MoleditPy-linux 4.0.2__tar.gz → 4.1.1__tar.gz

{moleditpy_linux-4.0.2 → moleditpy_linux-4.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.0.2
+Version: 4.1.1
 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
@@ -837,9 +837,9 @@ moleditpy
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
   * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
-## License
+## License & Disclaimer
 
-This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**. See the `LICENSE` file for details.
+This project is licensed under the GNU General Public License v3.0 (GPLv3) - see the [LICENSE](LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
 
 ## Citation
 
@@ -971,9 +971,9 @@ moleditpy
   * **化学計算 (RDKit / Open Babel):** 2DデータからRDKit分子オブジェクトを生成し、3D座標生成や分子特性計算を実行します。RDKitでの3D座標生成が失敗した際は、Open Babelにフォールバックします。重い計算処理は別スレッド (`QThread`) で実行し、GUIの応答性を維持しています。
   * **3D可視化 (PyVista / pyvistaqt):** RDKitのコンフォーマ座標からPyVistaのメッシュ（球や円柱）を生成して描画します。カスタムの`vtkInteractorStyle`を実装し、3Dビュー内での原子の直接的なドラッグ＆ドロップ編集を可能にしています。
 
-## ライセンス
+## ライセンス & 免責事項
 
-このプロジェクトは **GNU General Public License v3.0 (GPL-v3)** のもとで公開されています。詳細は `LICENSE` ファイルを参照してください。
+このプロジェクトは GNU General Public License v3.0 (GPLv3) のもとでライセンスされています。詳細は [LICENSE](LICENSE) ファイルを参照してください。オープンソースソフトウェアとして、本ソフトウェアは「現状のまま」提供され、いかなる明示または黙示の保証も行いません。また、本ソフトウェアを使用した結果について、作者は一切の責任や義務を負いません。出力結果は慎重に検証されていますが、学術論文の作成など重要な用途においては、ユーザーご自身で結果を独立して確認および検証することを強くお勧めします。バグに遭遇した場合は、Issueを作成してください。
 
 ## 引用
 

{moleditpy_linux-4.0.2 → moleditpy_linux-4.1.1}/README.md

@@ -134,9 +134,9 @@ moleditpy
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
   * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
-## License
+## License & Disclaimer
 
-This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**. See the `LICENSE` file for details.
+This project is licensed under the GNU General Public License v3.0 (GPLv3) - see the [LICENSE](LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
 
 ## Citation
 
@@ -268,9 +268,9 @@ moleditpy
   * **化学計算 (RDKit / Open Babel):** 2DデータからRDKit分子オブジェクトを生成し、3D座標生成や分子特性計算を実行します。RDKitでの3D座標生成が失敗した際は、Open Babelにフォールバックします。重い計算処理は別スレッド (`QThread`) で実行し、GUIの応答性を維持しています。
   * **3D可視化 (PyVista / pyvistaqt):** RDKitのコンフォーマ座標からPyVistaのメッシュ（球や円柱）を生成して描画します。カスタムの`vtkInteractorStyle`を実装し、3Dビュー内での原子の直接的なドラッグ＆ドロップ編集を可能にしています。
 
-## ライセンス
+## ライセンス & 免責事項
 
-このプロジェクトは **GNU General Public License v3.0 (GPL-v3)** のもとで公開されています。詳細は `LICENSE` ファイルを参照してください。
+このプロジェクトは GNU General Public License v3.0 (GPLv3) のもとでライセンスされています。詳細は [LICENSE](LICENSE) ファイルを参照してください。オープンソースソフトウェアとして、本ソフトウェアは「現状のまま」提供され、いかなる明示または黙示の保証も行いません。また、本ソフトウェアを使用した結果について、作者は一切の責任や義務を負いません。出力結果は慎重に検証されていますが、学術論文の作成など重要な用途においては、ユーザーご自身で結果を独立して確認および検証することを強くお勧めします。バグに遭遇した場合は、Issueを作成してください。
 
 ## 引用
 

{moleditpy_linux-4.0.2 → moleditpy_linux-4.1.1}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "4.0.2"
+version = "4.1.1"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-4.0.2 → moleditpy_linux-4.1.1}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.0.2
+Version: 4.1.1
 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
@@ -837,9 +837,9 @@ moleditpy
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
   * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
-## License
+## License & Disclaimer
 
-This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**. See the `LICENSE` file for details.
+This project is licensed under the GNU General Public License v3.0 (GPLv3) - see the [LICENSE](LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
 
