MoleditPy-linux 1.16.1a3__tar.gz → 1.16.3__tar.gz

{moleditpy_linux-1.16.1a3 → moleditpy_linux-1.16.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 1.16.1a3
+Version: 1.16.3
 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>
 Project-URL: Homepage, https://github.com/HiroYokoyama/python_molecular_editor
@@ -109,7 +109,14 @@ For detailed instructions, please refer to the project [Wiki](https://github.com
     moleditpy-installer
     ```
 
------
+
+To enable Open Babel features (e.g., alternative 3D structure generation), please install the package manually.
+**Note:** Open Babel is licensed under **GPL v2**. Installing this package combines GPL code with this software.
+
+
+```bash
+pip install "moleditpy[openbabel]"
+```
 
 #### Running the Application
 
@@ -225,6 +232,13 @@ This project is licensed under the **Apache-2.0 License**. See the `LICENSE` fil
     moleditpy-installer
     ```
 
+Open Babel 機能（代替的な3D構造生成など）を有効にする場合は、以下のコマンドで個別にインストールしてください。
+**注意:** Open Babel は **GPL v2** ライセンスです。このパッケージをインストールすると、GPLの条項が適用される可能性があります。
+
+```bash
+pip install "moleditpy[openbabel]"
+```
+
 #### アプリケーションの起動
 
 ```bash

{moleditpy_linux-1.16.1a3 → moleditpy_linux-1.16.3}/README.md

@@ -84,7 +84,14 @@ For detailed instructions, please refer to the project [Wiki](https://github.com
     moleditpy-installer
     ```
 
------
+
+To enable Open Babel features (e.g., alternative 3D structure generation), please install the package manually.
+**Note:** Open Babel is licensed under **GPL v2**. Installing this package combines GPL code with this software.
+
+
+```bash
+pip install "moleditpy[openbabel]"
+```
 
 #### Running the Application
 
@@ -200,6 +207,13 @@ This project is licensed under the **Apache-2.0 License**. See the `LICENSE` fil
     moleditpy-installer
     ```
 
+Open Babel 機能（代替的な3D構造生成など）を有効にする場合は、以下のコマンドで個別にインストールしてください。
+**注意:** Open Babel は **GPL v2** ライセンスです。このパッケージをインストールすると、GPLの条項が適用される可能性があります。
+
+```bash
+pip install "moleditpy[openbabel]"
+```
+
 #### アプリケーションの起動
 
 ```bash

{moleditpy_linux-1.16.1a3 → moleditpy_linux-1.16.3}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "1.16.1a3"
+version = "1.16.3"
 
 authors = [
   { name="HiroYokoyama", email="titech.yoko.hiro@gmail.com" },

{moleditpy_linux-1.16.1a3 → moleditpy_linux-1.16.3}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 1.16.1a3
+Version: 1.16.3
 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>
 Project-URL: Homepage, https://github.com/HiroYokoyama/python_molecular_editor
@@ -109,7 +109,14 @@ For detailed instructions, please refer to the project [Wiki](https://github.com
     moleditpy-installer
     ```
 
------
+
+To enable Open Babel features (e.g., alternative 3D structure generation), please install the package manually.
+**Note:** Open Babel is licensed under **GPL v2**. Installing this package combines GPL code with this software.
+
+
+```bash
+pip install "moleditpy[openbabel]"
+```
 
 #### Running the Application
 
@@ -225,6 +232,13 @@ This project is licensed under the **Apache-2.0 License**. See the `LICENSE` fil
     moleditpy-installer
     ```
 
+Open Babel 機能（代替的な3D構造生成など）を有効にする場合は、以下のコマンドで個別にインストールしてください。
+**注意:** Open Babel は **GPL v2** ライセンスです。このパッケージをインストールすると、GPLの条項が適用される可能性があります。
+
+```bash
+pip install "moleditpy[openbabel]"
+```
+
 #### アプリケーションの起動
 
 ```bash

{moleditpy_linux-1.16.1a3 → moleditpy_linux-1.16.3}/src/moleditpy_linux/modules/constants.py

@@ -4,7 +4,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '1.16.1a3'
+VERSION = '1.16.3'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy_linux-1.16.1a3 → moleditpy_linux-1.16.3}/src/moleditpy_linux/modules/main_window_main_init.py

@@ -1579,6 +1579,9 @@ class MainWindowMainInit(object):
             # Color overrides
             'ball_stick_bond_color': '#7F7F7F',
             'cpk_colors': {},  # symbol->hex overrides
+            # Whether to kekulize aromatic systems for 3D display
+            'display_kekule_3d': False,
+            'always_ask_charge': False,
         }
 
         try:

{moleditpy_linux-1.16.1a3 → moleditpy_linux-1.16.3}/src/moleditpy_linux/modules/main_window_molecular_parsers.py

@@ -557,92 +557,173 @@ class MainWindowMolecularParsers(object):
                     # Accept the candidate
                     return candidate_mol
 
-            # Silent first attempt
+            # Decide whether to silently try charge=0 first, or prompt user first.
