MoleditPy 4.9.0__tar.gz → 4.9.2__tar.gz

{moleditpy-4.9.0 → moleditpy-4.9.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 4.9.0
+Version: 4.9.2
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{moleditpy-4.9.0 → moleditpy-4.9.2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "4.9.0"
+version = "4.9.2"
 
 license = {file = "LICENSE"}
 

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 4.9.0
+Version: 4.9.2
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/core/mol_geometry.py

@@ -723,6 +723,7 @@ def resolve_2d_overlaps(
     parent = {aid: aid for aid in atom_ids}
 
     def find_set(aid: int) -> int:
+        """Find representative root for an element in disjoint-set."""
         # Iterative path compression avoids recursion limits
         root = aid
         while parent[root] != root:
@@ -732,6 +733,7 @@ def resolve_2d_overlaps(
         return root
 
     def unite_sets(aid1: int, aid2: int) -> None:
+        """Unite two sets in disjoint-set forest."""
         root1 = find_set(aid1)
         root2 = find_set(aid2)
         if root1 != root2:

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/core/molecular_data.py

@@ -126,6 +126,7 @@ class MolecularData:
     next_atom_id: int
 
     def __init__(self) -> None:
+        """Initialize MolecularData structure with atoms, bonds, and coordinates."""
         self.atoms = {}
         self.bonds = {}
         self.next_atom_id = 0
@@ -342,6 +343,7 @@ class MolecularData:
 
         # Helper: Pick neighbors prioritizing heavy atoms
         def pick_preferred_neighbor(atom: Chem.Atom, exclude_idx: int) -> Optional[int]:
+            """Select preferred neighbor atom for geometry alignment or reference."""
             for nbr in atom.GetNeighbors():
                 if nbr.GetIdx() == exclude_idx:
                     continue

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/main.py

@@ -77,6 +77,7 @@ class _ErrorDialogHandler(logging.Handler):
     _DEDUP_WINDOW_S = 10.0
 
     def __init__(self, log_path: Optional[str] = None) -> None:
+        """Initialize GUI error dialog logging handler with dedup tracking."""
         super().__init__(level=logging.ERROR)
         # signature -> monotonic timestamp of its last shown dialog.
         self._last_shown: Dict[str, float] = {}
@@ -85,6 +86,7 @@ class _ErrorDialogHandler(logging.Handler):
         self._log_path = log_path
 
     def emit(self, record: logging.LogRecord) -> None:
+        """Emit error dialog for unhandled error log record with deduplication."""
         try:
             if getattr(record, "no_dialog", False):
                 return

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/plugins/plugin_interface.py

@@ -21,6 +21,7 @@ class PluginContext:
     """
 
     def __init__(self, manager: Any, plugin_name: str) -> None:
+        """Initialize plugin execution context with host reference."""
         self._manager = manager
         self._plugin_name = plugin_name
 
@@ -206,6 +207,7 @@ class PluginContext:
 
     @current_mol.setter
     def current_mol(self, mol: Any) -> None:
+        """Set active RDKit molecule and redraw 3D view."""
         mw = self.get_main_window()
         if mw and hasattr(mw, "view_3d_manager"):
             mw.view_3d_manager.current_mol = mol
@@ -218,6 +220,7 @@ class PluginContext:
 
     @current_molecule.setter
     def current_molecule(self, mol: Any) -> None:
+        """Set active molecule via current_mol setter."""
         self.current_mol = mol
 
     @property
@@ -607,6 +610,7 @@ class Plugin3DController:
     """Helper to manipulate the 3D scene."""
 
     def __init__(self, main_window: Any) -> None:
+        """Initialize Plugin3DController with main window reference."""
         self._mw = main_window
 
     def _get_v3d(self) -> Optional[Any]:

