MoleditPy-linux 1.18.0__tar.gz → 1.18.1__tar.gz

{moleditpy_linux-1.18.0 → moleditpy_linux-1.18.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 1.18.0
+Version: 1.18.1
 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
@@ -684,7 +684,6 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11

{moleditpy_linux-1.18.0 → moleditpy_linux-1.18.1}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "1.18.0"
+version = "1.18.1"
 
 license = {file = "LICENSE"}
 
@@ -24,7 +24,6 @@ classifiers = [
     "Operating System :: OS Independent",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Chemistry",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",

{moleditpy_linux-1.18.0 → moleditpy_linux-1.18.1}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 1.18.0
+Version: 1.18.1
 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
@@ -684,7 +684,6 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11

{moleditpy_linux-1.18.0 → moleditpy_linux-1.18.1}/src/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-1.18.0 → moleditpy_linux-1.18.1}/src/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-1.18.0 → moleditpy_linux-1.18.1}/src/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-1.18.0 → moleditpy_linux-1.18.1}/src/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-1.18.0 → moleditpy_linux-1.18.1}/src/moleditpy_linux/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '1.18.0'
+VERSION = '1.18.1'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy_linux-1.18.0 → moleditpy_linux-1.18.1}/src/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-1.18.0 → moleditpy_linux-1.18.1}/src/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-1.18.0 → moleditpy_linux-1.18.1}/src/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-1.18.0 → moleditpy_linux-1.18.1}/src/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-1.18.0 → moleditpy_linux-1.18.1}/src/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-1.18.0 → moleditpy_linux-1.18.1}/src/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-1.18.0 → moleditpy_linux-1.18.1}/src/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-1.18.0 → moleditpy_linux-1.18.1}/src/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.")
 

{moleditpy_linux-1.18.0 → moleditpy_linux-1.18.1}/src/moleditpy_linux/modules/main_window_view_3d.py

@@ -19,6 +19,7 @@ MainWindow (main_window.py) から分離されたモジュール
 
 import numpy as np
 import vtk
+import logging
 
 
 # RDKit imports (explicit to satisfy flake8 and used features)
@@ -58,7 +59,7 @@ 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
 
@@ -201,7 +202,7 @@ class MainWindowView3d(object):
             resolution = self.settings.get('wireframe_resolution', 6)
             rad = np.array([0.01 for s in sym])  # 極小値（使用されない）
         elif self.current_3d_style == 'stick':
-            atom_radius = self.settings.get('stick_atom_radius', 0.15)
+            atom_radius = self.settings.get('stick_bond_radius', 0.15)  # Use bond radius for atoms
             resolution = self.settings.get('stick_resolution', 16)
             rad = np.array([atom_radius for s in sym])
         else:  # ball_and_stick
@@ -278,7 +279,7 @@ class MainWindowView3d(object):
                                         
                                         # 結合描画と同じ計算
                                         sphere_radius = cyl_radius * radius_factor
-                                    except:
+                                    except Exception:
                                         sphere_radius = 0.09  # デフォルト値
                                         offset_distance = 0.15  # デフォルト値
                                     
@@ -437,7 +438,7 @@ class MainWindowView3d(object):
                         double_radius_factor = self.settings.get('ball_stick_double_bond_radius_factor', 0.8)
                         triple_radius_factor = self.settings.get('ball_stick_triple_bond_radius_factor', 0.75)
                     elif self.current_3d_style == 'wireframe':
-                        double_radius_factor = self.settings.get('wireframe_double_bond_radius_factor', 1.0)
+                        double_radius_factor = self.settings.get('wireframe_double_bond_radius_factor', 0.8)
                         triple_radius_factor = self.settings.get('wireframe_triple_bond_radius_factor', 0.75)
                     elif self.current_3d_style == 'stick':
                         double_radius_factor = self.settings.get('stick_double_bond_radius_factor', 0.60)
@@ -660,7 +661,7 @@ class MainWindowView3d(object):
                     self.plotter.add_mesh(circle_line, color=torus_color, **mesh_props)
                     
             except Exception as e:
-                print(f"Error rendering aromatic circles: {e}")
+                logging.error(f"Error rendering aromatic circles: {e}")
 
         if getattr(self, 'show_chiral_labels', False):
             try:
@@ -820,7 +821,7 @@ class MainWindowView3d(object):
         try:
             # 既存のE/Zラベルを削除
             self.plotter.remove_actor('ez_labels')
-        except:
+        except Exception:
             pass
         
         pts, labels = [], []
@@ -837,7 +838,7 @@ class MainWindowView3d(object):
             # 3D座標からステレオ化学を再計算 (molに対して行う)
             # これにより、2Dでの描画状態に関わらず、現在の3D座標に基づいたE/Z判定が行われる
             Chem.AssignStereochemistry(mol, cleanIt=True, force=True, flagPossibleStereoCenters=True)
-        except:
+        except Exception:
             pass
 
         for bond in mol.GetBonds():
@@ -1171,7 +1172,7 @@ class MainWindowView3d(object):
                 for nm in self.atom_label_legend_names:
                     try:
                         self.plotter.remove_actor(nm)
-                    except:
+                    except Exception:
                         pass
             self.atom_label_legend_names = []
 
