MoleditPy-linux 1.17.1__py3-none-any.whl → 1.18.1__py3-none-any.whl

moleditpy_linux/modules/align_plane_dialog.py

@@ -194,7 +194,7 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog):
             for label_actor in self.selection_labels:
                 try:
                     self.main_window.plotter.remove_actor(label_actor)
-                except:
+                except Exception:
                     pass
             self.selection_labels = []
     

moleditpy_linux/modules/alignment_dialog.py

@@ -166,7 +166,7 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog):
             for label_actor in self.selection_labels:
                 try:
                     self.main_window.plotter.remove_actor(label_actor)
-                except:
+                except Exception:
                     pass
             self.selection_labels = []
     

moleditpy_linux/modules/angle_dialog.py

@@ -202,7 +202,7 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):
             for label_actor in self.selection_labels:
                 try:
                     self.main_window.plotter.remove_actor(label_actor)
-                except:
+                except Exception:
                     pass
             self.selection_labels = []
     
@@ -212,7 +212,7 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):
             for label_actor in self.selection_labels:
                 try:
                     self.main_window.plotter.remove_actor(label_actor)
-                except:
+                except Exception:
                     pass
             self.selection_labels = []
     

moleditpy_linux/modules/bond_item.py

@@ -216,11 +216,102 @@ class BondItem(QGraphicsItem):
                 offset = QPointF(v.dx(), v.dy()) * BOND_OFFSET
 
                 if self.order == 2:
-                    # -------------------- ここから差し替え --------------------)
-                    line1 = line.translated(offset)
-                    line2 = line.translated(-offset)
-                    painter.drawLine(line1)
-                    painter.drawLine(line2)
+                    # 環構造かどうかを判定し、描画方法を変更
+                    is_in_ring = False
+                    ring_center = None
+                    
+                    try:
+                        # シーンからRDKit分子を取得
+                        sc = self.scene()
+                        if sc and hasattr(sc, 'window') and sc.window:
+                            # 2DデータからRDKit分子を生成
+                            mol = sc.window.data.to_rdkit_mol(use_2d_stereo=False)
+                            if mol:
+                                # この結合に対応するRDKitボンドを探す
+                                atom1_id = self.atom1.atom_id
+                                atom2_id = self.atom2.atom_id
+                                
+                                # RDKitインデックスを取得
+                                rdkit_idx1 = None
+                                rdkit_idx2 = None
+                                for atom in mol.GetAtoms():
+                                    if atom.HasProp("_original_atom_id"):
+                                        orig_id = atom.GetIntProp("_original_atom_id")
+                                        if orig_id == atom1_id:
+                                            rdkit_idx1 = atom.GetIdx()
+                                        elif orig_id == atom2_id:
+                                            rdkit_idx2 = atom.GetIdx()
+                                
+                                if rdkit_idx1 is not None and rdkit_idx2 is not None:
+                                    bond = mol.GetBondBetweenAtoms(rdkit_idx1, rdkit_idx2)
+                                    if bond and bond.IsInRing():
+                                        is_in_ring = True
+                                        # 環の中心を計算（この結合を含む最小環）
+                                        from rdkit import Chem
+                                        ring_info = mol.GetRingInfo()
+                                        for ring in ring_info.AtomRings():
+                                            if rdkit_idx1 in ring and rdkit_idx2 in ring:
+                                                # 環の原子位置の平均を計算
+                                                ring_positions = []
+                                                for atom_idx in ring:
+                                                    # 対応するエディタ側の原子を探す
+                                                    rdkit_atom = mol.GetAtomWithIdx(atom_idx)
+                                                    if rdkit_atom.HasProp("_original_atom_id"):
+                                                        editor_atom_id = rdkit_atom.GetIntProp("_original_atom_id")
+                                                        if editor_atom_id in sc.window.data.atoms:
+                                                            atom_item = sc.window.data.atoms[editor_atom_id]['item']
+                                                            if atom_item:
+                                                                ring_positions.append(atom_item.pos())
+                                                
+                                                if ring_positions:
+                                                    # 環の中心を計算
+                                                    center_x = sum(p.x() for p in ring_positions) / len(ring_positions)
+                                                    center_y = sum(p.y() for p in ring_positions) / len(ring_positions)
+                                                    ring_center = QPointF(center_x, center_y)
+                                                    break
+                    except Exception as e:
+                        # エラーが発生した場合は通常の描画にフォールバック
+                        is_in_ring = False
+                    
+                    v = line.unitVector().normalVector()
+                    offset = QPointF(v.dx(), v.dy()) * BOND_OFFSET
+                    
+                    if is_in_ring and ring_center:
+                        # 環構造: 1本の中心線（単結合位置） + 1本の短い内側線
+                        # 結合の中心から環の中心への方向を計算
+                        bond_center = line.center()
+                        
+                        # ローカル座標系での環中心方向
+                        local_ring_center = self.mapFromScene(ring_center)
+                        local_bond_center = line.center()
+                        inward_vec = local_ring_center - local_bond_center
+                        
+                        # offsetとinward_vecの内積で内側を判定
+                        if QPointF.dotProduct(offset, inward_vec) > 0:
+                            # offsetが内側方向（2倍のオフセット）
+                            inner_offset = offset * 2
+                        else:
+                            # -offsetが内側方向（2倍のオフセット）
+                            inner_offset = -offset * 2
+                        
+                        # 中心線を描画（単結合と同じ位置）
+                        painter.drawLine(line)
+                        
+                        # 内側の短い線を描画（80%の長さ）
+                        inner_line = line.translated(inner_offset)
+                        shorten_factor = 0.8
+                        p1 = inner_line.p1()
+                        p2 = inner_line.p2()
+                        center = QPointF((p1.x() + p2.x()) / 2, (p1.y() + p2.y()) / 2)
+                        shortened_p1 = center + (p1 - center) * shorten_factor
+                        shortened_p2 = center + (p2 - center) * shorten_factor
+                        painter.drawLine(QLineF(shortened_p1, shortened_p2))
+                    else:
+                        # 非環構造: 従来の2本の平行線
+                        line1 = line.translated(offset)
+                        line2 = line.translated(-offset)
+                        painter.drawLine(line1)
+                        painter.drawLine(line2)
 