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/plugins/plugin_manager.py

@@ -76,6 +76,7 @@ class PluginManager:
             return "N/A"
 
     def __init__(self, main_window: Any = None) -> None:
+        """Initialize PluginManager with plugin search directories."""
         self.plugin_dir: str = os.path.join(
             os.path.expanduser("~"), ".moleditpy", "plugins"
         )

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/plugins/plugin_manager_window.py

@@ -37,6 +37,7 @@ class PluginManagerWindow(QDialog):
     """Dialog for browsing, installing, and removing plugins."""
 
     def __init__(self, plugin_manager: Any, parent: Optional[QWidget] = None) -> None:
+        """Initialize plugin management dialog window."""
         super().__init__(parent)
         self.btn_remove: Any = None
         self.table: Any = None

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/about_dialog.py

@@ -33,6 +33,7 @@ class AboutDialog(QDialog):
     """Dialog showing application version, icon, and project links."""
 
     def __init__(self, main_window: Any, parent: Optional[QWidget] = None) -> None:
+        """Initialize About dialog with version and author info."""
         super().__init__(parent)
         self.image_label: Any = None
         self.main_window = main_window

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/align_plane_dialog.py

@@ -45,6 +45,7 @@ class AlignPlaneDialog(BasePickingDialog):
         preselected_atoms: Optional[Sequence[int]] = None,
         parent: Optional[QWidget] = None,
     ) -> None:
+        """Initialize align plane dialog with target geometry settings."""
         super().__init__(mol, main_window, parent)
         self.plane = plane
         self._selected_atoms = SelectionList()

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/alignment_dialog.py

@@ -49,6 +49,7 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog):
         preselected_atoms: Optional[Sequence[int]] = None,
         parent: Optional[QWidget] = None,
     ) -> None:
+        """Initialize alignment dialog with reference axis settings."""
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
         self.mol = mol

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/analysis_window.py

@@ -41,6 +41,7 @@ class AnalysisWindow(QDialog):
         parent: Optional[QWidget] = None,
         is_xyz_derived: bool = False,
     ) -> None:
+        """Initialize analysis window for molecular properties."""
         super().__init__(parent)
         self.mol = mol
         self.is_xyz_derived = is_xyz_derived  # Flag indicating if derived from XYZ

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/angle_dialog.py

@@ -51,6 +51,7 @@ class AngleDialog(GeometryBaseDialog):
         preselected_atoms: Optional[Sequence[int]] = None,
         parent: Optional[QWidget] = None,
     ) -> None:
+        """Initialize bond angle adjustment dialog."""
         super().__init__(mol, main_window, parent)
         self._baseline_positions: Any = None
         self._snapshot_positions = None
@@ -384,6 +385,7 @@ class AngleDialog(GeometryBaseDialog):
         self._push_undo()
 
     def _is_selection_complete(self) -> bool:
+        """Check whether required three atoms have been picked."""
         return (
             self.atom1_idx is not None
             and self.atom2_idx is not None

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/app_state.py

@@ -74,6 +74,7 @@ class StateManager:
     """Manages serialized undo/redo state and document save state for MainWindow."""
 
     def __init__(self, host: MainWindow) -> None:
+        """Initialize StateManager with reference to host window."""
         self.host = host
         self.data: MolecularData  # Dynamically assigned in main_window_init.py
         self.has_unsaved_changes = False
@@ -139,6 +140,7 @@ class StateManager:
         file_version_str = loaded_data.get("version", "0.0.0")
 
         def parse_v(v_str: str) -> Tuple[int, ...]:
+            """Parse version string into tuple of integers."""
             if not v_str or not isinstance(v_str, str):
                 return (0, 0, 0)
             try:

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/atom_item.py

@@ -78,6 +78,7 @@ class AtomItem(QGraphicsItem):
     def __init__(
         self, atom_id: int, symbol: str, pos: QPointF, charge: int = 0, radical: int = 0
     ) -> None:
+        """Initialize 2D atom graphics item."""
         super().__init__()
         self.atom_id: int = atom_id
         self.symbol: str = symbol