+            always_ask = bool(self.settings.get('always_ask_charge', False))
+
             try:
-                final_mol = _process_with_charge(0)
-            except RuntimeError:
-                # DetermineBonds explicitly failed for charge=0. In this
-                # situation, repeatedly prompt the user for charges until
-                # DetermineBonds succeeds or the user cancels.
-                while True:
-                    charge_val, ok, skip_flag = prompt_for_charge()
-                    if not ok:
-                        # user cancelled the prompt -> abort
-                        return None
-                    if skip_flag:
-                        # User selected Skip chemistry: attempt distance-based salvage
-                        try:
-                            self.estimate_bonds_from_distances(mol)
-                        except Exception:
-                            pass
-                        salvaged = None
-                        try:
-                            salvaged = mol.GetMol()
-                        except Exception:
-                            salvaged = None
+                if not always_ask:
+                    # Silent first attempt (existing behavior)
+                    try:
+                        final_mol = _process_with_charge(0)
+                    except RuntimeError:
+                        # DetermineBonds explicitly failed for charge=0. In this
+                        # situation, repeatedly prompt the user for charges until
+                        # DetermineBonds succeeds or the user cancels.
+                        while True:
+                            charge_val, ok, skip_flag = prompt_for_charge()
+                            if not ok:
+                                # user cancelled the prompt -> abort
+                                return None
+                            if skip_flag:
+                                # User selected Skip chemistry: attempt distance-based salvage
+                                try:
+                                    self.estimate_bonds_from_distances(mol)
+                                except Exception:
+                                    pass
+                                salvaged = None
+                                try:
+                                    salvaged = mol.GetMol()
+                                except Exception:
+                                    salvaged = None
+
+                                if salvaged is not None:
+                                    try:
+                                        salvaged.SetIntProp("_xyz_skip_checks", 1)
+                                    except Exception:
+                                        try:
+                                            salvaged._xyz_skip_checks = True
+                                        except Exception:
+                                            pass
+                                    final_mol = salvaged
+                                    break
+                                else:
+                                    # Could not salvage; abort
+                                    try:
+                                        self.statusBar().showMessage("Skip chemistry selected but failed to create salvaged molecule.")
+                                    except Exception:
+                                        pass
+                                    return None
 
-                        if salvaged is not None:
                             try:
-                                salvaged.SetIntProp("_xyz_skip_checks", 1)
-                            except Exception:
+                                final_mol = _process_with_charge(charge_val)
+                                # success -> break out of prompt loop
+                                break
+                            except RuntimeError:
+                                # DetermineBonds still failing for this charge -> loop again
                                 try:
-                                    salvaged._xyz_skip_checks = True
+                                    self.statusBar().showMessage("DetermineBonds failed for that charge; please try a different total charge or cancel.")
                                 except Exception:
                                     pass
-                            final_mol = salvaged
-                            break
-                        else:
-                            # Could not salvage; abort
+                                continue
+                            except Exception as e_prompt:
+                                # Some other failure occurred after DetermineBonds or in
+                                # finalization. If skip_chemistry_checks is enabled we
+                                # try the salvaged mol once; otherwise prompt again.