@@ -1237,12 +1238,12 @@ class MainWindowView3d(object):
                     for a in list(self.current_atom_info_labels):
                         try:
                             self.plotter.remove_actor(a)
-                        except:
+                        except Exception:
                             pass
                 else:
                     try:
                         self.plotter.remove_actor(self.current_atom_info_labels)
-                    except:
+                    except Exception:
                         pass
         except Exception:
             pass
@@ -1255,7 +1256,7 @@ class MainWindowView3d(object):
                 for nm in list(self.atom_label_legend_names):
                     try:
                         self.plotter.remove_actor(nm)
-                    except:
+                    except Exception:
                         pass
         except Exception:
             pass
@@ -1401,7 +1402,7 @@ class MainWindowView3d(object):
         if renderer and hasattr(renderer, 'SetNumberOfLayers'):
             try:
                 renderer.SetNumberOfLayers(2)  # レイヤー0:3Dオブジェクト、レイヤー1:2Dオーバーレイ
-            except:
+            except Exception:
                 pass  # PyVistaのバージョンによってはサポートされていない場合がある  
 
         # --- 3D軸ウィジェットの設定 ---

{moleditpy_linux-1.18.0 → moleditpy_linux-1.18.1}/src/moleditpy_linux/modules/main_window_view_loaders.py

@@ -317,7 +317,7 @@ class MainWindowViewLoaders(object):
                             # Keep mol as-is (may lack conformer); downstream code checks for conformers
                         else:
                             raise
-                except:
+                except Exception:
                     self.statusBar().showMessage("Failed to generate 3D coordinates")
                     return
             

{moleditpy_linux-1.18.0 → moleditpy_linux-1.18.1}/src/moleditpy_linux/modules/molecule_scene.py

@@ -11,6 +11,7 @@ DOI: 10.5281/zenodo.17268532
 """
 
 import traceback
+import logging
 
 from PyQt6.QtWidgets import (
     QApplication, QGraphicsScene, QGraphicsItem,
@@ -203,9 +204,7 @@ class MoleculeScene(QGraphicsScene):
                             self.window.push_undo_state()
                             data_changed = False  # ここでundo済みなので以降で積まない
                     except Exception as e:
-                        print(f"Error clearing E/Z label: {e}")
-                        
-                        traceback.print_exc()
+                        logging.error(f"Error clearing E/Z label: {e}", exc_info=True)
                         if hasattr(self.window, 'statusBar'):
                             self.window.statusBar().showMessage(f"Error clearing E/Z label: {e}", 5000)
                 # AtomItemは何もしない
@@ -387,9 +386,7 @@ class MoleculeScene(QGraphicsScene):
                         self.update_bond_stereo(b, new_stereo)
                         self.window.push_undo_state()  # ここでUndo stackに積む
                 except Exception as e:
-                    print(f"Error in E/Z stereo toggle: {e}")
-                    
-                    traceback.print_exc()
+                    logging.error(f"Error in E/Z stereo toggle: {e}", exc_info=True)
                     if hasattr(self.window, 'statusBar'):
                         self.window.statusBar().showMessage(f"Error changing E/Z stereochemistry: {e}", 5000)
                 return # この後の処理は行わない
@@ -610,7 +607,7 @@ class MoleculeScene(QGraphicsScene):
     def create_bond(self, start_atom, end_atom, bond_order=None, bond_stereo=None):
         try:
             if start_atom is None or end_atom is None:
-                print("Error: Cannot create bond with None atoms")
+                logging.error("Error: Cannot create bond with None atoms")
                 return
                 
             exist_b = self.find_bond_between(start_atom, end_atom)
@@ -637,9 +634,7 @@ class MoleculeScene(QGraphicsScene):
                 end_atom.update_style()
                 
         except Exception as e:
-            print(f"Error creating bond: {e}")
-            
-            traceback.print_exc()
+            logging.error(f"Error creating bond: {e}", exc_info=True)
 
     def add_molecule_fragment(self, points, bonds_info, existing_items=None, symbol='C'):
         """
@@ -1668,9 +1663,9 @@ class MoleculeScene(QGraphicsScene):
                 elif key == Qt.Key.Key_1 and (bond.order != 1 or bond.stereo != 0):
                     bond.order = 1; bond.stereo = 0
                 elif key == Qt.Key.Key_2 and (bond.order != 2 or bond.stereo != 0):
-                    bond.order = 2; bond.stereo = 0; needs_update = True
+                    bond.order = 2; bond.stereo = 0
                 elif key == Qt.Key.Key_3 and bond.order != 3:
-                    bond.order = 3; bond.stereo = 0; needs_update = True
+                    bond.order = 3; bond.stereo = 0
 
