MoleditPy-linux 4.0.1__tar.gz → 4.1.0__tar.gz

{moleditpy_linux-4.0.1 → moleditpy_linux-4.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.0.1
+Version: 4.1.0
 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_linux-4.0.1 → moleditpy_linux-4.1.0}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "4.0.1"
+version = "4.1.0"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-4.0.1 → moleditpy_linux-4.1.0}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.0.1
+Version: 4.1.0
 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_linux-4.0.1 → moleditpy_linux-4.1.0}/src/moleditpy_linux/core/mol_geometry.py

@@ -13,7 +13,21 @@ DOI: 10.5281/zenodo.17268532
 from __future__ import annotations
 import math
 from collections import deque
-from typing import Any, Dict, Iterable, List, Optional, Set, Tuple, Union
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    Callable,
+    Dict,
+    Iterable,
+    List,
+    Optional,
+    Set,
+    Tuple,
+    Union,
+)
+
+if TYPE_CHECKING:
+    from rdkit import Chem
 
 import numpy as np
 
@@ -82,7 +96,7 @@ def calc_angle_deg(
 
 
 def get_connected_group(
-    mol: Any, start_atom: int, exclude: Optional[int] = None
+    mol: Chem.Mol, start_atom: int, exclude: Optional[int] = None
 ) -> Set[int]:
     """Return the set of atom indices reachable from *start_atom*
     without passing through *exclude*.
@@ -422,7 +436,9 @@ def is_problematic_valence(
 
 
 def inject_ez_stereo_to_mol_block(
-    mol_block: str, rdkit_mol: Any, bonds_data: Dict[Tuple[int, int], Any]
+    mol_block: str,
+    rdkit_mol: Chem.Mol,
+    bonds_data: Dict[Tuple[int, int], Dict[str, Any]],
 ) -> str:
     """Generate a modified MOL block with 'M CFG' lines for E/Z stereochemistry.
 
@@ -504,7 +520,7 @@ def identify_valence_problems(
     problem_atom_ids = []
 
     # Pre-calculate bond orders per atom
-    bond_orders: Dict[int, int] = {}
+    bond_orders: Dict[int, float] = {}
     for (id1, id2), bond in bonds_data.items():
         order = bond.get("order", 1)
         bond_orders[id1] = bond_orders.get(id1, 0) + order
@@ -521,7 +537,7 @@ def identify_valence_problems(
     return problem_atom_ids
 
 
-def optimize_2d_coords(mol: Any) -> Dict[int, Tuple[float, float]]:
+def optimize_2d_coords(mol: Chem.Mol) -> Dict[int, Tuple[float, float]]:
     """Generate 2D coordinates using RDKit and return a map of (x, y) tuples."""
     from rdkit.Chem import AllChem
 
@@ -572,7 +588,7 @@ def resolve_2d_overlaps(
     adjacency_list: Dict[int, List[int]],
     overlap_threshold: float = 0.5,
     move_distance: float = 20,
-    has_bond_check_func: Optional[Any] = None,
+    has_bond_check_func: Optional[Callable[[int, int], bool]] = None,
 ) -> List[Tuple[Set[int], Tuple[float, float]]]:
     """Detect and resolve overlapping atom groups in 2D.
 
@@ -601,13 +617,13 @@ def resolve_2d_overlaps(
     # Union-Find for overlap groups
     parent = {aid: aid for aid in atom_ids}
 
-    def find_set(aid: Any) -> Any:
+    def find_set(aid: int) -> int:
         if parent[aid] == aid:
             return aid
         parent[aid] = find_set(parent[aid])
         return parent[aid]
 
-    def unite_sets(aid1: Any, aid2: Any) -> None:
+    def unite_sets(aid1: int, aid2: int) -> None:
         root1 = find_set(aid1)
         root2 = find_set(aid2)
         if root1 != root2:

{moleditpy_linux-4.0.1 → moleditpy_linux-4.1.0}/src/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-4.0.1 → moleditpy_linux-4.1.0}/src/moleditpy_linux/main.py

@@ -11,36 +11,92 @@ DOI: 10.5281/zenodo.17268532
 """
 
 import ctypes
-import sys
-import argparse
+import json
 import logging
+import logging.handlers
 import os
+import sys
+import argparse
 from typing import Any
 
