Improve docstrings, add all_indices property

MDANSE/Src/MDANSE/Chemistry/ChemicalSystem.py

@@ -15,7 +15,7 @@
 #
 
 from __future__ import annotations
-from typing import List, Tuple, Dict, Any
+from typing import List, Tuple, Dict, Any, Set
 import copy
 from functools import reduce
 
@@ -229,6 +229,11 @@ def number_of_atoms(self) -> int:
         """The number of non-ghost atoms in the ChemicalSystem."""
         return self._total_number_of_atoms
 
+    @property
+    def all_indices(self) -> Set[int]:
+        """The number of non-ghost atoms in the ChemicalSystem."""
+        return set(self._atom_indices)
+
     @property
     def total_number_of_atoms(self) -> int:
         """The number of all atoms in the ChemicalSystem, including ghost ones."""

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

@@ -27,7 +27,7 @@ def select_atoms(
     index_slice: Sequence[int] = None,
     atom_types: Sequence[str] = (),
     atom_names: Sequence[str] = (),
-    **kwargs: str,
+    **_kwargs: str,
 ) -> Set[int]:
     """Selects specific atoms in the trajectory. These can be selected based
     on indices, atom type or trajectory-specific atom name.
@@ -60,7 +60,7 @@ def select_atoms(
     system = trajectory.chemical_system
     element_list = system.atom_list
     name_list = system.name_list
-    indices = set(range(len(element_list)))
+    indices = system.all_indices
     if index_list is not None:
         selection |= indices & set(index_list)
     if index_range is not None:

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

@@ -18,7 +18,7 @@
 from MDANSE.MolecularDynamics.Trajectory import Trajectory
 
 
-def select_all(trajectory: Trajectory, **kwargs: str) -> Set[int]:
+def select_all(trajectory: Trajectory, **_kwargs: str) -> Set[int]:
     """Selects all the atoms in the trajectory.
 
     Parameters
@@ -31,10 +31,10 @@ def select_all(trajectory: Trajectory, **kwargs: str) -> Set[int]:
     Set[int]
         Set of all the atom indices
     """
-    return set(range(len(trajectory.chemical_system.atom_list)))
+    return trajectory.chemical_system.all_indices
 
 
-def select_none(_trajectory: Trajectory, **kwargs: str) -> Set[int]:
+def select_none(_trajectory: Trajectory, **_kwargs: str) -> Set[int]:
     """Returns an empty selection.
 
     Parameters
@@ -51,7 +51,7 @@ def select_none(_trajectory: Trajectory, **kwargs: str) -> Set[int]:
 
 
 def invert_selection(
-    trajectory: Trajectory, selection: Set[int], **kwargs: str
+    trajectory: Trajectory, selection: Set[int], **_kwargs: str
 ) -> Set[int]:
     """Returns a set of all the indices that are present in the trajectory
     and were not included in the input selection.
@@ -66,7 +66,7 @@ def invert_selection(
     Returns
     -------
     Set[int]
-        set of all the indices in the trajectory which were not in the selection
+        set of all the indices in the trajectory which were not in the input selection
     """
     all_indices = select_all(trajectory)
     inverted = all_indices - selection

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

@@ -21,7 +21,7 @@
 
 
 def select_labels(
-    trajectory: Trajectory, atom_labels: Sequence[str] = (), **kwargs: str
+    trajectory: Trajectory, atom_labels: Sequence[str] = (), **_kwargs: str
 ) -> Set[int]:
     """Selects atoms with a specific label in the trajectory.
     A residue name can be read as a label by MDANSE.
@@ -46,7 +46,7 @@ def select_labels(
 
 
 def select_pattern(
-    trajectory: Trajectory, rdkit_pattern: str = "", **kwargs: str
+    trajectory: Trajectory, rdkit_pattern: str = "", **_kwargs: str
 ) -> Set[int]:
     """Selects atoms according to the SMARTS string given as input.
     This will only work if molecules and bonds have been detected in the system.