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/atom_picking.py

@@ -21,6 +21,7 @@ from ..utils.constants import VDW_DISPLAY_RADII, pt
 
 
 def _world_to_display(renderer: Any, pos: Any) -> Optional[tuple[float, float, float]]:
+    """Project 3D world coordinates to 2D display viewport pixels."""
     try:
         renderer.SetWorldPoint(float(pos[0]), float(pos[1]), float(pos[2]), 1.0)
         renderer.WorldToDisplay()
@@ -31,6 +32,7 @@ def _world_to_display(renderer: Any, pos: Any) -> Optional[tuple[float, float, f
 
 
 def _atom_world_radius(view_3d_manager: Any, mol: Any, atom_idx: int) -> float:
+    """Calculate effective atom sphere radius in 3D world units."""
     try:
         atom = mol.GetAtomWithIdx(int(atom_idx))
         symbol = atom.GetSymbol()
@@ -68,6 +70,7 @@ def _atom_world_radius(view_3d_manager: Any, mol: Any, atom_idx: int) -> float:
 def _projected_radius_px(
     renderer: Any, center: Any, world_radius: float
 ) -> Optional[float]:
+    """Calculate projected atom radius on screen in display pixels."""
     center_display = _world_to_display(renderer, center)
     if center_display is None:
         return None

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/base_picking_dialog.py

@@ -57,6 +57,7 @@ class BasePickingDialog(Dialog3DPickingMixin, QDialog):
         main_window: "MainWindow",
         parent: Optional[QWidget] = None,
     ) -> None:
+        """Initialize base atom picking dialog."""
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
         self.mol = mol

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/bond_item.py

@@ -120,6 +120,7 @@ class BondItem(QGraphicsItem):
         """Shorten inner ring double bonds based on the ring angle at both atoms."""
 
         def angle_between(v1: QPointF, v2: QPointF) -> Optional[float]:
+            """Calculate smaller unsigned angle between two 2D vectors in radians."""
             len1 = math.hypot(v1.x(), v1.y())
             len2 = math.hypot(v2.x(), v2.y())
             if len1 <= 1e-6 or len2 <= 1e-6:
@@ -158,6 +159,7 @@ class BondItem(QGraphicsItem):
         order: int = 1,
         stereo: int = 0,
     ) -> None:
+        """Initialize 2D bond graphics item between two atoms."""
         super().__init__()
         # Validate input parameters
         if atom1_item is None or atom2_item is None:

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/bond_length_dialog.py

@@ -48,6 +48,7 @@ class BondLengthDialog(GeometryBaseDialog):
         preselected_atoms: Optional[Sequence[int]] = None,
         parent: Optional[QWidget] = None,
     ) -> None:
+        """Initialize bond length adjustment dialog."""
         super().__init__(mol, main_window, parent)
         self._baseline_positions: Any = None
         self._snapshot_positions = None
@@ -325,6 +326,7 @@ class BondLengthDialog(GeometryBaseDialog):
         self._push_undo()
 
     def _is_selection_complete(self) -> bool:
+        """Check whether required two atoms have been picked."""
         return self.atom1_idx is not None and self.atom2_idx is not None
 
     def apply_geometry_update(self, new_distance: float) -> None:  # pylint: disable=arguments-renamed

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/calculation_worker.py

@@ -808,6 +808,7 @@ class CalculationWorker(QObject):
     start_work = pyqtSignal(str, object)
 
     def __init__(self, parent: Optional[QObject] = None) -> None:
+        """Initialize background calculation worker thread."""
         super().__init__(parent)
         self.halt_ids: Optional[Set[Any]] = None
         self.halt_all: bool = False
@@ -822,6 +823,7 @@ class CalculationWorker(QObject):
         w_id = options.get("worker_id")
 
