Trajectory tab and 3D view updates.

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[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[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
@@ -320,7 +326,7 @@ def center_and_moment_of_inertia(
         mr = Vector(0.0, 0.0, 0.0)
         t = Tensor(3 * [3 * [0.0]])
         for atom in self.atom_list:
-            ma = ATOMS_DATABASE[atom.symbol]["atomic_weight"]
+            ma = ATOMS_DATABASE.get_atom_property(atom.symbol, "atomic_weight")
             r = Vector(configuration["coordinates"][atom.index, :])
             m += ma
             mr += ma * r
@@ -473,7 +479,7 @@ def __init__(
 
         self._parent = None
 
-        self.element = ATOMS_DATABASE[self._symbol]["element"]
+        self.element = ATOMS_DATABASE.get_atom_property(self._symbol, "element")
 
         for k, v in kwargs.items():
             try:
@@ -2460,7 +2466,7 @@ def add_chemical_entity(self, chemical_entity: _ChemicalEntity) -> None:
 
             # add the atoms to the rdkit molecule, ghost atoms are
             # never added to the rdkit molecule object
-            atm_num = ATOMS_DATABASE[at.symbol]["atomic_number"]
+            atm_num = ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_number")
             rdkit_atm = Chem.Atom(atm_num)
 
             # makes sure that rdkit doesn't add extra hydrogens

MDANSE/Src/MDANSE/Chemistry/Databases.py

@@ -589,6 +589,24 @@ def save(self) -> None:
         with open(AtomsDatabase._USER_DATABASE, "w") as fout:
             json.dump(d, fout)
 
+    def get_atom_property(self, symbol: str, property: str) -> Union[int, float, str]:
+        """Faster access to the atom property as it avoids the deepcopy
+        in __getitem__.
+
+        Parameters
+        ----------
+        symbol : str
+            Symbol of the atom.
+        property : str
+            Property of the atoms to get.
+
+        Returns
+        -------
+        Union[int, float, str]
+            The atom property.
+        """
+        return self._data[symbol][property]
+
 
 class MoleculesDatabaseError(Error):
     """This class handles the exceptions related to MoleculesDatabase"""

MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py

@@ -65,10 +65,10 @@ def guess_element(atm_label: str, mass: Union[float, int, None] = None) -> str:
         if guess in ATOMS_DATABASE:
             if mass is None:
                 return guess
-            num = ATOMS_DATABASE[guess]["proton"]
+            num = ATOMS_DATABASE.get_atom_property(guess, "proton")
             atms = ATOMS_DATABASE.match_numeric_property("proton", num)
             for atm in atms:
-                atm_mass = ATOMS_DATABASE[atm]["atomic_weight"]
+                atm_mass = ATOMS_DATABASE.get_atom_property(atm, "atomic_weight")
                 diff = abs(mass - atm_mass)
                 if diff < best_diff:
                     best_match = atm

MDANSE/Src/MDANSE/Framework/AtomSelector/atom_selectors.py

@@ -30,7 +30,7 @@ def select_element(
     Union[set[int], bool]
         The atom indices of the matched atoms.
     """
-    pattern = f"[#{ATOMS_DATABASE[symbol]['atomic_number']}]"
+    pattern = f"[#{ATOMS_DATABASE.get_atom_property(symbol, 'atomic_number')}]"
     if check_exists:
         return system.has_substructure_match(pattern)
     else:
@@ -56,7 +56,7 @@ def select_hs_on_element(
     Union[set[int], bool]
         The atom indices of the matched atoms.
     """
-    num = ATOMS_DATABASE[symbol]["atomic_number"]
+    num = ATOMS_DATABASE.get_atom_property(symbol, "atomic_number")
     if check_exists:
         return system.has_substructure_match(f"[#{num}]~[H]")
     else:

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[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[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/Configurators/WeightsConfigurator.py

@@ -73,7 +73,7 @@ def get_weights(self):
         for i in range(ascfg["selection_length"]):
             name = ascfg["names"][i]
             for el in ascfg["elements"][i]:
-                p = ATOMS_DATABASE[el][self["property"]]
+                p = ATOMS_DATABASE.get_atom_property(el, self["property"])
                 if name in weights:
                     weights[name] += p
                 else:

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[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

@@ -160,7 +160,7 @@ def initialize(self):
         self._selectionTotalMass = np.sum(self._selectionMasses)
 
         self._comMasses = [
-            ATOMS_DATABASE[self._atoms[idx].symbol]["atomic_weight"]
+            ATOMS_DATABASE.get_atom_property(self._atoms[idx].symbol, "atomic_weight")
             for idx in self._comIndexes
         ]
 
@@ -196,7 +196,9 @@ def run_step(self, index):
             atomsCoordinates = series[idxs, :]
             difference = atomsCoordinates - com
 
-            w = ATOMS_DATABASE[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/McStasVirtualInstrument.py