+                                try:
+                                    skip_checks = bool(self.settings.get('skip_chemistry_checks', False))
+                                except Exception:
+                                    skip_checks = False
+
+                                salvaged = None
+                                try:
+                                    salvaged = mol.GetMol()
+                                except Exception:
+                                    salvaged = None
+
+                                if skip_checks and salvaged is not None:
+                                    final_mol = salvaged
+                                    # mark salvaged molecule as produced under skip_checks
+                                    try:
+                                        final_mol.SetIntProp("_xyz_skip_checks", 1)
+                                    except Exception:
+                                        try:
+                                            final_mol._xyz_skip_checks = True
+                                        except Exception:
+                                            pass
+                                    break
+                                else:
+                                    try:
+                                        self.statusBar().showMessage(f"Retry failed: {e_prompt}")
+                                    except Exception:
+                                        pass
+                                    # Continue prompting
+                                    continue
+                else:
+                    # User has requested to always be asked for charge — prompt before any silent try
+                    while True:
+                        charge_val, ok, skip_flag = prompt_for_charge()
+                        if not ok:
+                            # user cancelled the prompt -> abort
+                            return None
+                        if skip_flag:
+                            # User selected Skip chemistry: attempt distance-based salvage
                             try:
-                                self.statusBar().showMessage("Skip chemistry selected but failed to create salvaged molecule.")
+                                self.estimate_bonds_from_distances(mol)
                             except Exception:
                                 pass
-                            return None
-
-                    try:
-                        final_mol = _process_with_charge(charge_val)
-                        # success -> break out of prompt loop
-                        break
-                    except RuntimeError:
-                        # DetermineBonds still failing for this charge -> loop again
-                        try:
-                            self.statusBar().showMessage("DetermineBonds failed for that charge; please try a different total charge or cancel.")
-                        except Exception:
-                            pass
-                        continue
-                    except Exception as e_prompt:
-                        # Some other failure occurred after DetermineBonds or in
-                        # finalization. If skip_chemistry_checks is enabled we
-                        # try the salvaged mol once; otherwise prompt again.
-                        try:
-                            skip_checks = bool(self.settings.get('skip_chemistry_checks', False))
-                        except Exception:
-                            skip_checks = False
-
-                        salvaged = None
-                        try:
-                            salvaged = mol.GetMol()
-                        except Exception:
                             salvaged = None
-
-                        if skip_checks and salvaged is not None:
-                            final_mol = salvaged
-                            # mark salvaged molecule as produced under skip_checks
                             try:
-                                final_mol.SetIntProp("_xyz_skip_checks", 1)
+                                salvaged = mol.GetMol()
                             except Exception:
+                                salvaged = None
+    
+                            if salvaged is not None:
                                 try:
-                                    final_mol._xyz_skip_checks = True
+                                    salvaged.SetIntProp("_xyz_skip_checks", 1)
+                                except Exception:
+                                    try:
+                                        salvaged._xyz_skip_checks = True
+                                    except Exception:
+                                        pass
+                                final_mol = salvaged
+                                break
+                            else:
+                                try:
+                                    self.statusBar().showMessage("Skip chemistry selected but failed to create salvaged molecule.")
                                 except Exception:
                                     pass
+                                return None
+    
+                        try:
+                            final_mol = _process_with_charge(charge_val)
+                            # success -> break out of prompt loop
                             break
-                        else:
+                        except RuntimeError:
+                            # DetermineBonds still failing for this charge -> loop again
                             try:
-                                self.statusBar().showMessage(f"Retry failed: {e_prompt}")
+                                self.statusBar().showMessage("DetermineBonds failed for that charge; please try a different total charge or cancel.")
                             except Exception:
                                 pass
-                            # Continue prompting
                             continue
+                        except Exception as e_prompt:
+                            try:
+                                skip_checks = bool(self.settings.get('skip_chemistry_checks', False))
+                            except Exception:
+                                skip_checks = False
+    
+                            salvaged = None
+                            try:
+                                salvaged = mol.GetMol()
+                            except Exception:
+                                salvaged = None
+    
+                            if skip_checks and salvaged is not None:
+                                final_mol = salvaged
+                                try:
+                                    final_mol.SetIntProp("_xyz_skip_checks", 1)
+                                except Exception:
+                                    try:
+                                        final_mol._xyz_skip_checks = True
+                                    except Exception:
+                                        pass
+                                break
+                            else:
+                                try:
+                                    self.statusBar().showMessage(f"Retry failed: {e_prompt}")
+                                except Exception:
+                                    pass
+                                continue
+                
             except Exception:
                 # If the silent attempt failed for reasons other than
                 # DetermineBonds failing (e.g., finalization errors), fall

{moleditpy_linux-1.16.1a3 → moleditpy_linux-1.16.3}/src/moleditpy_linux/modules/main_window_view_3d.py

@@ -156,11 +156,30 @@ class MainWindowView3d(object):
             self.plotter.add_light(light)
             
         # 5. 分子描画ロジック
+        # Optionally kekulize aromatic systems for 3D visualization.