         def _check_halted() -> bool:
+            """Check if current calculation worker has been requested to halt."""
             h_ids = getattr(self, "halt_ids", None)
             if self.halt_all:
                 return True  # type: ignore[return-value]
@@ -836,18 +838,21 @@ class CalculationWorker(QObject):
             # pylint: enable=unsupported-membership-test
 
         def _safe_status(msg: str) -> None:
+            """Emit calculation status update checking halt state."""
             if _check_halted():
                 raise WorkerHaltError("Halted")
             with suppress_log(AttributeError, RuntimeError):
                 self.status_update.emit(msg)
 
         def _safe_finished(payload: Any) -> None:
+            """Emit calculation finished signal checking halt state."""
             if _check_halted():
                 raise WorkerHaltError("Halted")
             with suppress_log(AttributeError, RuntimeError, TypeError):
                 self.finished.emit(payload)
 
         def _safe_error(msg: str) -> None:
+            """Emit calculation error signal handling graceful halt state."""
             # If we're already halting, don't raise another error
             if msg == "Halted":
                 with suppress_log(AttributeError, RuntimeError, TypeError):

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/chain_mixin.py

@@ -38,6 +38,7 @@ class ChainMixin:
     template_preview: Any
 
     def __init__(self, *args: Any, **kwargs: Any) -> None:
+        """Initialize aliphatic chain drawing tool mixin."""
         self.chain_anchor: Optional[QPointF] = None
         self.chain_start_atom: Optional[AtomItem] = None
         self.chain_end_atom: Optional[AtomItem] = None

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/color_settings_dialog.py

@@ -37,6 +37,7 @@ class ColorSettingsDialog(QDialog):
     """
 
     def __init__(self, current_settings: Any, parent: Optional[QWidget] = None) -> None:
+        """Initialize CPK element color customization dialog."""
         super().__init__(parent)
         self.setWindowTitle("CPK Colors")
         self.parent_window: Any = parent

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/compute_logic.py

@@ -48,6 +48,7 @@ class ComputeManager:
     """Independent manager for molecular computations, ported from MainWindowCompute mixin."""
 
     def __init__(self, host: MainWindow) -> None:
+        """Initialize ComputeManager with reference to host window."""
         self._calculating_text_actor: Any = None
         self.original_atom_properties: Dict[int, int] = {}
         self.host = host
@@ -180,6 +181,7 @@ class ComputeManager:
         menu.exec(self.host.init_manager.convert_button.mapToGlobal(pos))  # type: ignore[union-attr]
 
     def _trigger_conversion_with_temp_mode(self, mode_key: str) -> None:
+        """Trigger 2D to 3D conversion with temporary mode override."""
         # Store mode as instance attribute so it reaches trigger_conversion
         # without passing a kwarg — plugins may wrap trigger_conversion without
         # forwarding **kwargs, which would cause a TypeError.
@@ -203,6 +205,7 @@ class ComputeManager:
         menu.exec(self.host.init_manager.optimize_3d_button.mapToGlobal(pos))  # type: ignore[union-attr]
 
     def _trigger_optimize_with_temp_method(self, method_key: str) -> None:
+        """Trigger 3D optimization with temporary method override."""
         QTimer.singleShot(0, lambda: self.optimize_3d_structure(method_key))
 
     def trigger_conversion(
@@ -429,6 +432,7 @@ class ComputeManager:
         self.host.update_status_message(f"Process completed ({label}).")
 
     def _prepare_rdkit_mol_for_conversion(self) -> Optional[Chem.Mol]:
+        """Prepare and sanitize RDKit molecule for 3D conversion."""
         mol = self.host.state_manager.data.to_rdkit_mol(use_2d_stereo=False)
         if not mol or mol.GetNumAtoms() == 0:
             self.check_chemistry_problems_fallback()
@@ -457,6 +461,7 @@ class ComputeManager:
     def _handle_chemistry_problems(
         self, mol: Chem.Mol, problems: Sequence[Any]
     ) -> None:
+        """Handle chemical sanitization issues before conversion."""
         self.host.init_manager.scene.clear_all_problem_flags()
         msg = f"Error: {len(problems)} chemistry problem(s) found (e.g., hypervalency). Fix the 2D layout before converting."
         self.host.statusBar().showMessage(msg)  # type: ignore[union-attr]
@@ -498,6 +503,7 @@ class ComputeManager:
             return None
 