                     # E/Z ラベルの描画処理
                     if self.stereo in [3, 4]:

moleditpy_linux/modules/bond_length_dialog.py

@@ -190,7 +190,7 @@ class BondLengthDialog(Dialog3DPickingMixin, QDialog):
             for label_actor in self.selection_labels:
                 try:
                     self.main_window.plotter.remove_actor(label_actor)
-                except:
+                except Exception:
                     pass
             self.selection_labels = []
     
@@ -200,7 +200,7 @@ class BondLengthDialog(Dialog3DPickingMixin, QDialog):
             for label_actor in self.selection_labels:
                 try:
                     self.main_window.plotter.remove_actor(label_actor)
-                except:
+                except Exception:
                     pass
             self.selection_labels = []
     

moleditpy_linux/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '1.17.1'
+VERSION = '1.18.1'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

moleditpy_linux/modules/constrained_optimization_dialog.py

@@ -394,7 +394,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
         for label_actor in self.constraint_labels:
             try:
                 self.main_window.plotter.remove_actor(label_actor)
-            except:
+            except Exception:
                 pass
         self.constraint_labels = []
 
@@ -595,7 +595,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
             for label_actor in self.selection_labels:
                 try:
                     self.main_window.plotter.remove_actor(label_actor)
-                except:
+                except Exception:
                     pass
             self.selection_labels = []
 

moleditpy_linux/modules/dihedral_dialog.py

@@ -207,7 +207,7 @@ class DihedralDialog(Dialog3DPickingMixin, QDialog):
             for label_actor in self.selection_labels:
                 try:
                     self.main_window.plotter.remove_actor(label_actor)
-                except:
+                except Exception:
                     pass
             self.selection_labels = []
     