+        mol_to_draw = mol
+        if self.settings.get('display_kekule_3d', False):
+            try:
+                # Operate on a copy to avoid mutating the original molecule
+                mol_to_draw = Chem.Mol(mol)
+                Chem.Kekulize(mol_to_draw, clearAromaticFlags=True)
+            except Exception as e:
+                # Kekulize failed; keep original and warn user
+                try:
+                    self.statusBar().showMessage(f"Kekulize failed: {e}")
+                except Exception:
+                    pass
+                mol_to_draw = mol
+
+        # Use the original molecule's conformer (positions) to ensure coordinates
+        # are preserved even when we create a kekulized copy for bond types.
         conf = mol.GetConformer()
 
-        self.atom_positions_3d = np.array([list(conf.GetAtomPosition(i)) for i in range(mol.GetNumAtoms())])
+        # Use the kekulized molecule's atom ordering for color/size decisions
+        self.atom_positions_3d = np.array([list(conf.GetAtomPosition(i)) for i in range(mol_to_draw.GetNumAtoms())])
 
-        sym = [a.GetSymbol() for a in mol.GetAtoms()]
+        # Use the possibly-kekulized molecule for symbol/bond types
+        sym = [a.GetSymbol() for a in mol_to_draw.GetAtoms()]
         col = np.array([CPK_COLORS_PV.get(s, [0.5, 0.5, 0.5]) for s in sym])
 
         # スタイルに応じて原子の半径を設定（設定から読み込み）
@@ -239,7 +258,7 @@ class MainWindowView3d(object):
                 except Exception:
                     bs_bond_rgb = [127, 127, 127]
             
-            for bond in mol.GetBonds():
+            for bond in mol_to_draw.GetBonds():
                 begin_atom_idx = bond.GetBeginAtomIdx()
                 end_atom_idx = bond.GetEndAtomIdx()
                 sp = np.array(conf.GetAtomPosition(begin_atom_idx))
@@ -313,7 +332,7 @@ class MainWindowView3d(object):
                     if bt == Chem.rdchem.BondType.DOUBLE:
                         r = cyl_radius * double_radius_factor
                         # 二重結合の場合、結合している原子の他の結合を考慮してオフセット方向を決定
-                        off_dir = self._calculate_double_bond_offset(mol, bond, conf)
+                        off_dir = self._calculate_double_bond_offset(mol_to_draw, bond, conf)
                         # 設定から二重結合のオフセットファクターを適用
                         s_double = cyl_radius * double_offset_factor
                         c1, c2 = c + off_dir * (s_double / 2), c - off_dir * (s_double / 2)
@@ -432,7 +451,10 @@ class MainWindowView3d(object):
         # E/Zラベルも表示
         if getattr(self, 'show_chiral_labels', False):
             try:
-                self.show_ez_labels_3d(mol)
+                # If we drew a kekulized molecule use it for E/Z detection so
+                # E/Z labels reflect Kekulé rendering; pass mol_to_draw as the
+                # molecule to scan for bond stereochemistry.
+                self.show_ez_labels_3d(mol, scan_mol=mol_to_draw)
             except Exception as e: 
                 self.statusBar().showMessage(f"3D E/Z label drawing error: {e}")
 
@@ -561,7 +583,7 @@ class MainWindowView3d(object):
 
 
 
-    def show_ez_labels_3d(self, mol):
+    def show_ez_labels_3d(self, mol, scan_mol=None):
         """3DビューでE/Zラベルを表示する（RDKitのステレオ化学判定を使用）"""
         if not mol:
             return
@@ -588,11 +610,19 @@ class MainWindowView3d(object):
             pass
         
         # 二重結合でRDKitが判定したE/Z立体化学を表示
-        for bond in mol.GetBonds():
+        # `scan_mol` is used for stereochemistry detection (bond types); default
+        # to the provided molecule if not supplied.