     def _setup_mol_block_for_worker(self, mol: Chem.Mol) -> str:
+        """Construct molecule block data for background worker."""
         ez_block = self._ez_consistent_mol_block()
         if ez_block:
             return ez_block
@@ -511,6 +517,7 @@ class ComputeManager:
     def _start_calculation_worker(
         self, mol_block: str, options: Dict[str, Any], run_id: int
     ) -> None:
+        """Start background thread calculation worker."""
         thread = QThread()
         worker = CalculationWorker()
         worker.halt_ids = self.halt_ids
@@ -518,6 +525,7 @@ class ComputeManager:
         worker.status_update.connect(self.host.ui_manager.update_status_bar)
 
         def _cleanup() -> None:
+            """Clean up calculation worker thread references."""
             thread.quit()
             thread.finished.connect(thread.deleteLater)
             worker.deleteLater()
@@ -525,12 +533,14 @@ class ComputeManager:
                 self._active_calc_threads.remove(thread)
 
         def _on_finished(result: Any) -> None:
+            """Handle successful background calculation completion."""
             try:
                 self.on_calculation_finished(result)
             finally:
                 _cleanup()
 
         def _on_error(msg: Any) -> None:
+            """Handle background calculation failure."""
             try:
                 self.on_calculation_error(msg)
             finally:

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/constrained_optimization_dialog.py

@@ -40,6 +40,7 @@ class ConstrainedOptimizationThread(QThread):
     error_occurred = pyqtSignal(str)
 
     def __init__(self, ff: Any, max_iters: int = 20000, parent: Any = None) -> None:
+        """Initialize constrained optimization worker thread."""
         super().__init__(parent)
         self.ff = ff
         self.max_iters = max_iters
@@ -57,6 +58,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
     """Dialog for constrained optimization."""
 
     def __init__(self, mol: Any, main_window: Any, parent: Any = None) -> None:
+        """Initialize constrained force field optimization dialog."""
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
         self.mol = mol
@@ -251,6 +253,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
         layout.addLayout(main_buttons)
 
     def on_atom_picked(self, atom_idx: int) -> None:
+        """Handle atom selection event from 3D viewport."""
         if atom_idx in self.selected_atoms:
             self.selected_atoms.remove(atom_idx)
         else:
@@ -603,6 +606,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
             self.optimize_button.setEnabled(True)
 
     def _on_optimization_error(self, err_msg: str) -> None:
+        """Handle optimization thread failure callback."""
         if self._closed:
             logging.warning(
                 "Constrained optimization failed after dialog close: %s", err_msg
@@ -615,6 +619,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
         QMessageBox.critical(self, "Error", f"Optimization error: {err_msg}")
 
     def _on_optimization_finished(self, ff_name: str, conf: Any) -> None:
+        """Handle optimization thread completion callback."""
         if self._closed:
             logging.info("Discarding constrained optimization result after close.")
             return

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/custom_interactor_style.py

@@ -72,6 +72,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
     """VTK interactor style extending trackball-camera with 3D atom drag and measurement."""
 