moleditpy_linux/modules/main_window_app_state.py

@@ -574,7 +574,7 @@ class MainWindowAppState(object):
                         inchi_key = Chem.MolToInchiKey(self.current_mol)
                         json_data["identifiers"]["inchi"] = inchi
                         json_data["identifiers"]["inchi_key"] = inchi_key
-                    except:
+                    except Exception:
                         pass  # InChI生成に失敗した場合は無視
                         
                 except Exception as e:

moleditpy_linux/modules/main_window_compute.py

@@ -958,6 +958,12 @@ class MainWindowCompute(object):
         try:
             if mol.GetNumConformers() > 0:
                 # 初回変換では、2Dで設定したwedge/dashボンドの立体情報を保持
+                
+                # 3D立体化学計算で上書きされる前に、2D由来の立体化学情報をプロパティとして保存
+                for bond in mol.GetBonds():
+                    if bond.GetBondType() == Chem.BondType.DOUBLE:
+                        bond.SetIntProp("_original_2d_stereo", bond.GetStereo())
+
                 # 立体化学の割り当てを行うが、既存の2D立体情報を尊重
                 Chem.AssignStereochemistry(mol, cleanIt=False, force=True)
             

moleditpy_linux/modules/main_window_edit_3d.py

@@ -119,7 +119,7 @@ class MainWindowEdit3d(object):
         for dialog in dialogs_to_close:
             try:
                 dialog.close()
-            except:
+            except Exception:
                 pass
         self.active_3d_dialogs.clear()
 
@@ -169,7 +169,7 @@ class MainWindowEdit3d(object):
         try:
             # 既存の測定ラベルを削除
             self.plotter.remove_actor('measurement_labels')
-        except:
+        except Exception:
             pass
         
         if not self.measurement_labels or not self.current_mol:
@@ -208,7 +208,7 @@ class MainWindowEdit3d(object):
         self.measurement_labels.clear()
         try:
             self.plotter.remove_actor('measurement_labels')
-        except:
+        except Exception:
             pass
         
         # 2Dビューの測定ラベルも削除
@@ -219,7 +219,7 @@ class MainWindowEdit3d(object):
             try:
                 self.plotter.remove_actor(self.measurement_text_actor)
                 self.measurement_text_actor = None
-            except:
+            except Exception:
                 pass
         
         self.plotter.render()
@@ -434,7 +434,7 @@ class MainWindowEdit3d(object):
         if self.measurement_text_actor:
             try:
                 self.plotter.remove_actor(self.measurement_text_actor)
-            except:
+            except Exception:
                 pass
         
         if not measurement_lines:
@@ -453,7 +453,7 @@ class MainWindowEdit3d(object):
                 text_color = 'black' if luminance > 128 else 'white'
             else:
                 text_color = 'white'
-        except:
+        except Exception:
             text_color = 'white'
         
         # 左上に表示（小さな等幅フォント）
@@ -496,7 +496,7 @@ class MainWindowEdit3d(object):
         try:
             # 既存の選択ハイライトを削除
             self.plotter.remove_actor('selection_highlight')
-        except:
+        except Exception:
             pass
         
         if not self.selected_atoms_3d or not self.current_mol:

moleditpy_linux/modules/main_window_export.py

@@ -178,11 +178,6 @@ class MainWindowExport(object):
         except Exception as e:
             self.statusBar().showMessage(f"Error exporting OBJ/MTL: {e}")
 
-            return meshes_with_colors
-            
-        except Exception:
-            return []
-
 
 
     def create_multi_material_obj(self, meshes_with_colors, obj_path, mtl_path):
@@ -199,17 +194,17 @@ class MainWindowExport(object):
                     material_name = f"material_{i}_{mesh_data['name'].replace(' ', '_')}"
                     
                     mtl_file.write(f"newmtl {material_name}\n")
-                    mtl_file.write("Ka 0.2 0.2 0.2\n")  # Ambient
+                    mtl_file.write(f"Ka 0.2 0.2 0.2\n")  # Ambient
                     mtl_file.write(f"Kd {color[0]/255.0:.3f} {color[1]/255.0:.3f} {color[2]/255.0:.3f}\n")  # Diffuse
-                    mtl_file.write("Ks 0.5 0.5 0.5\n")  # Specular
-                    mtl_file.write("Ns 32.0\n")          # Specular exponent
-                    mtl_file.write("illum 2\n")          # Illumination model
-                    mtl_file.write("\n")
+                    mtl_file.write(f"Ks 0.5 0.5 0.5\n")  # Specular
+                    mtl_file.write(f"Ns 32.0\n")          # Specular exponent
+                    mtl_file.write(f"illum 2\n")          # Illumination model
+                    mtl_file.write(f"\n")
             
