularViewer/MolecularViewer.py +++ b/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( diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/JobTab.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/JobTab.py index ddda4597c1..77d22b6e07 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/JobTab.py +++ b/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