MoleditPy-linux 4.0.0__py3-none-any.whl → 4.0.2__py3-none-any.whl

moleditpy_linux/core/molecular_data.py

@@ -22,13 +22,17 @@ class PointTuple(tuple):
     """Backward-compatible tuple that allows .x() and .y() access like QPointF."""
 
     def x(self) -> float:
+        """Return the x coordinate as a float."""
         return float(self[0])
 
     def y(self) -> float:
+        """Return the y coordinate as a float."""
         return float(self[1])
 
 
 class MolecularData:
+    """In-memory graph of atoms and bonds, independent of any UI framework."""
+
     atoms: Dict[int, Dict[str, Any]]
     bonds: Dict[Tuple[int, int], Dict[str, Any]]
     adjacency_list: Dict[int, List[int]]
@@ -47,6 +51,7 @@ class MolecularData:
         charge: int = 0,
         radical: int = 0,
     ) -> int:
+        """Add a new atom and return its auto-assigned integer ID."""
         atom_id = self.next_atom_id
         # Internalize position as raw floats to decouple from UI types (QPointF)
         if hasattr(pos, "x") and hasattr(pos, "y"):
@@ -77,6 +82,7 @@ class MolecularData:
     def add_bond(
         self, id1: int, id2: int, order: Union[int, float] = 1, stereo: int = 0
     ) -> Tuple[Tuple[int, int], str]:
+        """Add or update a bond between two atoms; return its canonical key and 'created'/'updated'."""
         # For stereo bonds, do not sort because ID order determines direction.
         # For non-stereo bonds, sort to normalize the key.
         if stereo == 0:
@@ -100,6 +106,7 @@ class MolecularData:
             return (id1, id2), "created"
 
     def remove_atom(self, atom_id: int) -> None:
+        """Remove an atom and all bonds involving it from the data model."""
         if atom_id in self.atoms:
             # Safely get neighbors before deleting the atom's own entry
             neighbors = self.adjacency_list.get(atom_id, [])
@@ -123,6 +130,7 @@ class MolecularData:
                 self.bonds.pop(key, None)
 
     def remove_bond(self, id1: int, id2: int) -> None:
+        """Remove the bond between two atoms, handling stereo and non-stereo key variants."""
         # Look for directional stereo bonds (forward/reverse) and normalized non-stereo bond keys.
         key_to_remove = None
         if (id1, id2) in self.bonds:
@@ -318,6 +326,7 @@ class MolecularData:
         return final_mol
 
     def to_mol_block(self) -> Optional[str]:
+        """Serialize the molecule to an MDL MOL block string, or None on failure."""
         mol = self.to_rdkit_mol()
         if mol:
             try:

moleditpy_linux/main.py

@@ -21,12 +21,33 @@ from .utils.constants import VERSION
 
 # VERSION is resolved above (before Qt) so --version works without launching the app.
 
+from PyQt6.QtCore import QtMsgType, qInstallMessageHandler
 from PyQt6.QtWidgets import QApplication
 
 from .ui.main_window import MainWindow
 
+_QT_LOG_LEVEL = {
+    QtMsgType.QtDebugMsg: logging.DEBUG,
+    QtMsgType.QtInfoMsg: logging.INFO,
+    QtMsgType.QtWarningMsg: logging.WARNING,
+    QtMsgType.QtCriticalMsg: logging.ERROR,
+    QtMsgType.QtFatalMsg: logging.CRITICAL,
+}
+
+_DOWNGRADED_QT_PATTERNS = ("Retrying to obtain clipboard",)
+
+
+def _qt_message_handler(mode: QtMsgType, _context: Any, message: str) -> None:
+    """Route Qt log messages to Python logging, downgrading known noisy warnings."""
+    for pattern in _DOWNGRADED_QT_PATTERNS:
+        if pattern in message:
+            logging.debug("Qt: %s", message)
+            return
+    logging.log(_QT_LOG_LEVEL.get(mode, logging.WARNING), "Qt: %s", message)
+
 
 def setup_logging() -> None:
+    """Configure root logger and install a global unhandled-exception handler."""
     logging.basicConfig(
         level=logging.INFO,
         format="%(asctime)s [%(levelname)s] %(name)s (%(pathname)s:%(lineno)d): %(message)s",
@@ -49,12 +70,11 @@ def setup_logging() -> None:
 
 
 def main() -> None:
-    # Setup logging as early as possible
+    """Parse CLI arguments, configure logging, and launch the GUI."""
     setup_logging()
 