             # OBJファイルを作成
             with open(obj_path, 'w') as obj_file:
-                obj_file.write("# OBJ file with multiple materials\n")
-                obj_file.write("# Generated with individual object colors\n")
+                obj_file.write(f"# OBJ file with multiple materials\n")
+                obj_file.write(f"# Generated with individual object colors\n")
                 obj_file.write(f"mtllib {os.path.basename(mtl_path)}\n\n")
                 
                 vertex_offset = 1  # OBJファイルの頂点インデックスは1から始まる
@@ -229,6 +224,7 @@ class MainWindowExport(object):
                         obj_file.write(f"v {point[0]:.6f} {point[1]:.6f} {point[2]:.6f}\n")
                     
                     # 面を書き込み
+                    faces_written = 0
                     for j in range(mesh.n_cells):
                         cell = mesh.get_cell(j)
                         if cell.type == 5:  # VTK_TRIANGLE
@@ -237,6 +233,25 @@ class MainWindowExport(object):
                             v2 = points_in_cell[1] + vertex_offset
                             v3 = points_in_cell[2] + vertex_offset
                             obj_file.write(f"f {v1} {v2} {v3}\n")
+                            faces_written += 1
+                        elif cell.type == 6:  # VTK_TRIANGLE_STRIP
+                            # Triangle strips share vertices between adjacent triangles
+                            # For n points, we get (n-2) triangles
+                            points_in_cell = cell.point_ids
+                            n_points = len(points_in_cell)
+                            for k in range(n_points - 2):
+                                if k % 2 == 0:
+                                    # Even triangles: use points k, k+1, k+2
+                                    v1 = points_in_cell[k] + vertex_offset
+                                    v2 = points_in_cell[k+1] + vertex_offset
+                                    v3 = points_in_cell[k+2] + vertex_offset
+                                else:
+                                    # Odd triangles: reverse winding to maintain consistent orientation
+                                    v1 = points_in_cell[k+1] + vertex_offset
+                                    v2 = points_in_cell[k] + vertex_offset
+                                    v3 = points_in_cell[k+2] + vertex_offset
+                                obj_file.write(f"f {v1} {v2} {v3}\n")
+                                faces_written += 1
                         elif cell.type == 9:  # VTK_QUAD
                             points_in_cell = cell.point_ids
                             v1 = points_in_cell[0] + vertex_offset
@@ -244,10 +259,12 @@ class MainWindowExport(object):
                             v3 = points_in_cell[2] + vertex_offset
                             v4 = points_in_cell[3] + vertex_offset
                             obj_file.write(f"f {v1} {v2} {v3} {v4}\n")
+                            faces_written += 1
                     
-                    vertex_offset += mesh.n_points
-                    obj_file.write("\n")
                     
+                    vertex_offset += mesh.n_points
+                    obj_file.write(f"\n")
+                
         except Exception as e:
             raise Exception(f"Failed to create multi-material OBJ: {e}")
 
@@ -310,24 +327,25 @@ class MainWindowExport(object):
                     # VTKアクターからポリデータを取得する複数の方法を試行
                     mesh = None
                     