 ## Citation
 
@@ -971,9 +971,9 @@ moleditpy
   * **化学計算 (RDKit / Open Babel):** 2DデータからRDKit分子オブジェクトを生成し、3D座標生成や分子特性計算を実行します。RDKitでの3D座標生成が失敗した際は、Open Babelにフォールバックします。重い計算処理は別スレッド (`QThread`) で実行し、GUIの応答性を維持しています。
   * **3D可視化 (PyVista / pyvistaqt):** RDKitのコンフォーマ座標からPyVistaのメッシュ（球や円柱）を生成して描画します。カスタムの`vtkInteractorStyle`を実装し、3Dビュー内での原子の直接的なドラッグ＆ドロップ編集を可能にしています。
 
-## ライセンス
+## ライセンス & 免責事項
 
-このプロジェクトは **GNU General Public License v3.0 (GPL-v3)** のもとで公開されています。詳細は `LICENSE` ファイルを参照してください。
+このプロジェクトは GNU General Public License v3.0 (GPLv3) のもとでライセンスされています。詳細は [LICENSE](LICENSE) ファイルを参照してください。オープンソースソフトウェアとして、本ソフトウェアは「現状のまま」提供され、いかなる明示または黙示の保証も行いません。また、本ソフトウェアを使用した結果について、作者は一切の責任や義務を負いません。出力結果は慎重に検証されていますが、学術論文の作成など重要な用途においては、ユーザーご自身で結果を独立して確認および検証することを強くお勧めします。バグに遭遇した場合は、Issueを作成してください。
 
 ## 引用
 

{moleditpy_linux-4.0.2 → moleditpy_linux-4.1.1}/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-4.0.2 → moleditpy_linux-4.1.1}/src/moleditpy_linux/main.py

@@ -11,10 +11,12 @@ 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
@@ -46,22 +48,55 @@ def _qt_message_handler(mode: QtMsgType, _context: Any, message: str) -> None:
     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)
         )

{moleditpy_linux-4.0.2 → moleditpy_linux-4.1.1}/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-4.0.2 → moleditpy_linux-4.1.1}/src/moleditpy_linux/plugins/plugin_manager_window.py

@@ -213,7 +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}"
                         )

{moleditpy_linux-4.0.2 → moleditpy_linux-4.1.1}/src/moleditpy_linux/ui/app_state.py

@@ -542,13 +542,9 @@ class StateManager:
         # 3D viewer mode
         is_3d_mode = json_data.get("is_3d_viewer_mode", False)
         # Restore last successful optimization method if present in file
-        try:
-            method = json_data.get("last_successful_optimization_method", None)
-            with contextlib.suppress(AttributeError, RuntimeError, TypeError):
-                self.host.set_last_successful_optimization_method(method)
-        except (AttributeError, RuntimeError, TypeError):
-            # Safe defensive fallback catching AttributeError, RuntimeError, TypeError
-            pass
+        method = json_data.get("last_successful_optimization_method", None)
+        with contextlib.suppress(AttributeError, RuntimeError, TypeError):
+            self.host.set_last_successful_optimization_method(method)
 
         # Plugin State Restoration (Phase 3)
         self._preserved_plugin_data = {}  # Reset preserved data on new load

{moleditpy_linux-4.0.2 → moleditpy_linux-4.1.1}/src/moleditpy_linux/ui/atom_item.py

@@ -11,7 +11,7 @@ DOI: 10.5281/zenodo.17268532
 """
 
 from __future__ import annotations
-from typing import Any, List, Optional
+from typing import TYPE_CHECKING, Any, List, Optional
 
 from PyQt6.QtCore import QPointF, QRectF, Qt
 from PyQt6.QtGui import (
@@ -23,7 +23,12 @@ from PyQt6.QtGui import (
     QPainterPath,
     QPen,
 )
-from PyQt6.QtWidgets import QGraphicsItem, QWidget
+from PyQt6.QtWidgets import (
+    QGraphicsItem,
+    QGraphicsSceneHoverEvent,
+    QStyleOptionGraphicsItem,
+    QWidget,
+)
 
 from ..utils.constants import (
     ATOM_RADIUS,
@@ -34,6 +39,9 @@ from ..utils.constants import (
 )
 from ..utils.sip_isdeleted_safe import sip_isdeleted_safe
 
+if TYPE_CHECKING:
+    from .bond_item import BondItem
+
 
 class AtomItem(QGraphicsItem):
     """2D scene item representing a single atom in the molecule editor."""
@@ -46,7 +54,7 @@ class AtomItem(QGraphicsItem):
         self.symbol: str = symbol
         self.charge: int = charge
         self.radical: int = radical
-        self.bonds: List[Any] = []
+        self.bonds: List[BondItem] = []
         self.chiral_label: Optional[str] = None
 
         self.setPos(pos)
@@ -67,16 +75,24 @@ class AtomItem(QGraphicsItem):
         """Refresh font, color, and visibility based on current scene settings."""
         if sip_isdeleted_safe(self):
             return
-        # Allow updating font preference dynamically
         font_size = 20
         font_family = FONT_FAMILY
+        font_bold = True
+        font_italic = False
+        font_underline = False
 
         scene = self.scene()
         if scene is not None and hasattr(scene, "get_setting"):
             font_size = scene.get_setting("atom_font_size_2d", 20)
             font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
-
-        self.font = QFont(font_family, font_size, FONT_WEIGHT_BOLD)
+            font_bold = scene.get_setting("atom_font_bold_2d", True)
+            font_italic = scene.get_setting("atom_font_italic_2d", False)
+            font_underline = scene.get_setting("atom_font_underline_2d", False)
+
+        weight = QFont.Weight.Bold if font_bold else QFont.Weight.Normal
+        self.font = QFont(font_family, font_size, weight)
+        self.font.setItalic(font_italic)
+        self.font.setUnderline(font_underline)
         self.prepareGeometryChange()
 
         self.is_visible = not (
@@ -89,16 +105,23 @@ class AtomItem(QGraphicsItem):
 
     def boundingRect(self) -> QRectF:
         """Calculate the bounding rectangle for the atom item."""
-        # --- Calculate text position and size using logic matching paint() ---
-        # Get dynamic font size and family
         font_size = 20
         font_family = FONT_FAMILY
+        font_bold = True
+        font_italic = False
+        font_underline = False
         scene = self.scene()
         if scene is not None and hasattr(scene, "get_setting"):
             font_size = scene.get_setting("atom_font_size_2d", 20)
             font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
-
-        font = QFont(font_family, font_size, FONT_WEIGHT_BOLD)
+            font_bold = scene.get_setting("atom_font_bold_2d", True)
+            font_italic = scene.get_setting("atom_font_italic_2d", False)
+            font_underline = scene.get_setting("atom_font_underline_2d", False)
+
+        weight = QFont.Weight.Bold if font_bold else QFont.Weight.Normal
+        font = QFont(font_family, font_size, weight)
+        font.setItalic(font_italic)
+        font.setUnderline(font_underline)
         fm = QFontMetricsF(font)
 
         hydrogen_part = ""
@@ -207,13 +230,21 @@ class AtomItem(QGraphicsItem):
 
         font_size = 20
         font_family = FONT_FAMILY
+        font_bold = True
+        font_italic = False
+        font_underline = False
         scene = self.scene()
-        if scene is not None:
-            if hasattr(scene, "get_setting"):
-                font_size = scene.get_setting("atom_font_size_2d", 20)
-                font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
-
-        font = QFont(font_family, font_size, FONT_WEIGHT_BOLD)
+        if scene is not None and hasattr(scene, "get_setting"):
+            font_size = scene.get_setting("atom_font_size_2d", 20)
+            font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
+            font_bold = scene.get_setting("atom_font_bold_2d", True)
+            font_italic = scene.get_setting("atom_font_italic_2d", False)
+            font_underline = scene.get_setting("atom_font_underline_2d", False)
+
+        weight = QFont.Weight.Bold if font_bold else QFont.Weight.Normal
+        font = QFont(font_family, font_size, weight)
+        font.setItalic(font_italic)
+        font.setUnderline(font_underline)
         fm = QFontMetricsF(font)
 
         hydrogen_part = ""
@@ -292,7 +323,7 @@ class AtomItem(QGraphicsItem):
     def paint(
         self,
         painter: Optional[QPainter],
-        option: Any,
+        option: QStyleOptionGraphicsItem,
         widget: Optional[QWidget] = None,
     ) -> None:
         """Paint the atom symbol and its associated labels (charge, radical)."""
@@ -484,14 +515,14 @@ class AtomItem(QGraphicsItem):
                 self.update_style()
         return res
 
-    def hoverEnterEvent(self, event: Any) -> None:
+    def hoverEnterEvent(self, event: QGraphicsSceneHoverEvent) -> 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:
+    def hoverLeaveEvent(self, event: QGraphicsSceneHoverEvent) -> None:
         """Remove hover highlight when the mouse leaves."""
         if self.hovered:
             self.hovered = False