-    # --- Additional handling for Windows taskbar icon ---
     if sys.platform == "win32":
-        myappid = "hyoko.moleditpy_linux.1.0"  # Application-specific ID (arbitrary)
+        myappid = "hyoko.moleditpy_linux.1.0"
         ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
 
     parser = argparse.ArgumentParser(
@@ -80,7 +100,6 @@ def main() -> None:
     # parse_known_args so Qt's own argv flags (e.g. -platform) are passed through
     args, remaining = parser.parse_known_args()
 
-    # --- Headless Plugin Installation ---
     if args.install_plugin:
         plugin_path = os.path.abspath(args.install_plugin)
         if not os.path.exists(plugin_path):
@@ -95,7 +114,6 @@ def main() -> None:
         pm = PluginManager()
         sha256 = pm.compute_sha256(plugin_path)
 
-        # Extract metadata
         metadata_file = plugin_path
         if os.path.isdir(plugin_path):
             init_py = os.path.join(plugin_path, "__init__.py")
@@ -136,10 +154,10 @@ def main() -> None:
             sys.exit(0)
 
     app = QApplication([sys.argv[0]] + remaining)
+    qInstallMessageHandler(_qt_message_handler)
     window = MainWindow(initial_file=args.file, safe_mode=args.safe)
     window.show()
 
-    # Force Windows to refresh taskbar/titlebar icon after event loop starts
     if sys.platform == "win32":
         try:
             from PyQt6.QtCore import QTimer

moleditpy_linux/plugins/plugin_manager.py

@@ -29,6 +29,8 @@ from .plugin_interface import PluginContext
 
 
 class PluginManager:
+    """Discovers, loads, and manages lifecycle of all installed plugins."""
+
     def compute_sha256(self, path: str) -> str:
         """Computes SHA-256 for a file or a directory (concatenated hashes of all files)."""
         if os.path.isfile(path):
@@ -98,9 +100,11 @@ class PluginManager:
         ] = {}  # Map of plugin_name -> {window_id -> window}
 
     def get_main_window(self) -> Any:
+        """Return the current main window reference."""
         return self.main_window
 
     def set_main_window(self, mw: Any) -> None:
+        """Set the main window reference."""
         self.main_window = mw
 
     def ensure_plugin_dir(self) -> None:
@@ -420,6 +424,7 @@ class PluginManager:
         icon: str,
         shortcut: str,
     ) -> None:
+        """Register a plugin menu action with its path, callback, and display metadata."""
         self.menu_actions.append(
             {
                 "plugin": plugin_name,
@@ -434,6 +439,7 @@ class PluginManager:
     def register_toolbar_action(
         self, plugin_name: str, callback: Callable, text: str, icon: str, tooltip: str
     ) -> None:
+        """Register a plugin toolbar button with its callback and display metadata."""
         self.toolbar_actions.append(
             {
                 "plugin": plugin_name,
@@ -447,6 +453,7 @@ class PluginManager:
     def register_drop_handler(
         self, plugin_name: str, callback: Callable, priority: int
     ) -> None:
+        """Register a drag-and-drop handler with a given priority."""
         self.drop_handlers.append(
             {"priority": priority, "plugin": plugin_name, "callback": callback}
         )
@@ -456,6 +463,7 @@ class PluginManager:
     def register_export_action(
         self, plugin_name: str, label: str, callback: Callable
     ) -> None:
+        """Register a plugin export action with its label and callback."""
         self.export_actions.append(
             {"plugin": plugin_name, "label": label, "callback": callback}
         )
@@ -463,6 +471,7 @@ class PluginManager:
     def register_optimization_method(
         self, plugin_name: str, method_name: str, callback: Callable
     ) -> None:
+        """Register a named 3D optimization method provided by a plugin."""
         # Key by upper-case method name for consistency
         self.optimization_methods[method_name.upper()] = {
             "plugin": plugin_name,
@@ -473,6 +482,7 @@ class PluginManager:
     def register_file_opener(
         self, plugin_name: str, extension: str, callback: Callable, priority: int = 0
     ) -> None:
+        """Register a file-type handler for the given extension."""
         # Normalize extension to lowercase
         ext = extension.lower()
         if not ext.startswith("."):
@@ -492,20 +502,24 @@ class PluginManager:
     def register_analysis_tool(
         self, plugin_name: str, label: str, callback: Callable
     ) -> None:
+        """Register a plugin analysis tool with its label and callback."""
         self.analysis_tools.append(
             {"plugin": plugin_name, "label": label, "callback": callback}
         )
 