-                    # 方法1: mapperのinputから取得
+                    # 方法1: mapperのinputから取得 (Improved)
+                    mapper = None
                     if hasattr(actor, 'mapper') and actor.mapper is not None:
-                        if hasattr(actor.mapper, 'input') and actor.mapper.input is not None:
-                            mesh = actor.mapper.input
-                        elif hasattr(actor.mapper, 'GetInput') and actor.mapper.GetInput() is not None:
-                            mesh = actor.mapper.GetInput()
+                        mapper = actor.mapper
+                    elif hasattr(actor, 'GetMapper'):
+                        mapper = actor.GetMapper()
+                    
+                    if mapper is not None:
+                        if hasattr(mapper, 'input') and mapper.input is not None:
+                            mesh = mapper.input
+                        elif hasattr(mapper, 'GetInput') and mapper.GetInput() is not None:
+                            mesh = mapper.GetInput()
+                        elif hasattr(mapper, 'GetInputAsDataSet'):
+                            mesh = mapper.GetInputAsDataSet()
                     
                     # 方法2: PyVistaプロッターの内部データから取得
                     if mesh is None and actor_name in self.plotter.mesh:
                         mesh = self.plotter.mesh[actor_name]
                     
-                    # 方法3: PyVistaのメッシュデータベースから検索
-                    if mesh is None:
-                        for mesh_name, mesh_data in self.plotter.mesh.items():
-                            if mesh_data is not None and mesh_data.n_points > 0:
-                                mesh = mesh_data
-                                break
-                    
                     if mesh is not None and hasattr(mesh, 'n_points') and mesh.n_points > 0:
                         # PyVistaメッシュに変換（必要な場合）
                         if not isinstance(mesh, pv.PolyData):
@@ -391,23 +409,26 @@ class MainWindowExport(object):
                     # VTKアクターからポリデータを取得する複数の方法を試行
                     mesh = None
                     
-                    # 方法1: mapperのinputから取得
+                    # 方法1: mapperのinputから取得 (Improved)
+                    mapper = None
                     if hasattr(actor, 'mapper') and actor.mapper is not None:
-                        if hasattr(actor.mapper, 'input') and actor.mapper.input is not None:
-                            mesh = actor.mapper.input
-                        elif hasattr(actor.mapper, 'GetInput') and actor.mapper.GetInput() is not None:
-                            mesh = actor.mapper.GetInput()
+                        mapper = actor.mapper
+                    elif hasattr(actor, 'GetMapper'):
+                        mapper = actor.GetMapper()
+                    
+                    if mapper is not None:
+                        if hasattr(mapper, 'input') and mapper.input is not None:
+                            mesh = mapper.input
+                        elif hasattr(mapper, 'GetInput') and mapper.GetInput() is not None:
+                            mesh = mapper.GetInput()
+                        elif hasattr(mapper, 'GetInputAsDataSet'):
+                            mesh = mapper.GetInputAsDataSet()
                     
                     # 方法2: PyVistaプロッターの内部データから取得
                     if mesh is None and actor_name in self.plotter.mesh:
                         mesh = self.plotter.mesh[actor_name]
                     
-                    # 方法3: PyVistaのメッシュデータベースから検索
-                    if mesh is None:
-                        for mesh_name, mesh_data in self.plotter.mesh.items():
-                            if mesh_data is not None and mesh_data.n_points > 0:
-                                mesh = mesh_data
-                                break
+                    # 方法3: Removed unsafe fallback
                     
                     if mesh is not None and hasattr(mesh, 'n_points') and mesh.n_points > 0:
                         # PyVistaメッシュに変換（必要な場合）
@@ -447,17 +468,26 @@ class MainWindowExport(object):
             actors = renderer.actors
             
             actor_count = 0
+            
             for actor_name, actor in actors.items():
                 try:
                     # VTKアクターからポリデータを取得
                     mesh = None
                     
-                    # 方法1: mapperのinputから取得
+                    # 方法1: mapperのinputから取得 (Improved)
+                    mapper = None
                     if hasattr(actor, 'mapper') and actor.mapper is not None:
-                        if hasattr(actor.mapper, 'input') and actor.mapper.input is not None:
-                            mesh = actor.mapper.input
-                        elif hasattr(actor.mapper, 'GetInput') and actor.mapper.GetInput() is not None:
-                            mesh = actor.mapper.GetInput()
+                        mapper = actor.mapper
+                    elif hasattr(actor, 'GetMapper'):
+                        mapper = actor.GetMapper()
+                    
+                    if mapper is not None:
+                        if hasattr(mapper, 'input') and mapper.input is not None:
+                            mesh = mapper.input
+                        elif hasattr(mapper, 'GetInput') and mapper.GetInput() is not None:
+                            mesh = mapper.GetInput()
+                        elif hasattr(mapper, 'GetInputAsDataSet'):
+                            mesh = mapper.GetInputAsDataSet()
                     