     def __init__(self, main_window: Any = None, **kwargs: Any) -> None:
+        """Initialize custom PyVista interactor style with mouse handlers."""
         super().__init__(**kwargs)
         self.main_window = main_window
         # Custom state flags
@@ -416,6 +417,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                     if type(move_group_dialog).__name__ == "MoveSelectedAtomsDialog":
                         # For MoveSelectedAtomsDialog, we toggle ONLY the clicked atom, no BFS!
                         def _deferred_toggle() -> None:
+                            """Toggle atom selection state in deferred callback."""
                             try:
                                 move_group_dialog.on_atom_picked(clicked_atom_idx)
                             except (AttributeError, RuntimeError):
@@ -477,6 +479,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                     move_group_dialog.selected_atoms.add(clicked_atom_idx)
 
                     def _deferred_move_group_update() -> None:
+                        """Update selected group translation in deferred callback."""
                         try:
                             move_group_dialog.show_atom_labels()
                             move_group_dialog.update_display()
@@ -527,6 +530,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                         if True:
 
                             def _deferred_measure() -> None:
+                                """Measure distance between picked atoms in deferred callback."""
                                 try:
                                     mw.edit_3d_manager.handle_measurement_atom_selection(
                                         closest_atom_idx
@@ -846,6 +850,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             _rt_mol = mw.view_3d_manager.current_mol
 
             def _deferred_rt_atom() -> None:
+                """Execute deferred real-time atom drag update."""
                 try:
                     mw.view_3d_manager.draw_molecule_3d(_rt_mol)
                 except (AttributeError, RuntimeError, ValueError, TypeError):
@@ -906,6 +911,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             _rt_dlg = move_group_dialog
 
             def _deferred_rt_grp() -> None:
+                """Execute deferred real-time group translation update."""
                 try:
                     mw.view_3d_manager.draw_molecule_3d(_rt_mol)
                     _rt_dlg.show_atom_labels()
@@ -1054,6 +1060,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             _rt_dlg = move_group_dialog
 
             def _deferred_rt_rot() -> None:
+                """Execute deferred real-time group rotation update."""
                 try:
                     mw.view_3d_manager.draw_molecule_3d(_rt_mol)
                     _rt_dlg.show_atom_labels()
@@ -1161,6 +1168,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                     _grp_dlg = move_group_dialog
 
                     def _deferred_group_redraw() -> None:
+                        """Redraw moving group geometry in deferred callback."""
                         mw.view_3d_manager.draw_molecule_3d(_grp_mol)
                         mw.view_3d_manager.update_chiral_labels()
                         _grp_dlg.show_atom_labels()
@@ -1186,6 +1194,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             if not self._mouse_moved_during_drag and self._mouse_press_pos is not None:
                 # Background click: deselect
                 def _deferred_clear_move_group() -> None:
+                    """Clear active move group selection in deferred callback."""
                     try:
                         move_group_dialog.group_atoms.clear()
                         move_group_dialog.selected_atoms.clear()
@@ -1205,6 +1214,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         ):
             # Background click -> clear selection
             def _deferred_clear_measurement() -> None:
+                """Clear active measurement lines in deferred callback."""
                 try:
                     mw.edit_3d_manager.clear_measurement_selection()
                 except (AttributeError, RuntimeError):
@@ -1314,6 +1324,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                     _atom_mol = mw.view_3d_manager.current_mol
 
                     def _deferred_atom_redraw() -> None:
+                        """Redraw moved atom geometry in deferred callback."""
                         try:
                             mw.view_3d_manager.draw_molecule_3d(_atom_mol)
                         except (AttributeError, RuntimeError, ValueError, TypeError):
@@ -1340,6 +1351,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                 ]
 
                 def _deferred_updates() -> None:
+                    """Process pending deferred viewport updates."""
                     for fn in _update_calls:
                         try:
                             fn()

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/custom_qt_interactor.py

@@ -32,6 +32,7 @@ class CustomQtInteractor(QtInteractor):
         main_window: Optional[Any] = None,
         **kwargs: Any,
     ) -> None:
+        """Initialize embedded PyVista Qt interactor widget."""
         super().__init__(parent, **kwargs)
         self.main_window = main_window
 

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/dialog_3d_picking_mixin.py

@@ -86,6 +86,7 @@ class Dialog3DPickingMixin(_MixinBase):
                             self.main_window.picking_consumed = True
 