     # State Persistence registration
     def register_save_handler(self, plugin_name: str, callback: Callable) -> None:
+        """Register a plugin session-save callback."""
         self.save_handlers[plugin_name] = callback
 
     def register_load_handler(self, plugin_name: str, callback: Callable) -> None:
+        """Register a plugin session-load callback."""
         self.load_handlers[plugin_name] = callback
 
     def register_3d_style(
         self, plugin_name: str, style_name: str, callback: Callable
     ) -> None:
+        """Register a named custom 3D rendering style."""
         self.custom_3d_styles[style_name] = {
             "plugin": plugin_name,
             "callback": callback,

moleditpy_linux/plugins/plugin_manager_window.py

@@ -33,6 +33,8 @@ from PyQt6.QtWidgets import (
 
 
 class PluginManagerWindow(QDialog):
+    """Dialog for browsing, installing, and removing plugins."""
+
     def __init__(self, plugin_manager: Any, parent: Optional[QWidget] = None) -> None:
         super().__init__(parent)
         self.btn_remove = None
@@ -46,6 +48,7 @@ class PluginManagerWindow(QDialog):
         self.refresh_plugin_list()
 
     def init_ui(self) -> None:
+        """Build the plugin manager UI with table, buttons, and drag-and-drop support."""
         layout = QVBoxLayout(self)
 
         lbl_info = QLabel("Drag & Drop .py or .zip files here to install plugins.")
@@ -106,6 +109,7 @@ class PluginManagerWindow(QDialog):
         layout.addLayout(btn_layout)
 
     def refresh_plugin_list(self) -> None:
+        """Repopulate the plugin table from the current plugin registry."""
         self.table.setRowCount(0)
         plugins = self.plugin_manager.plugins
 
@@ -146,11 +150,13 @@ class PluginManagerWindow(QDialog):
                 self.table.item(row, 0).setForeground(color)
 
     def update_button_state(self) -> None:
+        """Enable or disable the Remove button based on table selection."""
         has_selection = self.table.currentRow() >= 0
         if hasattr(self, "btn_remove"):
             self.btn_remove.setEnabled(has_selection)
 
     def on_reload(self, silent: bool = False) -> None:
+        """Reload all plugins from disk and refresh the table."""
         # Trigger reload in main manager
         if self.plugin_manager.main_window:
             self.plugin_manager.discover_plugins(self.plugin_manager.main_window)
@@ -164,6 +170,7 @@ class PluginManagerWindow(QDialog):
             self.refresh_plugin_list()
 
     def on_remove_plugin(self) -> None:
+        """Delete the selected plugin file or folder and reload."""
         row = self.table.currentRow()
         if row < 0:
             QMessageBox.warning(self, "Warning", "Please select a plugin to remove.")
@@ -216,6 +223,7 @@ class PluginManagerWindow(QDialog):
                 )
 
     def show_plugin_details(self, item: QTableWidgetItem) -> None:
+        """Show a message box with full metadata for the double-clicked plugin."""
         row = item.row()
         if row < len(self.plugin_manager.plugins):
             p = self.plugin_manager.plugins[row]
@@ -231,6 +239,7 @@ class PluginManagerWindow(QDialog):
 