+        if scan_mol is None:
+            scan_mol = mol
+
+        for bond in scan_mol.GetBonds():
             if bond.GetBondType() == Chem.BondType.DOUBLE:
                 stereo = bond.GetStereo()
                 if stereo in [Chem.BondStereo.STEREOE, Chem.BondStereo.STEREOZ]:
                     # 結合の中心座標を計算
+                    # Use positions from the original molecule's conformer; `bond` may
+                    # come from `scan_mol` which can be kekulized but position indices
+                    # correspond to the original `mol`.
                     begin_pos = np.array(conf.GetAtomPosition(bond.GetBeginAtomIdx()))
                     end_pos = np.array(conf.GetAtomPosition(bond.GetEndAtomIdx()))
                     center_pos = (begin_pos + end_pos) / 2
@@ -1083,15 +1113,33 @@ class MainWindowView3d(object):
         Only keys present in self.settings['cpk_colors'] are changed; other elements keep the defaults.
         """
         try:
+            # Overridden CPK settings are stored in self.settings['cpk_colors'].
+            # To ensure that 2D modules (e.g., atom_item.py) which imported the
+            # `CPK_COLORS` mapping from `modules.constants` at import time see
+            # updates, mutate the mapping in-place on the constants module
+            # instead of rebinding a new local variable here.
             overrides = self.settings.get('cpk_colors', {}) or {}
-            # Start from a clean copy of the defaults
-            global CPK_COLORS, CPK_COLORS_PV
-            CPK_COLORS = {k: QColor(v) if not isinstance(v, QColor) else QColor(v) for k, v in DEFAULT_CPK_COLORS.items()}
+
+            # Import the constants module so we can update mappings directly
+            try:
+                from . import constants as constants_mod
+            except Exception:
+                import modules.constants as constants_mod
+
+            # Reset constants.CPK_COLORS to defaults but keep the same dict
+            constants_mod.CPK_COLORS.clear()
+            for k, v in DEFAULT_CPK_COLORS.items():
+                constants_mod.CPK_COLORS[k] = QColor(v) if not isinstance(v, QColor) else v
+
+            # Apply overrides from settings
             for k, hexv in overrides.items():
                 if isinstance(hexv, str) and hexv:
-                    CPK_COLORS[k] = QColor(hexv)
-            # Rebuild PV version
-            CPK_COLORS_PV = {k: [c.redF(), c.greenF(), c.blueF()] for k, c in CPK_COLORS.items()}
+                    constants_mod.CPK_COLORS[k] = QColor(hexv)
+
+            # Rebuild the PV representation in-place too
+            constants_mod.CPK_COLORS_PV.clear()
+            for k, c in constants_mod.CPK_COLORS.items():
+                constants_mod.CPK_COLORS_PV[k] = [c.redF(), c.greenF(), c.blueF()]
         except Exception as e:
             print(f"Failed to update CPK colors from settings: {e}")
 

{moleditpy_linux-1.16.1a3 → moleditpy_linux-1.16.3}/src/moleditpy_linux/modules/molecule_scene.py

@@ -727,61 +727,130 @@ class MoleculeScene(QGraphicsScene):
 
                 # --- フューズされた辺の数による条件分岐 ---
                 if len(existing_orders) >= 2:
-                    # 2辺以上フューズ: 単純に既存の辺の次数とテンプレートの辺の次数が一致するものを最優先する
-                    # (この場合、新しい環を交互配置にするのは難しく、単に既存の構造を壊さないことを優先)
+                    
                     for rot in range(num_points):
-                        current_score = sum(100 for k, exist_order in existing_orders.items() 
-                                            if orig_orders[(k + rot) % num_points] == exist_order)
+                        match_double_count = 0
+                        match_bonus = 0
+                        mismatch_penalty = 0
+                        
+                        # 【新規追加】接続部（Legs）の安全性チェック
+                        # フューズ領域の両隣（テンプレート側）が「単結合(1)」であることを強く推奨する
+                        # これにより、既存構造との接続点での原子価オーバー（手が5本になる）を防ぐ
+                        safe_connection_score = 0
+                        
+                        # フューズ領域の開始と終了を探す（インデックス集合から判定）
+                        fused_indices = sorted(list(existing_orders.keys()))
+                        # 連続領域と仮定して、端のインデックスを取得
+                        # (0と5がつながっている環状のケースも考慮すべきだが、簡易的に最小/最大で判定し、