                         def _deferred_pick() -> None:
+                            """Process deferred atom pick event in 3D viewport."""
                             try:
                                 self.on_atom_picked(int(closest_atom_idx))
                             except (AttributeError, RuntimeError):
@@ -140,6 +141,7 @@ class Dialog3DPickingMixin(_MixinBase):
                     if hasattr(self, "clear_selection"):
 
                         def _deferred_clear() -> None:
+                            """Clear deferred picking state in 3D viewport."""
                             try:
                                 self.clear_selection()
                             except (AttributeError, RuntimeError):

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/dialog_logic.py

@@ -52,6 +52,7 @@ class DialogManager:
     """
 
     def __init__(self, host: Any) -> None:
+        """Initialize DialogManager coordinating application dialogs."""
         self.host = host
 
     def _get_preselected_atoms_3d(self) -> List[int]:

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/dihedral_dialog.py

@@ -51,6 +51,7 @@ class DihedralDialog(GeometryBaseDialog):
         preselected_atoms: Optional[Sequence[int]] = None,
         parent: Optional[QWidget] = None,
     ) -> None:
+        """Initialize dihedral angle adjustment dialog."""
         super().__init__(mol, main_window, parent)
         self._baseline_positions: Any = None
         self._snapshot_positions = None

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/edit_3d_logic.py

@@ -39,6 +39,7 @@ class Edit3DManager:
     """Independent manager for 3D editing logic, ported from MainWindowEdit3d mixin."""
 
     def __init__(self, host: Any) -> None:
+        """Initialize 3D geometric transformation and editing manager."""
         self.host = host
         # State variables previously held by mixin
         self.measurement_mode = False

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/edit_actions_logic.py

@@ -75,6 +75,7 @@ class Rotate2DDialog(QDialog):
     def __init__(
         self, parent: Optional[QWidget] = None, initial_angle: float = 0
     ) -> None:
+        """Initialize 2D structure rotation dialog."""
         super().__init__(parent)
         self.setWindowTitle("Rotate 2D")
         self.setFixedWidth(300)
@@ -122,6 +123,7 @@ class EditActionsManager:
     """Independent manager for molecular editing actions, ported from MainWindowEditActions mixin."""
 
     def __init__(self, host: MainWindow) -> None:
+        """Initialize EditActionsManager for clipboard and editing tools."""
         self.dragged_atom_info = None
         self.host = host
         # State variables previously held by mixin
@@ -665,6 +667,7 @@ class EditActionsManager:
 
                 # Helper: determine bond_stereo for hydrogen
                 def _choose_stereo(i: int) -> int:
+                    """Determine stereo wedge or dash representation for bond."""
                     # 0: plain, 1: wedge, 2: dash, 3: plain, 4+: all plain
                     if i == 0:
                         return 0
@@ -1122,6 +1125,7 @@ class EditActionsManager:
             problem_map = self._detect_chemistry_problems(mol)
 
             def _ui_closure() -> None:
+                """Execute UI update closure callback."""
                 self._apply_ui_h_counts(h_count_map, problem_map, my_token)
 
             try:
@@ -1265,6 +1269,7 @@ class EditActionsManager:
         from moleditpy.core.mol_geometry import resolve_2d_overlaps
 
         def has_bond_check(id1: int, id2: int) -> bool:
+            """Check if bond already exists between atom pair."""
             item1 = self.host.init_manager.scene.atom_items.get(id1)
             item2 = self.host.init_manager.scene.atom_items.get(id2)
             return (

{moleditpy-4.9.0 → moleditpy-4.9.2}/src/moleditpy/ui/export_logic.py

@@ -35,6 +35,7 @@ class ExportManager:
     """Independent manager for export logic, ported from MainWindowExport mixin."""
 
     def __init__(self, host: Any) -> None:
+        """Initialize ExportManager for file and scene exports."""
         self.host = host
 
     def _get_default_basename(self) -> str: