Save selection as array of bool values

MDANSE/Src/MDANSE/Framework/AtomSelector/atom_selection.py

@@ -20,7 +20,9 @@
 from MDANSE.MolecularDynamics.Trajectory import Trajectory
 
 
-def select_atoms(trajectory: Trajectory, **function_parameters: Dict[str, Any]) -> Set[int]:
+def select_atoms(
+    trajectory: Trajectory, **function_parameters: Dict[str, Any]
+) -> Set[int]:
     """Selects all the atoms in the trajectory.
 
     Parameters
@@ -46,7 +48,9 @@ def select_atoms(trajectory: Trajectory, **function_parameters: Dict[str, Any])
     if index_list is not None:
         selection = selection.union(indices.intersection(index_list))
     if index_range is not None:
-        selection = selection.union(indices.intersection(range(index_range[0], index_range[1])))
+        selection = selection.union(
+            indices.intersection(range(index_range[0], index_range[1]))
+        )
     if index_slice is not None:
         selection = selection.union(
             indices.intersection(range(index_slice[0], index_slice[1], index_slice[2]))

MDANSE/Src/MDANSE/Framework/AtomSelector/general_selection.py

@@ -19,7 +19,9 @@
 from MDANSE.MolecularDynamics.Trajectory import Trajectory
 
 
-def select_all(trajectory: Trajectory, **function_parameters: Dict[str, Any]) -> Set[int]:
+def select_all(
+    trajectory: Trajectory, **function_parameters: Dict[str, Any]
+) -> Set[int]:
     """Selects all the atoms in the trajectory.
 
     Parameters
@@ -37,7 +39,9 @@ def select_all(trajectory: Trajectory, **function_parameters: Dict[str, Any]) ->
     return set(range(len(trajectory.chemical_system.atom_list)))
 
 
-def select_none(trajectory: Trajectory, **function_parameters: Dict[str, Any]) -> Set[int]:
+def select_none(
+    trajectory: Trajectory, **function_parameters: Dict[str, Any]
+) -> Set[int]:
     """Returns an empty selection.
 
     Parameters

MDANSE/Src/MDANSE/Framework/AtomSelector/group_selection.py

@@ -21,7 +21,9 @@
 from MDANSE.MolecularDynamics.Trajectory import Trajectory
 
 
-def select_labels(trajectory: Trajectory, **function_parameters: Dict[str, Any]) -> Set[int]:
+def select_labels(
+    trajectory: Trajectory, **function_parameters: Dict[str, Any]
+) -> Set[int]:
     """Selects all the atoms in the trajectory.
 
     Parameters
@@ -45,7 +47,9 @@ def select_labels(trajectory: Trajectory, **function_parameters: Dict[str, Any])
     return selection
 
 
-def select_pattern(trajectory: Trajectory, **function_parameters: Dict[str, Any]) -> Set[int]:
+def select_pattern(
+    trajectory: Trajectory, **function_parameters: Dict[str, Any]
+) -> Set[int]:
     """Selects all the atoms in the trajectory.
 
     Parameters

MDANSE/Src/MDANSE/Framework/AtomSelector/molecule_selection.py

@@ -21,7 +21,9 @@
 from MDANSE.MolecularDynamics.Trajectory import Trajectory
 
 
-def select_molecules(trajectory: Trajectory, **function_parameters: Dict[str, Any]) -> Set[int]:
+def select_molecules(
+    trajectory: Trajectory, **function_parameters: Dict[str, Any]
+) -> Set[int]:
     """Selects all the atoms in the trajectory.
 
     Parameters
@@ -41,5 +43,7 @@ def select_molecules(trajectory: Trajectory, **function_parameters: Dict[str, An
     molecule_names = function_parameters.get("molecule_names", None)
     for molecule in molecule_names:
         if molecule in system._clusters:
-            selection = selection.union(reduce(list.__add__, system._clusters[molecule]))
+            selection = selection.union(
+                reduce(list.__add__, system._clusters[molecule])
+            )
     return selection

MDANSE/Src/MDANSE/Framework/AtomSelector/selector.py

@@ -113,9 +113,15 @@ def validate_selection_string(
                 selection = selection.difference(temp_selection)
             else:
                 selection = temp_selection
-        if len(selection.difference(current_selection)) > 0 and operation_type == "union":
+        if (
+            len(selection.difference(current_selection)) > 0
+            and operation_type == "union"
+        ):
             return True
-        elif len(current_selection.difference(selection)) > 0 and operation_type != "union":
+        elif (
+            len(current_selection.difference(selection)) > 0
+            and operation_type != "union"
+        ):
             return True
         return False
 