 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 _read_startup_log_settings() -> tuple[bool, bool]:
+    """Read log_to_file and log_level_debug from settings.json before Qt starts.
+
+    Returns (log_to_file, log_level_debug). Falls back to (False, False) on any error.
+    """
+    settings_path = os.path.join(os.path.expanduser("~"), ".moleditpy", "settings.json")
+    try:
+        with open(settings_path, encoding="utf-8") as f:
+            data = json.load(f)
+        return bool(data.get("log_to_file", False)), bool(
+            data.get("log_level_debug", False)
+        )
+    except (OSError, json.JSONDecodeError, ValueError):
+        return False, False
+
 
 def setup_logging() -> None:
+    """Configure root logger and install a global unhandled-exception handler."""
+    log_to_file, log_level_debug = _read_startup_log_settings()
+    level = logging.DEBUG if log_level_debug else logging.INFO
+    fmt = "%(asctime)s [%(levelname)s] %(name)s (%(pathname)s:%(lineno)d): %(message)s"
+
     logging.basicConfig(
-        level=logging.INFO,
-        format="%(asctime)s [%(levelname)s] %(name)s (%(pathname)s:%(lineno)d): %(message)s",
+        level=level,
+        format=fmt,
         stream=sys.stdout,
         force=True,
     )
 
+    if log_to_file:
+        log_dir = os.path.join(os.path.expanduser("~"), ".moleditpy")
+        try:
+            os.makedirs(log_dir, exist_ok=True)
+            log_path = os.path.join(log_dir, "moleditpy_linux.log")
+            fh = logging.handlers.RotatingFileHandler(
+                log_path, maxBytes=1_048_576, backupCount=3, encoding="utf-8"
+            )
+            fh.setLevel(level)
+            fh.setFormatter(logging.Formatter(fmt))
+            logging.getLogger().addHandler(fh)
+            logging.info("File logging enabled: %s", log_path)
+        except OSError as e:
+            logging.warning("Could not open log file: %s", e)
+
     def handle_exception(exc_type: Any, exc_value: Any, exc_traceback: Any) -> None:
         """Log unhandled exceptions using the configured logging system."""
         if issubclass(exc_type, KeyboardInterrupt):
-            # Allow keyboard interrupt to exit normally
             sys.__excepthook__(exc_type, exc_value, exc_traceback)
             return
-
         logging.error(
             "Uncaught exception", exc_info=(exc_type, exc_value, exc_traceback)
         )
@@ -49,12 +105,11 @@ 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 +135,6 @@ 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 +149,6 @@ 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 +189,10 @@ 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-4.0.1 → moleditpy_linux-4.1.0}/src/moleditpy_linux/plugins/plugin_interface.py

@@ -10,6 +10,7 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
+import logging
 from typing import Any, Callable, List, Optional, Union
 
 
@@ -173,10 +174,11 @@ class PluginContext:
         """Switch the application UI layout to 3D viewer mode (Public API)."""
         mw = self.get_main_window()
         if mw is not None and hasattr(mw, "ui_manager"):
-            if hasattr(mw.ui_manager, "enter_3d_viewer_mode"):
-                mw.ui_manager.enter_3d_viewer_mode()
-            elif hasattr(mw.ui_manager, "enter_3d_viewer_ui_mode"):
-                mw.ui_manager.enter_3d_viewer_ui_mode()
+            fn = getattr(mw.ui_manager, "enter_3d_viewer_mode", None) or getattr(
+                mw.ui_manager, "enter_3d_viewer_ui_mode", None
+            )
+            if fn:
+                fn()
 
     def enter_3d_mode(self) -> None:
         """Switch UI layout to 3D viewer mode. Alias for enter_3d_viewer_mode."""
@@ -240,16 +242,11 @@ class PluginContext:
         """Force the 3D window to redraw using the current molecule."""
         mw = self.get_main_window()
         if mw and hasattr(mw, "view_3d_manager"):
-            mol = getattr(mw.view_3d_manager, "current_mol", None)
+            mol = mw.view_3d_manager.current_mol
             if mol:
                 mw.view_3d_manager.draw_molecule_3d(mol)
-            else:
-                # Also redraw/clear plotter if no molecule
-                if (
-                    hasattr(mw.view_3d_manager, "plotter")
-                    and mw.view_3d_manager.plotter
-                ):
-                    mw.view_3d_manager.plotter.render()
+            elif mw.view_3d_manager.plotter:
+                mw.view_3d_manager.plotter.render()
 
     def reset_3d_camera(self) -> None:
         """Zoom in and re-center the 3D viewport to fit the current molecule."""
@@ -370,7 +367,7 @@ class PluginContext:
             default: Value to return if the setting is not found.
         """
         mw = self.get_main_window()
-        if mw and hasattr(mw, "init_manager") and hasattr(mw.init_manager, "settings"):
+        if mw and hasattr(mw, "init_manager"):
             namespaced = f"plugin.{self._plugin_name}.{key}"
             return mw.init_manager.settings.get(namespaced, default)
         return default
@@ -387,11 +384,10 @@ class PluginContext:
             value: Value to store (must be JSON-serializable).
         """
         mw = self.get_main_window()
-        if mw and hasattr(mw, "init_manager") and hasattr(mw.init_manager, "settings"):
+        if mw and hasattr(mw, "init_manager"):
             namespaced = f"plugin.{self._plugin_name}.{key}"
             mw.init_manager.settings[namespaced] = value
-            if hasattr(mw.init_manager, "settings_dirty"):
-                mw.init_manager.settings_dirty = True
+            mw.init_manager.settings_dirty = True
 