                 # 4. 実際に変更があった場合のみデータモデルを更新
                 if old_order != bond.order or old_stereo != bond.stereo:

{moleditpy_linux-1.18.0 → moleditpy_linux-1.18.1}/src/moleditpy_linux/modules/planarize_dialog.py

@@ -157,7 +157,7 @@ class PlanarizeDialog(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-1.18.0 → moleditpy_linux-1.18.1}/src/moleditpy_linux/modules/settings_dialog.py

@@ -53,7 +53,6 @@ class SettingsDialog(QDialog):
             '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)
@@ -278,8 +277,8 @@ class SettingsDialog(QDialog):
         # Aromatic torus thickness factor
         self.aromatic_torus_thickness_slider = QSlider(Qt.Orientation.Horizontal)
         self.aromatic_torus_thickness_slider.setRange(10, 300)  # 0.1x to 3.0x
-        self.aromatic_torus_thickness_slider.setValue(100)  # Default 1.0x
-        self.aromatic_torus_thickness_label = QLabel("1.0")
+        self.aromatic_torus_thickness_slider.setValue(60)  # Default 0.6x
+        self.aromatic_torus_thickness_label = QLabel("0.6")
         self.aromatic_torus_thickness_slider.valueChanged.connect(
             lambda v: self.aromatic_torus_thickness_label.setText(f"{v/100:.1f}")
         )
@@ -564,17 +563,7 @@ class SettingsDialog(QDialog):
         info_label.setStyleSheet("color: #666; font-style: italic; margin-top: 10px;")
         form_layout.addRow(info_label)
         
-        # 原子半径
-        self.stick_atom_radius_slider = QSlider(Qt.Orientation.Horizontal)
-        self.stick_atom_radius_slider.setRange(5, 50)  # 0.05 ~ 0.5
-        self.stick_atom_radius_label = QLabel("0.15")
-        self.stick_atom_radius_slider.valueChanged.connect(lambda v: self.stick_atom_radius_label.setText(f"{v/100:.2f}"))
-        atom_radius_layout = QHBoxLayout()
-        atom_radius_layout.addWidget(self.stick_atom_radius_slider)
-        atom_radius_layout.addWidget(self.stick_atom_radius_label)
-        form_layout.addRow("Atom Radius:", atom_radius_layout)
-        
-        # ボンド半径
+        # ボンド半径（原子半径も同じ値を使用）
         self.stick_bond_radius_slider = QSlider(Qt.Orientation.Horizontal)
         self.stick_bond_radius_slider.setRange(5, 50)  # 0.05 ~ 0.5
         self.stick_bond_radius_label = QLabel("0.15")
@@ -673,7 +662,7 @@ class SettingsDialog(QDialog):
                 'display_kekule_3d': self.default_settings.get('display_kekule_3d', False),
                 'always_ask_charge': self.default_settings.get('always_ask_charge', False),
                 'display_aromatic_circles_3d': self.default_settings.get('display_aromatic_circles_3d', False),
-                'aromatic_torus_thickness_factor': self.default_settings.get('aromatic_torus_thickness_factor', 1.0),
+                'aromatic_torus_thickness_factor': self.default_settings.get('aromatic_torus_thickness_factor', 0.6),
             },
             "Ball & Stick": {
                 'ball_stick_atom_scale': self.default_settings['ball_stick_atom_scale'],
@@ -700,7 +689,6 @@ class SettingsDialog(QDialog):
                 'wireframe_triple_bond_radius_factor': self.default_settings.get('wireframe_triple_bond_radius_factor', 0.75)
             },
             "Stick": {
-                'stick_atom_radius': self.default_settings['stick_atom_radius'],
                 'stick_bond_radius': self.default_settings['stick_bond_radius'],
                 'stick_resolution': self.default_settings['stick_resolution'],
                 'stick_double_bond_offset_factor': self.default_settings.get('stick_double_bond_offset_factor', 1.5),
@@ -844,7 +832,6 @@ class SettingsDialog(QDialog):
             'wireframe_bond_radius': self.wf_bond_radius_slider.value() / 100.0,
             'wireframe_resolution': self.wf_resolution_slider.value(),
             # Stick settings
-            'stick_atom_radius': self.stick_atom_radius_slider.value() / 100.0,
             'stick_bond_radius': self.stick_bond_radius_slider.value() / 100.0,
             'stick_resolution': self.stick_resolution_slider.value(),
             # Multi-bond settings (per-model)
@@ -944,10 +931,6 @@ class SettingsDialog(QDialog):
         self.wf_resolution_label.setText(str(settings_dict.get('wireframe_resolution', self.default_settings['wireframe_resolution'])))
         