+                        #  もし飛び地なら不整合ペナルティで自然と落ちる)
+                        
+                        # 簡易的な隣接チェック: 
+                        # フューズに使われる辺集合に含まれない「その隣」の辺を見る
+                        for k in existing_orders:
+                            # 左隣を見る
+                            prev_idx = (k - 1 + rot) % num_points
+                            # 右隣を見る
+                            next_idx = (k + 1 + rot) % num_points
+                            
+                            # もし隣がフューズ領域外（＝接続部）なら、その次数をチェック
+                            # 注意: existing_ordersのキーは「配置位置(k)」
+                            # rotはテンプレートのズレ。
+                            # テンプレート上の該当エッジの次数は orig_orders[(neighbor_k + rot)] ではなく
+                            # orig_orders[neighbor_template_index]
+                            
+                            # 正確なロジック:
+                            # 今、配置位置 k にテンプレートの bond (k+rot) が来ている。
+                            # 配置位置 k の「隣のボンド」ではなく、
+                            # 「テンプレート上で」そのボンドの両隣にあるボンドが、今回のフューズに使われていないか確認する。
+                            pass 
+
+                        # --- シンプルな実装: 全ての非フューズ辺（外周になる辺）をチェック ---
+                        # 「フューズに使われていない辺」が単結合か二重結合かで加点
+                        # ピレンの場合(3辺フューズ)、残り3辺が外周。
+                        # ベンゼン(D-S-D-S-D-S)において、D-S-Dでフューズすると、残りはS-D-S。
+                        # 接合部(Legs)にあたるのは、残りのS-D-Sの両端のS。これが重要。
+                        
+                        # テンプレートの結合次数配列
+                        current_template_orders = [orig_orders[(i + rot) % num_points] for i in range(num_points)]
+                        
+                        # フューズ領域の両端を特定するために、
+                        # 「フューズしているk」に対応するテンプレート側のインデックスを集める
+                        used_template_indices = set((k + rot) % num_points for k in existing_orders)
+                        
+                        # テンプレート上で「使われている領域」の両隣（接続部）が「1(単結合)」なら超高得点
+                        for t_idx in used_template_indices:
+                            # そのボンドのテンプレート上の左隣
+                            adj_l = (t_idx - 1) % num_points
+                            # そのボンドのテンプレート上の右隣
+                            adj_r = (t_idx + 1) % num_points
+                            
+                            # もし隣が「使われていない」なら、それは接続部である
+                            if adj_l not in used_template_indices:
+                                if orig_orders[adj_l] == 1: safe_connection_score += 5000
+                            
+                            if adj_r not in used_template_indices:
+                                if orig_orders[adj_r] == 1: safe_connection_score += 5000
+
+                        # 既存のスコア計算
+                        for k, exist_order in existing_orders.items():
+                            template_ord = orig_orders[(k + rot) % num_points]
+                            if template_ord == exist_order:
+                                match_bonus += 100
+                                if exist_order == 2: match_double_count += 1
+                            else:
+                                # 不一致でも、Legsが安全なら許容したいのでペナルティは控えめに、
+                                # または safe_connection_score が圧倒的に勝つようにする
+                                mismatch_penalty += 50
+                        
+                        # 最終スコア: 接続部の安全性を最優先
+                        current_score = safe_connection_score + (match_double_count * 1000) + match_bonus - mismatch_penalty
+
                         if current_score > max_score:
                             max_score = current_score
                             best_rot = rot
 
                 elif len(existing_orders) == 1:
-                    # 1辺フューズ: 既存の辺を維持しつつ、その両隣で「反転一致」を達成し、新しい環を交互配置にする
-                    
-                    # フューズされた辺のインデックスと次数を取得
+                    # 1辺フューズ
                     k_fuse = next(iter(existing_orders.keys()))
                     exist_order = existing_orders[k_fuse]
                     
-                    # 目標: フューズされた辺の両隣（k-1とk+1）に来るテンプレートの次数が、既存の辺の次数と逆であること
-                    # k_adj_1 -> (k_fuse - 1) % 6
-                    # k_adj_2 -> (k_fuse + 1) % 6
-                    
                     for rot in range(num_points):