                     # 方法2: PyVistaプロッターの内部データから取得
                     if mesh is None and actor_name in self.plotter.mesh:
@@ -484,7 +514,7 @@ class MainWindowExport(object):
                                 if prop is not None:
                                     vtk_color = prop.GetColor()
                                     color = [int(c * 255) for c in vtk_color]
-                        except:
+                        except Exception:
                             # 色取得に失敗した場合はデフォルト色をそのまま使用
                             pass
                         
@@ -513,6 +543,16 @@ class MainWindowExport(object):
                             # 単一の colors 配列があればそれを使う
                             elif 'colors' in pd:
                                 colors = np.asarray(pd['colors'])
+                            
+                            # cell_dataのcolorsも確認（Tubeフィルタなどはcell_dataに色を持つ場合がある）
+                            if colors is None and 'colors' in mesh_copy.cell_data:
+                                try:
+                                    # cell_dataをpoint_dataに変換
+                                    temp_mesh = mesh_copy.cell_data_to_point_data()
+                                    if 'colors' in temp_mesh.point_data:
+                                        colors = np.asarray(temp_mesh.point_data['colors'])
+                                except Exception:
+                                    pass
 
                             if colors is not None and colors.size > 0:
                                 # 整数に変換。colors が 0-1 の float の場合は 255 倍して正規化する。
@@ -539,18 +579,26 @@ class MainWindowExport(object):
 
                                 # 一意な色ごとにサブメッシュを抽出して追加
                                 unique_colors, inverse = np.unique(colors_int, axis=0, return_inverse=True)
+                                
+                                split_success = False
                                 if unique_colors.shape[0] > 1:
                                     for uc_idx, uc in enumerate(unique_colors):
                                         point_inds = np.where(inverse == uc_idx)[0]
                                         if point_inds.size == 0:
                                             continue
                                         try:
-                                            submesh = mesh_copy.extract_points(point_inds, adjacent_cells=True)
+                                            # Use temp_mesh if available (has point data), else mesh_copy
+                                            target_mesh = temp_mesh if 'temp_mesh' in locals() else mesh_copy
+                                            
+                                            # extract_points with adjacent_cells=False to avoid pulling in neighbors
+                                            submesh = target_mesh.extract_points(point_inds, adjacent_cells=False) 
+                                            
                                         except Exception:
                                             # extract_points が利用できない場合はスキップ
                                             continue
                                         if submesh is None or getattr(submesh, 'n_points', 0) == 0:
                                             continue
+                                        
                                         color_rgb = [int(uc[0]), int(uc[1]), int(uc[2])]
                                         meshes_with_colors.append({
                                             'mesh': submesh,
@@ -559,13 +607,22 @@ class MainWindowExport(object):
                                             'type': 'display_actor',
                                             'actor_name': actor_name
                                         })
-                                    actor_count += 1
-                                    # 分割したので以下の通常追加は行わない
-                                    continue
+                                        split_success = True
+                                    
+                                    if split_success:
+                                        actor_count += 1
+                                        # 分割に成功したので以下の通常追加は行わない
+                                        continue
+                                    # If splitting failed (no submeshes added), fall through to default
+                                else:
+                                    # 色が1色のみの場合は、その色を使用してメッシュ全体を出力
+                                    uc = unique_colors[0]
+                                    color = [int(uc[0]), int(uc[1]), int(uc[2])]
+                                    # ここでは continue せず、下のデフォルト追加処理に任せる（colorを更新したため）
                         except Exception:
                             # 分割処理に失敗した場合はフォールバックで単体メッシュを追加
                             pass
-
+                        
                         meshes_with_colors.append({
                             'mesh': mesh_copy,
                             'color': color,
@@ -577,9 +634,9 @@ class MainWindowExport(object):
                         actor_count += 1
                             
                 except Exception as e:
-                    print(f"Error processing actor {actor_name}: {e}")
                     continue
             
+            
             return meshes_with_colors
             
         except Exception as e:

moleditpy_linux/modules/main_window_main_init.py

@@ -1563,7 +1563,6 @@ class MainWindowMainInit(object):
             'wireframe_bond_radius': 0.01,
             'wireframe_resolution': 6,
             # Stick model parameters
-            'stick_atom_radius': 0.15,
             'stick_bond_radius': 0.15,
             'stick_resolution': 16,
             # Multiple bond offset parameters (per-model)
@@ -1573,12 +1572,13 @@ class MainWindowMainInit(object):
             'ball_stick_triple_bond_radius_factor': 0.75,
             'wireframe_double_bond_offset_factor': 3.0,
             'wireframe_triple_bond_offset_factor': 3.0,
-            'wireframe_double_bond_radius_factor': 1.0,
+            'wireframe_double_bond_radius_factor': 0.8,
             'wireframe_triple_bond_radius_factor': 0.75,
             'stick_double_bond_offset_factor': 1.5,
             'stick_triple_bond_offset_factor': 1.0,
             'stick_double_bond_radius_factor': 0.60,
             'stick_triple_bond_radius_factor': 0.40,
+            'aromatic_torus_thickness_factor': 0.6,
             # Ensure conversion/optimization defaults are present
             # If True, attempts to be permissive when RDKit raises chemical/sanitization errors
             # during file import (useful for viewing malformed XYZ/MOL files).
@@ -1629,7 +1629,7 @@ class MainWindowMainInit(object):
                         ('ball_stick_triple_bond_radius_factor', 'triple_bond_radius_factor', 0.75),
                         ('wireframe_double_bond_offset_factor', 'double_bond_offset_factor', 3.0),
                         ('wireframe_triple_bond_offset_factor', 'triple_bond_offset_factor', 3.0),
-                        ('wireframe_double_bond_radius_factor', 'double_bond_radius_factor', 1.0),
+                        ('wireframe_double_bond_radius_factor', 'double_bond_radius_factor', 0.8),
                         ('wireframe_triple_bond_radius_factor', 'triple_bond_radius_factor', 0.75),
                         ('stick_double_bond_offset_factor', 'double_bond_offset_factor', 1.5),
                         ('stick_triple_bond_offset_factor', 'triple_bond_offset_factor', 1.0),

moleditpy_linux/modules/main_window_molecular_parsers.py

@@ -22,6 +22,7 @@ import io
 import os
 import contextlib
 import traceback
+import logging
 
 
 # RDKit imports (explicit to satisfy flake8 and used features)
@@ -59,7 +60,7 @@ if OBABEL_AVAILABLE:
         # If import fails here, disable OBABEL locally; avoid raising
         pybel = None
         OBABEL_AVAILABLE = False
-        print("Warning: openbabel.pybel not available. Open Babel fallback and OBabel-based options will be disabled.")
+        logging.warning("Warning: openbabel.pybel not available. Open Babel fallback and OBabel-based options will be disabled.")
 else:
     pybel = None
     
@@ -901,12 +902,12 @@ class MainWindowMolecularParsers(object):
                     try:
                         mol.AddBond(i, j, Chem.BondType.SINGLE)
                         bonds_added.append((i, j, distance))
-                    except:
+                    except Exception:
                         # 既に結合が存在する場合はスキップ
                         pass
         
         # デバッグ情報（オプション）
-        # print(f"Added {len(bonds_added)} bonds based on distance analysis")
+        # Added bonds based on distance analysis
         
         return len(bonds_added)
 

moleditpy_linux/modules/main_window_project_io.py

@@ -430,9 +430,9 @@ class MainWindowProjectIo(object):
             # 拡張子不明の場合はJSONとして試行
             try:
                 self.load_json_data(file_path)
-            except:
+            except Exception:
                 try:
                     self.load_raw_data(file_path)
-                except:
+                except Exception:
                     self.statusBar().showMessage("Error: Unable to determine file format.")