     # --- Drag & Drop Support ---
     def dragEnterEvent(self, event: Optional[QDragEnterEvent]) -> None:
+        """Accept drag events carrying file URLs."""
         if event is None:
             return
         if event.mimeData().hasUrls():
@@ -239,6 +248,7 @@ class PluginManagerWindow(QDialog):
             event.ignore()
 
     def dropEvent(self, event: Optional[QDropEvent]) -> None:
+        """Install dropped plugin .py files, folders, or zip archives."""
         if event is None:
             return
         files_installed = []

moleditpy_linux/ui/about_dialog.py

@@ -30,6 +30,8 @@ from ..utils.constants import VERSION
 
 
 class AboutDialog(QDialog):
+    """Dialog showing application version, icon, and project links."""
+
     def __init__(self, main_window: Any, parent: Optional[QWidget] = None) -> None:
         super().__init__(parent)
         self.image_label = None
@@ -39,6 +41,7 @@ class AboutDialog(QDialog):
         self.init_ui()
 
     def init_ui(self) -> None:
+        """Build the about dialog layout with icon, version text, and links."""
         layout = QVBoxLayout(self)
 
         # Create a clickable image label

moleditpy_linux/ui/analysis_window.py

@@ -33,6 +33,8 @@ from rdkit.Chem import inchi as rd_inchi
 
 
 class AnalysisWindow(QDialog):
+    """Dialog displaying molecular formula, weight, and other computed properties."""
+
     def __init__(
         self,
         mol: Chem.Mol,
@@ -47,6 +49,7 @@ class AnalysisWindow(QDialog):
         self.init_ui()
 
     def init_ui(self) -> None:
+        """Build the analysis layout with computed molecular properties."""
         main_layout = QVBoxLayout(self)
         grid_layout = QGridLayout()
 
@@ -230,6 +233,7 @@ class AnalysisWindow(QDialog):
         self.setLayout(main_layout)
 
     def copy_to_clipboard(self, text: str) -> None:
+        """Copy text to the system clipboard and show a status bar message."""
         clipboard = QApplication.clipboard()
         clipboard.setText(text)
         if self.parent() and hasattr(self.parent(), "statusBar"):

moleditpy_linux/ui/angle_dialog.py

@@ -40,6 +40,8 @@ if TYPE_CHECKING:
 
 
 class AngleDialog(GeometryBaseDialog):
+    """Dialog for interactively viewing and adjusting a bond angle."""
+
     def __init__(
         self,
         mol: Chem.Mol,
@@ -73,6 +75,7 @@ class AngleDialog(GeometryBaseDialog):
         self.init_ui()
 
     def init_ui(self) -> None:
+        """Build the angle adjustment UI with atom picker, slider, and input field."""
         self.setWindowTitle("Adjust Angle")
         self.setModal(False)
         layout = QVBoxLayout(self)

moleditpy_linux/ui/app_state.py

@@ -71,6 +71,8 @@ def _deserialize_constraints(raw: list) -> list:
 
 
 class StateManager:
+    """Manages serialized undo/redo state and document save state for MainWindow."""
+
     def __init__(self, host: MainWindow) -> None:
         self.host = host
         self.data: MolecularData  # Dynamically assigned in main_window_init.py
@@ -80,6 +82,7 @@ class StateManager:
         self.saved_state: Optional[Dict[str, Any]] = None
 
     def get_current_state(self) -> Dict[str, Any]:
+        """Snapshot the current document into a serializable state dict."""
         atoms = {
             atom_id: {
                 "symbol": data["symbol"],
@@ -126,6 +129,7 @@ class StateManager:
         return state
 
     def set_state_from_data(self, state_data: Dict[str, Any]) -> None:
+        """Restore the document from a previously captured state dict."""
         self.dragged_atom_info = None
         self.host.edit_actions_manager.clear_2d_editor(push_to_undo=False)
 