                         current_score = 0
                         rotated_template_order = orig_orders[(k_fuse + rot) % num_points]
 
-                        # 1. まず、フューズされた辺自体が次数を反転させられる位置にあるかチェック（必須ではないが、回転を絞る）
+                        # 1. 接合部の次数マッチング
+                        
+                        # パターンA: 交互配置（既存と逆）
                         if (exist_order == 1 and rotated_template_order == 2) or \
                            (exist_order == 2 and rotated_template_order == 1):
-                            current_score += 100 # 大幅ボーナス: 理想的な回転
+                            current_score += 100 
 
-                        # 2. 次に、両隣の辺の次数をチェック（交互配置維持の主目的）
-                        # 既存辺の両隣は、新規に作成されるため、テンプレートの次数でボンドが作成されます。
-                        # ここで、テンプレートの次数が既存辺の次数と逆になる回転を選ぶ必要があります。
-                        
-                        # テンプレートの辺は、回転後のk_fuseの両隣（m_adj1, m_adj2）
+                        # 【追加変更点2】二重結合の重ね合わせ（共役維持）
+                        # 既存が二重結合で、テンプレートも二重結合なら、ここで1つ消費される
+                        elif (exist_order == 2 and rotated_template_order == 2):
+                            current_score += 100
+
+                        # 2. 両隣の辺の次数チェック（交互配置の維持を確認）
                         m_adj1 = (k_fuse - 1 + rot) % num_points 
                         m_adj2 = (k_fuse + 1 + rot) % num_points
-                        
                         neighbor_order_1 = orig_orders[m_adj1]
                         neighbor_order_2 = orig_orders[m_adj2]
 
-                        # 既存が単結合(1)の場合、両隣は二重結合(2)であってほしい
                         if exist_order == 1:
+                            # 接合部が単なら、隣は二重であってほしい
                             if neighbor_order_1 == 2: current_score += 50
                             if neighbor_order_2 == 2: current_score += 50
                         
-                        # 既存が二重結合(2)の場合、両隣は単結合(1)であってほしい
                         elif exist_order == 2:
+                            # 接合部が二重なら、隣は単であってほしい
                             if neighbor_order_1 == 1: current_score += 50
                             if neighbor_order_2 == 1: current_score += 50
                             
-                        # 3. タイブレーク: その他の既存結合（フューズ辺ではない）との次数一致度も加味
+                        # 3. タイブレーク（他の接触しない辺との整合性など）
                         for k, e_order in existing_orders.items():
                              if k != k_fuse:
                                 r_t_order = orig_orders[(k + rot) % num_points]
-                                if r_t_order == e_order: current_score += 10 # 既存構造維持のボーナス
+                                if r_t_order == e_order: current_score += 10
                         
                         if current_score > max_score:
                             max_score = current_score

{moleditpy_linux-1.16.1a3 → moleditpy_linux-1.16.3}/src/moleditpy_linux/modules/settings_dialog.py

@@ -62,11 +62,18 @@ class SettingsDialog(QDialog):
             # element symbol recognition will be coerced where possible and Chem.SanitizeMol
             # failures will be ignored so the 3D viewer can still display the structure.
             'skip_chemistry_checks': False,
+            # When True, always prompt the user for molecular charge on XYZ import
+            # instead of silently trying charge=0 first. Default True to disable
+            # the silent 'charge=0' test.
+            'always_ask_charge': False,
             # 3D conversion/optimization defaults
             '3d_conversion_mode': 'fallback',
             'optimization_method': 'MMFF_RDKIT',
             'ball_stick_bond_color': '#7F7F7F',
             'cpk_colors': {},
+            # If True, RDKit will attempt to kekulize aromatic systems for 3D display
+            # (shows alternating single/double bonds rather than aromatic circles)
+            'display_kekule_3d': False,
         }
         
         # --- 選択された色を管理する専用のインスタンス変数 ---
@@ -197,7 +204,7 @@ class SettingsDialog(QDialog):
 
         # 化学チェックスキップオプション（otherタブに移動）
         self.skip_chem_checks_checkbox = QCheckBox()
-        self.skip_chem_checks_checkbox.setToolTip("When enabled, file import will try to ignore chemical/sanitization errors and allow viewing malformed files.")