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

@@ -33,7 +33,7 @@ class AtomSelectionConfigurator(IConfigurator):
         The defaults selection setting.
     """
 
-    _default = '{}'
+    _default = "{}"
 
     def configure(self, value: str) -> None:
         """Configure an input value.
@@ -43,6 +43,8 @@ def configure(self, value: str) -> None:
         value : str
             The selection setting in a json readable format.
         """
+        self._original_input = value
+
         trajConfig = self._configurable[self._dependencies["trajectory"]]
         self.selector = ReusableSelection()
 
@@ -67,6 +69,7 @@ def configure(self, value: str) -> None:
         self["flatten_indices"] = sorted(list(indices))
 
         atoms = trajConfig["instance"].chemical_system.atom_list
+        self["total_number_of_atoms"] = len(atoms)
         selectedAtoms = [atoms[idx] for idx in self["flatten_indices"]]
 
         self["selection_length"] = len(self["flatten_indices"])
@@ -93,7 +96,7 @@ def get_natoms(self) -> dict[str, int]:
             A dictionary of the number of atom per element.
         """
         names, counts = np.unique(self["names"], return_counts=True)
-        nAtomsPerElement = {names[n]:counts[n] for n in range(len(names))}
+        nAtomsPerElement = {names[n]: counts[n] for n in range(len(names))}
 
         return nAtomsPerElement
 
@@ -132,7 +135,7 @@ def get_information(self) -> str:
 
         return "\n".join(info) + "\n"
 
-    def get_selector(self) -> 'ReusableSelection':
+    def get_selector(self) -> "ReusableSelection":
         """
         Returns
         -------

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

@@ -41,9 +41,7 @@ def __init__(self, trajectory: Trajectory) -> None:
         self._new_map = {}
         self._current_trajectory = trajectory
 
-    def apply_transmutation(
-        self, selection_string: str, symbol: str
-    ) -> None:
+    def apply_transmutation(self, selection_string: str, symbol: str) -> None:
         """With the selection dictionary update selector and then
         update the transmutation map.
 

MDANSE/Src/MDANSE/Framework/Configurators/PartialChargeConfigurator.py

@@ -44,9 +44,7 @@ def __init__(self, trajectory: Trajectory) -> None:
                 self._original_map[at_num] = 0.0
         self._new_map = {}
 
-    def update_charges(
-        self, selection_string: str, charge: float
-    ) -> None:
+    def update_charges(self, selection_string: str, charge: float) -> None:
         """With the selection dictionary update the selector and then
         update the partial charge map.
 

MDANSE/Src/MDANSE/Framework/Jobs/IJob.py

@@ -169,6 +169,22 @@ def initialize(self):
                 )
         except KeyError:
             LOG.error("IJob did not find 'write_logs' in output_files")
+        if "atom_selection" in self.configuration:
+            try:
+                array_length = self.configuration["atom_selection"][
+                    "total_number_of_atoms"
+                ]
+            except KeyError:
+                LOG.warning(
+                    "Job could not find total number of atoms in atom selection."
+                )
+            else:
+                valid_indices = self.configuration["atom_selection"]["flatten_indices"]
+                self._outputData.add(
+                    "selected_atoms",
+                    "LineOutputVariable",
+                    [index in valid_indices for index in range(array_length)],
+                )
 
     @abc.abstractmethod
     def run_step(self, index):

MDANSE_GUI/Src/MDANSE_GUI/Widgets/SelectionWidgets.py

@@ -95,10 +95,8 @@ def __init__(
         self.atom_names = []
         if trajectory:
             self.atom_types = list(np.unique(trajectory.chemical_system.atom_list))
-            if trajectory.chemical_system._atom_names:
-                self.atom_names = list(
-                    np.unique(trajectory.chemical_system._atom_names)
-                )
+            if trajectory.chemical_system.name_list:
+                self.atom_names = list(np.unique(trajectory.chemical_system.name_list))
         self.selection_types = []
         self.selection_keyword = ""
         if self.atom_types:
@@ -127,7 +125,7 @@ def switch_mode(self, new_mode: str):
             self.selection_field.addItems(self.atom_types)
             self.selection_keyword = "atom_types"
         elif new_mode == "name":
-            self.selection_field.addItems(self.atom_types)
+            self.selection_field.addItems(self.atom_names)
             self.selection_keyword = "atom_names"
 
     def parameter_dictionary(self):