@@ -256,6 +260,7 @@ class StateManager:
         self.host.edit_3d_manager.update_2d_measurement_labels()
 
     def push_undo_state(self) -> None:
+        """Push the current state onto the undo stack."""
         self.host.edit_actions_manager.push_undo_state()
 
     def update_window_title(self) -> None:
@@ -307,6 +312,7 @@ class StateManager:
             return False  # Cancel
 
     def reset_undo_stack(self) -> None:
+        """Clear the undo and redo stacks."""
         self.host.reset_undo_redo_stacks()
 
     def update_realtime_info(self) -> None:

moleditpy_linux/ui/atom_item.py

@@ -36,6 +36,8 @@ from ..utils.sip_isdeleted_safe import sip_isdeleted_safe
 
 
 class AtomItem(QGraphicsItem):
+    """2D scene item representing a single atom in the molecule editor."""
+
     def __init__(
         self, atom_id: int, symbol: str, pos: QPointF, charge: int = 0, radical: int = 0
     ) -> None:
@@ -62,6 +64,7 @@ class AtomItem(QGraphicsItem):
         self.font: QFont = QFont(FONT_FAMILY, 20, FONT_WEIGHT_BOLD)
 
     def update_style(self) -> None:
+        """Refresh font, color, and visibility based on current scene settings."""
         if sip_isdeleted_safe(self):
             return
         # Allow updating font preference dynamically
@@ -197,6 +200,7 @@ class AtomItem(QGraphicsItem):
         return full_visual_rect.adjusted(-3, -3, 3, 3)
 
     def get_bg_ellipse_path(self) -> QPainterPath:
+        """Return the elliptical background path used for bond endpoint clipping."""
         path = QPainterPath()
         if not self.is_visible:
             return path
@@ -468,6 +472,7 @@ class AtomItem(QGraphicsItem):
             painter.drawRect(self.boundingRect())
 
     def itemChange(self, change: QGraphicsItem.GraphicsItemChange, value: Any) -> Any:
+        """Propagate position and scene changes to connected bond items."""
         res = super().itemChange(change, value)
         if change == QGraphicsItem.GraphicsItemChange.ItemPositionHasChanged:
             if self.flags() & QGraphicsItem.GraphicsItemFlag.ItemIsMovable:
@@ -480,12 +485,14 @@ class AtomItem(QGraphicsItem):
         return res
 
     def hoverEnterEvent(self, event: Any) -> None:
+        """Highlight the atom on mouse hover."""
         # Enable highlight on hover regardless of scene mode
         self.hovered = True
         self.update()
         super().hoverEnterEvent(event)
 
     def hoverLeaveEvent(self, event: Any) -> None:
+        """Remove hover highlight when the mouse leaves."""
         if self.hovered:
             self.hovered = False
             self.update()

moleditpy_linux/ui/bond_item.py

@@ -159,6 +159,7 @@ class BondItem(QGraphicsItem):
         self.ring_center: Optional[Union[QPointF, Tuple[float, float]]] = None
 
     def get_line_in_local_coords(self) -> QLineF:
+        """Return the visible bond line trimmed back to avoid overlapping atom symbol backgrounds."""
         if self.atom1 is None or self.atom2 is None:
             return QLineF(0, 0, 0, 0)
         try:
@@ -214,6 +215,7 @@ class BondItem(QGraphicsItem):
             return QLineF(0, 0, 0, 0)
 
     def boundingRect(self) -> QRectF:
+        """Return the bounding rect encompassing all visual bond representations."""
         try:
             line = self.get_line_in_local_coords()
         except (AttributeError, RuntimeError, ValueError, TypeError):
@@ -315,6 +317,7 @@ class BondItem(QGraphicsItem):
         option: Any,
         widget: Optional[QWidget] = None,
     ) -> None:
+        """Render the bond as single, double, triple, wedge, or dashed line."""
         if painter is None or self.atom1 is None or self.atom2 is None:
             return
         line = self.get_line_in_local_coords()
@@ -584,6 +587,7 @@ class BondItem(QGraphicsItem):
         painter.restore()
 