+        self.skip_chem_checks_checkbox.setToolTip("When enabled, XYZ file import will try to ignore chemical/sanitization errors and allow viewing malformed files.")
         # Immediately persist change to settings when user toggles the checkbox
         try:
             self.skip_chem_checks_checkbox.stateChanged.connect(lambda s: self._on_skip_chem_checks_changed(s))
@@ -206,7 +213,27 @@ class SettingsDialog(QDialog):
 
         # Add the checkbox to the other tab's form
         try:
-            self.other_form_layout.addRow("Skip chemistry checks on import xyz file:", self.skip_chem_checks_checkbox)
+            self.other_form_layout.addRow("Skip chemistry checks on import XYZ file:", self.skip_chem_checks_checkbox)
+        except Exception:
+            pass
+
+        # 3D Kekule display option (under Other) will be added below the
+        # 'Always ask molecular charge on import' option so ordering is clear
+        # in the UI.
+        self.kekule_3d_checkbox = QCheckBox()
+        self.kekule_3d_checkbox.setToolTip("When enabled, aromatic bonds will be kekulized in the 3D view (show alternating single/double bonds).")
+        # Don't persist kekule state immediately; Apply/OK should commit setting.
+        # Always ask charge on XYZ import (skip silent charge=0 test)
+        self.always_ask_charge_checkbox = QCheckBox()
+        self.always_ask_charge_checkbox.setToolTip("Prompt for overall molecular charge when importing XYZ files instead of silently trying charge=0 first.")
+        try:
+            self.other_form_layout.addRow("Always ask molecular charge on import XYZ file:", self.always_ask_charge_checkbox)
+        except Exception:
+            pass
+
+        # Place the Kekulé option after the always-ask-charge option
+        try:
+            self.other_form_layout.addRow("Display Kekulé bonds in 3D:", self.kekule_3d_checkbox)
         except Exception:
             pass
 
@@ -578,6 +605,8 @@ class SettingsDialog(QDialog):
             "Other": {
                 # other options
                 'skip_chemistry_checks': self.default_settings.get('skip_chemistry_checks', False),
+                'display_kekule_3d': self.default_settings.get('display_kekule_3d', False),
+                'always_ask_charge': self.default_settings.get('always_ask_charge', False),
             },
             "Ball & Stick": {
                 'ball_stick_atom_scale': self.default_settings['ball_stick_atom_scale'],
@@ -899,6 +928,10 @@ class SettingsDialog(QDialog):
         self.projection_combo.setCurrentIndex(idx if idx != -1 else 0)
         # skip chemistry checks
         self.skip_chem_checks_checkbox.setChecked(settings_dict.get('skip_chemistry_checks', self.default_settings.get('skip_chemistry_checks', False)))
+        # kekule setting
+        self.kekule_3d_checkbox.setChecked(settings_dict.get('display_kekule_3d', self.default_settings.get('display_kekule_3d', False)))
+        # always ask for charge on XYZ imports
+        self.always_ask_charge_checkbox.setChecked(settings_dict.get('always_ask_charge', self.default_settings.get('always_ask_charge', False)))
       
     def select_color(self):
         """カラーピッカーを開き、選択された色を内部変数とUIに反映させる"""
@@ -950,7 +983,9 @@ class SettingsDialog(QDialog):
             'stick_triple_bond_offset_factor': self.stick_triple_offset_slider.value() / 100.0,
             'stick_double_bond_radius_factor': self.stick_double_radius_slider.value() / 100.0,
             'stick_triple_bond_radius_factor': self.stick_triple_radius_slider.value() / 100.0,
+            'display_kekule_3d': self.kekule_3d_checkbox.isChecked(),
             'skip_chemistry_checks': self.skip_chem_checks_checkbox.isChecked(),
+            'always_ask_charge': self.always_ask_charge_checkbox.isChecked(),
             # Ball & Stick bond color (3D grey/uniform color)
             'ball_stick_bond_color': getattr(self, 'bs_bond_color', self.default_settings.get('ball_stick_bond_color', '#7F7F7F')),
         }
@@ -1027,6 +1062,8 @@ class SettingsDialog(QDialog):
         except Exception:
             pass
 
+    # Note: Kekule display is applied only when user clicks Apply/OK.
+
     def accept(self):
         """ダイアログの設定を適用してから閉じる"""
         # apply_settingsを呼び出して設定を適用