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

@@ -20,7 +20,7 @@
 
 
 def select_molecules(
-    trajectory: Trajectory, molecule_names: Sequence[str] = (), **kwargs: str
+    trajectory: Trajectory, molecule_names: Sequence[str] = (), **_kwargs: str
 ) -> Set[int]:
     """Selects all the atoms belonging to the specified molecule types.
 

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

@@ -63,6 +63,7 @@ def __init__(self) -> None:
         self.reset()
 
     def reset(self):
+        """Initialises the attributes to an empty list of operations."""
         self.system = None
         self.trajectory = None
         self.all_idxs = set()
@@ -71,6 +72,15 @@ def reset(self):
     def set_selection(
         self, number: Union[int, None] = None, function_parameters: Dict[str, Any] = {}
     ):
+        """Appends a new selection operation, or overwrites an existing one.
+
+        Parameters
+        ----------
+        number : Union[int, None], optional
+            the position of the new selection in the sequence of operations, by default None
+        function_parameters : Dict[str, Any], optional
+            the dictionary of keyword arguments defining a selection operation, by default {}
+        """
         if number is None:
             number = len(self.operations)
         else:
@@ -132,8 +142,21 @@ def validate_selection_string(
         return False
 
     def select_in_trajectory(self, trajectory: Trajectory) -> Set[int]:
+        """Applies all the selection operations in sequence to the
+        input trajectory, and returns the resulting set of indices.
+
+        Parameters
+        ----------
+        trajectory : Trajectory
+            trajectory object in which the atoms will be selected
+
+        Returns
+        -------
+        Set[int]
+            set of atom indices that have been selected in the input trajectory
+        """
         selection = set()
-        self.all_idxs = set(range(len(trajectory.chemical_system.atom_list)))
+        self.all_idxs = trajectory.chemical_system.all_indices
         sequence = sorted(map(int, self.operations))
         if not sequence:
             return self.all_idxs
@@ -169,7 +192,8 @@ def convert_to_json(self) -> str:
         return json.dumps(self.operations)
 
     def load_from_json(self, json_string: str):
-        """_summary_
+        """Loads the atom selection operations from a JSON string.
+        Adds the operations to the selection sequence.
 
         Parameters
         ----------

MDANSE/Src/MDANSE/Framework/AtomSelector/spatial_selection.py

@@ -28,7 +28,7 @@ def select_positions(
     frame_number: int = 0,
     position_minimum: Union[Sequence[float], None] = None,
     position_maximum: Union[Sequence[float], None] = None,
-    **kwargs: str,
+    **_kwargs: str,
 ) -> Set[int]:
     """Selects atoms based on their positions at a specified frame number.
     Lower and upper limits of x, y and z coordinates can be given as input.
@@ -70,7 +70,7 @@ def select_sphere(
     frame_number: int = 0,
     sphere_centre: Sequence[float],
     sphere_radius: float,
-    **kwargs: str,
+    **_kwargs: str,
 ) -> Set[int]:
     """Selects atoms within a distance from a fixed point in space,
     based on coordinates at a specific frame number.

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/AtomSelectionWidget.py

@@ -148,7 +148,7 @@ def __init__(
         self.selection_model = SelectionModel(self.trajectory)
         self._field = field
         self.atm_full_names = self.system.name_list
-        self.molecule_names = list(map(str, self.system._clusters))
+        self.molecule_names = self.system.unique_molecules()
         self.labels = list(map(str, self.system._labels))
 
         self.selection_textbox = QPlainTextEdit()

MDANSE_GUI/Src/MDANSE_GUI/Widgets/SelectionWidgets.py

@@ -251,7 +251,7 @@ def __init__(
     ):
         self.molecule_names = []
         if trajectory:
-            self.molecule_names = list(trajectory.chemical_system._clusters.keys())
+            self.molecule_names = trajectory.chemical_system.unique_molecules()
         super().__init__(parent, widget_label)
 
     def add_specific_widgets(self):