     def update_position(self, notify: bool = True) -> None:
+        """Reposition the bond item relative to its first atom's scene position."""
         try:
             if notify:
                 self.prepareGeometryChange()
@@ -595,6 +599,7 @@ class BondItem(QGraphicsItem):
             # Continue without crashing
 
     def hoverEnterEvent(self, event: Any) -> None:
+        """Highlight the bond on mouse hover."""
         self.hovered = True
         self.update()
         if self.scene():
@@ -602,6 +607,7 @@ class BondItem(QGraphicsItem):
         super().hoverEnterEvent(event)
 
     def hoverLeaveEvent(self, event: Any) -> None:
+        """Remove hover highlight when the mouse leaves."""
         if self.hovered:
             self.hovered = False
             self.update()

moleditpy_linux/ui/bond_length_dialog.py

@@ -37,6 +37,8 @@ if TYPE_CHECKING:
 
 
 class BondLengthDialog(GeometryBaseDialog):
+    """Dialog for interactively viewing and adjusting a bond length."""
+
     def __init__(
         self,
         mol: Chem.Mol,
@@ -68,6 +70,7 @@ class BondLengthDialog(GeometryBaseDialog):
         self.init_ui()
 
     def init_ui(self) -> None:
+        """Build the bond length adjustment UI with atom picker, slider, and input field."""
         self.setWindowTitle("Adjust Bond Length")
         self.setModal(False)
 

moleditpy_linux/ui/calculation_worker.py

@@ -696,6 +696,8 @@ print(ob_mol.write("mol"))
 
 
 class CalculationWorker(QObject):
+    """QObject worker that runs 3D geometry optimization on a background QThread."""
+
     status_update = pyqtSignal(str)
     finished = pyqtSignal(object)
     error = pyqtSignal(object)

moleditpy_linux/ui/color_settings_dialog.py

@@ -240,6 +240,7 @@ class ColorSettingsDialog(QDialog):
         layout.addLayout(h)
 
     def on_element_clicked(self) -> None:
+        """Open a color picker for the clicked element button and update its swatch."""
         btn = self.sender()
         symbol = btn.text()
         cur = self.current_settings.get("cpk_colors", {}).get(symbol)
@@ -257,6 +258,7 @@ class ColorSettingsDialog(QDialog):
             )
 
     def reset_all(self) -> None:
+        """Revert all CPK and ball-and-stick colors to their defaults."""
         self.changed_cpk = {}
         self._reset_all_flag = True
 
@@ -284,6 +286,7 @@ class ColorSettingsDialog(QDialog):
         self.bs_button.setToolTip(hexv)
 
     def apply_changes(self) -> None:
+        """Write changed color settings to the application settings and redraw."""
         if not self.parent_window or not hasattr(self.parent_window, "init_manager"):
             return
 
@@ -370,10 +373,12 @@ class ColorSettingsDialog(QDialog):
                 self.parent_window.view_3d_manager.draw_molecule_3d(mol)
 
     def accept(self) -> None:
+        """Apply changes and close the dialog."""
         self.apply_changes()
         super().accept()
 
     def pick_bs_bond_color(self) -> None:
+        """Open a color picker for the ball-and-stick bond color."""
         settings = self.current_settings or {}
         cur = getattr(self, "changed_bs_color", None) or settings.get(
             "ball_stick_bond_color"

moleditpy_linux/ui/compute_logic.py

@@ -450,6 +450,7 @@ class ComputeManager:
     def on_calculation_finished(
         self, result: Union[Chem.Mol, Tuple[int, Chem.Mol]]
     ) -> None:
+        """Handle a completed 3D optimization result from the background worker."""
         worker_id, mol = result if isinstance(result, tuple) else (None, result)
         if worker_id is not None:
             if worker_id not in self.active_worker_ids:
@@ -500,6 +501,7 @@ class ComputeManager:
         self.host.view_3d_manager.update_atom_id_menu_state()
 