     def mark_project_modified(self) -> None:
         """Mark the current project as having unsaved changes and update the window title."""
@@ -399,8 +395,9 @@ class PluginContext:
         if mw and hasattr(mw, "state_manager"):
             try:
                 mw.state_manager.has_unsaved_changes = True
-                if hasattr(mw.state_manager, "update_window_title"):
-                    mw.state_manager.update_window_title()
+                fn = getattr(mw.state_manager, "update_window_title", None)
+                if fn:
+                    fn()
             except Exception:
                 pass
 
@@ -414,14 +411,16 @@ class PluginContext:
         if mw is None:
             return
         if hasattr(mw, "state_manager"):
-            if hasattr(mw.state_manager, "update_realtime_info"):
-                mw.state_manager.update_realtime_info()
-            if hasattr(mw.state_manager, "update_window_title"):
-                mw.state_manager.update_window_title()
-        if hasattr(mw, "edit_actions_manager") and hasattr(
-            mw.edit_actions_manager, "update_undo_redo_actions"
-        ):
-            mw.edit_actions_manager.update_undo_redo_actions()
+            fn = getattr(mw.state_manager, "update_realtime_info", None)
+            if fn:
+                fn()
+            fn = getattr(mw.state_manager, "update_window_title", None)
+            if fn:
+                fn()
+        if hasattr(mw, "edit_actions_manager"):
+            fn = getattr(mw.edit_actions_manager, "update_undo_redo_actions", None)
+            if fn:
+                fn()
 
     def fit_3d_view(self) -> None:
         """Zoom and re-center the 3D viewport to fit the current molecule."""
@@ -489,8 +488,10 @@ class PluginContext:
         mw = self.get_main_window()
         if mw and hasattr(mw, "init_manager"):
             scene = getattr(mw.init_manager, "scene", None)
-            if scene is not None and hasattr(scene, "update_all_items"):
-                scene.update_all_items()
+            if scene is not None:
+                fn = getattr(scene, "update_all_items", None)
+                if fn:
+                    fn()
 
     def load_from_smiles(self, smiles: str) -> None:
         """Add a molecule from a SMILES string to the 2D editor."""
@@ -518,6 +519,7 @@ class PluginContext:
 
             return "\n".join(xyz_lines)
         except Exception:
+            logging.debug("to_xyz_block failed", exc_info=True)
             return None
 
 
@@ -541,8 +543,8 @@ class Plugin3DController:
         v3d = self._get_v3d()
         if v3d:
             v3d.update_atom_color_override(atom_index, color_hex)
-            if hasattr(self._mw, "plotter") and self._mw.plotter:
-                self._mw.plotter.render()
+            if v3d.plotter:
+                v3d.plotter.render()
 
     def set_bond_color(self, bond_index: int, color_hex: str) -> None:
         """
@@ -555,8 +557,8 @@ class Plugin3DController:
         v3d = self._get_v3d()
         if v3d:
             v3d.update_bond_color_override(bond_index, color_hex)
-            if hasattr(self._mw, "plotter") and self._mw.plotter:
-                self._mw.plotter.render()
+            if v3d.plotter:
+                v3d.plotter.render()
 
     def set_bond_color_by_atoms(
         self, atom_idx1: int, atom_idx2: int, color_hex: str
@@ -569,7 +571,8 @@ class Plugin3DController:
             atom_idx2: Second RDKit atom index.
             color_hex: Hex string e.g., "#00FF00".
         """
-        mol = getattr(self._mw, "current_mol", None)
+        v3d = self._get_v3d()
+        mol = v3d.current_mol if v3d else None
         if not mol:
             return
 

{moleditpy_linux-4.0.1 → moleditpy_linux-4.1.0}/src/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-4.0.1 → moleditpy_linux-4.1.0}/src/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.")
@@ -206,7 +213,7 @@ class PluginManagerWindow(QDialog):
                             "Success",
                             f"Removed '{plugin.get('name', 'Unknown')}'.",
                         )
-                    except (AttributeError, RuntimeError, ValueError) as e:
+                    except OSError as e:
                         QMessageBox.critical(
                             self, "Error", f"Failed to delete plugin: {e}"
                         )
@@ -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-4.0.1 → moleditpy_linux-4.1.0}/src/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-4.0.1 → moleditpy_linux-4.1.0}/src/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"):