@@ -125,18 +125,18 @@ def initialize(self):
         # Compute some parameters used for a proper McStas run
         self._mcStasPhysicalParameters = {"density": 0.0}
         self._mcStasPhysicalParameters["weight"] = sum(
-            [ATOMS_DATABASE[s]["atomic_weight"] for s in symbols]
+            [ATOMS_DATABASE.get_atom_property(s, "atomic_weight") for s in symbols]
         )
         self._mcStasPhysicalParameters["sigma_abs"] = (
-            sum([ATOMS_DATABASE[s]["xs_absorption"] for s in symbols])
+            sum([ATOMS_DATABASE.get_atom_property(s, "xs_absorption") for s in symbols])
             * MCSTAS_UNITS_LUT["nm2"]
         )
         self._mcStasPhysicalParameters["sigma_coh"] = (
-            sum([ATOMS_DATABASE[s]["xs_coherent"] for s in symbols])
+            sum([ATOMS_DATABASE.get_atom_property(s, "xs_coherent") for s in symbols])
             * MCSTAS_UNITS_LUT["nm2"]
         )
         self._mcStasPhysicalParameters["sigma_inc"] = (
-            sum([ATOMS_DATABASE[s]["xs_incoherent"] for s in symbols])
+            sum([ATOMS_DATABASE.get_atom_property(s, "xs_incoherent") for s in symbols])
             * MCSTAS_UNITS_LUT["nm2"]
         )
         for frameIndex in self.configuration["frames"]["value"]:

MDANSE/Src/MDANSE/Framework/Jobs/NeutronDynamicTotalStructureFactor.py

@@ -447,8 +447,8 @@ def finalize(self):
 
         # Compute coherent functions and structure factor
         for pair in self._elementsPairs:
-            bi = ATOMS_DATABASE[pair[0]]["b_coherent"]
-            bj = ATOMS_DATABASE[pair[1]]["b_coherent"]
+            bi = ATOMS_DATABASE.get_atom_property(pair[0], "b_coherent")
+            bj = ATOMS_DATABASE.get_atom_property(pair[1], "b_coherent")
             ni = nAtomsPerElement[pair[0]]
             nj = nAtomsPerElement[pair[1]]
             ci = ni / nTotalAtoms
@@ -483,7 +483,7 @@ def finalize(self):
 
         # Compute incoherent functions and structure factor
         for element, ni in nAtomsPerElement.items():
-            bi = ATOMS_DATABASE[element]["b_incoherent2"]
+            bi = ATOMS_DATABASE.get_atom_property(element, "b_incoherent2")
             ni = nAtomsPerElement[element]
             ci = ni / nTotalAtoms
 

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[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/Temperature.py

@@ -115,7 +115,7 @@ def run_step(self, index):
 
         symbol = atom.symbol
 
-        mass = ATOMS_DATABASE[symbol]["atomic_weight"]
+        mass = ATOMS_DATABASE.get_atom_property(symbol, "atomic_weight")
 
         trajectory = self.configuration["trajectory"]["instance"]
 

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

@@ -24,18 +24,18 @@
 
 def atomic_scattering_factor(element, qvalues):
     a = np.empty((4,), dtype=np.float64)
-    a[0] = ATOMS_DATABASE[element]["xray_asf_a1"]
-    a[1] = ATOMS_DATABASE[element]["xray_asf_a2"]
-    a[2] = ATOMS_DATABASE[element]["xray_asf_a3"]
-    a[3] = ATOMS_DATABASE[element]["xray_asf_a4"]
+    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")
 
     b = np.empty((4,), dtype=np.float64)
-    b[0] = ATOMS_DATABASE[element]["xray_asf_b1"]
-    b[1] = ATOMS_DATABASE[element]["xray_asf_b2"]
-    b[2] = ATOMS_DATABASE[element]["xray_asf_b3"]
-    b[3] = ATOMS_DATABASE[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[element]["xray_asf_c"]
+    c = ATOMS_DATABASE.get_atom_property(element, "xray_asf_c")
 
     return c + np.sum(
         a[:, np.newaxis]

MDANSE/Src/MDANSE/Mathematics/Graph.py

@@ -56,11 +56,12 @@ def build_connected_components(self):
 
         # Make a copy of the set, so we can modify it.
         nodes = [self._nodes[k] for k in sorted(self._nodes.keys())]
+        nodes.reverse()
 
         # Iterate while we still have nodes to process.
         while nodes:
             # Get a random node and remove it from the global set.
-            n = nodes.pop(0)
+            n = nodes.pop()
 
             # This set will contain the next group of nodes connected to each other.
             group = set([n])

MDANSE/Src/MDANSE/MolecularDynamics/Connectivity.py

@@ -49,7 +49,7 @@ def check_composition(self, chemical: ChemicalSystem):
         atom_elements = [atom.symbol for atom in chemical.atoms]
         unique_elements = np.unique(atom_elements)
         radii = {
-            element: ATOMS_DATABASE[element]["covalent_radius"]
+            element: ATOMS_DATABASE.get_atom_property(element, "covalent_radius")
             for element in unique_elements
         }
         self._elements = atom_elements

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[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

@@ -77,8 +77,6 @@ def __init__(self, h5_filename):
         # Define a default name for all chemical entities which have no name
         resolve_undefined_molecules_name(self._chemical_system)
 
-        # Retrieve the connectivity
-        build_connectivity(self._chemical_system)
         ic("Trajectory.__init__ ended")
 
     def close(self):
@@ -231,7 +229,12 @@ def read_com_trajectory(
             last = len(self)
 
         indexes = [at.index for at in atoms]
-        masses = np.array([ATOMS_DATABASE[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)
@@ -615,7 +618,9 @@ def __init__(
 
         atoms = chemical_entity.atom_list
 
-        masses = [ATOMS_DATABASE[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[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