     def on_calculation_error(self, message: Union[str, Tuple[int, str]]) -> None:
+        """Handle an error or halt signal from the background optimization worker."""
         # Accept either a string or (worker_id, message) tuple from the worker signal
         if isinstance(message, tuple) and len(message) == 2:
             worker_id, msg = message
@@ -567,6 +569,7 @@ class ComputeManager:
                 continue
 
     def check_chemistry_problems_fallback(self) -> None:
+        """Mark valence-problem atoms in the 2D scene when RDKit validation is unavailable."""
         problem_atom_ids = identify_valence_problems(
             self.host.state_manager.data.atoms, self.host.state_manager.data.bonds
         )

moleditpy_linux/ui/constrained_optimization_dialog.py

@@ -34,6 +34,8 @@ from .dialog_3d_picking_mixin import Dialog3DPickingMixin
 
 
 class ConstrainedOptimizationThread(QThread):
+    """QThread that runs a force-field minimization with atom constraints."""
+
     optimization_finished = pyqtSignal()
     error_occurred = pyqtSignal(str)
 
@@ -43,6 +45,7 @@ class ConstrainedOptimizationThread(QThread):
         self.max_iters = max_iters
 
     def run(self) -> None:
+        """Execute force-field minimization and emit finished or error signal."""
         try:
             self.ff.Minimize(maxIts=self.max_iters)
             self.optimization_finished.emit()
@@ -156,6 +159,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
             logging.exception("Could not set default force field")
 
     def init_ui(self) -> None:
+        """Build the constrained optimization dialog with constraint table and controls."""
         self.setWindowTitle("Constrained Optimization")
         self.setModal(False)
         self.resize(450, 500)
@@ -256,6 +260,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
         self.update_selection_display()
 
     def update_selection_display(self) -> None:
+        """Update the selection label and Add Constraint button state."""
         self.show_selection_labels()
         n = len(self.selected_atoms)
 
@@ -292,6 +297,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
         self.add_button.setEnabled(can_add)
 
     def add_constraint(self) -> None:
+        """Read the current atom selection, compute its geometry value, and add a row to the table."""
         n = len(self.selected_atoms)
         conf = self.mol.GetConformer()
 
@@ -368,6 +374,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
         self.update_selection_display()
 
     def remove_constraint(self) -> None:
+        """Delete the selected constraint rows from the table."""
         selected_rows = sorted(
             list(set(index.row() for index in self.constraint_table.selectedIndexes())),
             reverse=True,
@@ -405,6 +412,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
         self.remove_button.setEnabled(False)
 
     def show_constraint_labels(self) -> None:
+        """Display 3D atom labels for the selected constraint rows."""
         self.clear_constraint_labels()
         selected_items = self.constraint_table.selectedItems()
         if not selected_items:
@@ -474,6 +482,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
                         logging.debug(f"Could not restore camera position: {e}")
 
     def clear_constraint_labels(self) -> None:
+        """Remove all constraint label actors from the 3D plotter."""
         for label_actor in self.constraint_labels:
             try:
                 plotter = self.main_window.view_3d_manager.plotter
@@ -487,6 +496,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
         self.constraint_labels = []
 
     def apply_optimization(self) -> None:
+        """Run force-field minimization with the configured constraints."""
         if not self.mol or self.mol.GetNumConformers() == 0:
             QMessageBox.warning(self, "Error", "No valid 3D molecule found.")
             return
@@ -666,10 +676,12 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
             QMessageBox.critical(self, "Error", f"Optimization failed: {e}")
 
     def closeEvent(self, event: Any) -> None:
+        """Delegate window close to reject."""
         self.reject()
         event.accept()
 
     def reject(self) -> None:
+        """Clear labels, disable picking, and save constraints before closing."""
         self.clear_constraint_labels()
         self.clear_selection_labels()
         self.disable_picking()

moleditpy_linux/ui/custom_interactor_style.py

@@ -27,6 +27,8 @@ from rdkit import Geometry
 
 
 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:
         super().__init__(**kwargs)
         self.main_window = main_window