         # Stick設定
-        stick_atom_radius = int(settings_dict.get('stick_atom_radius', self.default_settings['stick_atom_radius']) * 100)
-        self.stick_atom_radius_slider.setValue(stick_atom_radius)
-        self.stick_atom_radius_label.setText(f"{stick_atom_radius/100:.2f}")
-        
         stick_bond_radius = int(settings_dict.get('stick_bond_radius', self.default_settings['stick_bond_radius']) * 100)
         self.stick_bond_radius_slider.setValue(stick_bond_radius)
         self.stick_bond_radius_label.setText(f"{stick_bond_radius/100:.2f}")
@@ -1019,7 +1002,7 @@ class SettingsDialog(QDialog):
         self.always_ask_charge_checkbox.setChecked(settings_dict.get('always_ask_charge', self.default_settings.get('always_ask_charge', False)))
         # Aromatic ring circle display and torus thickness factor
         self.aromatic_circle_checkbox.setChecked(settings_dict.get('display_aromatic_circles_3d', self.default_settings.get('display_aromatic_circles_3d', False)))
-        thickness_factor = float(settings_dict.get('aromatic_torus_thickness_factor', self.default_settings.get('aromatic_torus_thickness_factor', 1.0)))
+        thickness_factor = float(settings_dict.get('aromatic_torus_thickness_factor', self.default_settings.get('aromatic_torus_thickness_factor', 0.6)))
         try:
             self.aromatic_torus_thickness_slider.setValue(int(thickness_factor * 100))
             self.aromatic_torus_thickness_label.setText(f"{thickness_factor:.1f}")
@@ -1060,7 +1043,6 @@ class SettingsDialog(QDialog):
             'wireframe_bond_radius': self.wf_bond_radius_slider.value() / 100.0,
             'wireframe_resolution': self.wf_resolution_slider.value(),
             # Stick settings
-            'stick_atom_radius': self.stick_atom_radius_slider.value() / 100.0,
             'stick_bond_radius': self.stick_bond_radius_slider.value() / 100.0,
             'stick_resolution': self.stick_resolution_slider.value(),
             # Multiple bond offset settings (per-model)

{moleditpy_linux-1.18.0 → moleditpy_linux-1.18.1}/src/moleditpy_linux/modules/user_template_dialog.py

@@ -23,6 +23,7 @@ except Exception:
     from modules.constants import VERSION, CPK_COLORS
 import os
 import json
+import logging
 
 class UserTemplateDialog(QDialog):
     """ユーザーテンプレート管理ダイアログ"""
@@ -106,7 +107,7 @@ class UserTemplateDialog(QDialog):
                         elif hasattr(child, 'refit_view'):
                             child.refit_view()
         except Exception as e:
-            print(f"Warning: Failed to refit template previews: {e}")
+            logging.warning(f"Warning: Failed to refit template previews: {e}")
     
     def showEvent(self, event):
         """ダイアログ表示時にプレビューを適切にフィット"""
@@ -136,7 +137,7 @@ class UserTemplateDialog(QDialog):
                         template_data['filepath'] = filepath
                         self.user_templates.append(template_data)
         except Exception as e:
-            print(f"Error loading user templates: {e}")
+            logging.error(f"Error loading user templates: {e}")
         
         self.update_template_grid()
     
@@ -146,7 +147,7 @@ class UserTemplateDialog(QDialog):
             with open(filepath, 'r', encoding='utf-8') as f:
                 return json.load(f)
         except Exception as e:
-            print(f"Error loading template file {filepath}: {e}")
+            logging.error(f"Error loading template file {filepath}: {e}")
             return None
     
     def save_template_file(self, filepath, template_data):
@@ -156,7 +157,7 @@ class UserTemplateDialog(QDialog):
                 json.dump(template_data, f, indent=2, ensure_ascii=False)
             return True
         except Exception as e:
-            print(f"Error saving template file {filepath}: {e}")
+            logging.error(f"Error saving template file {filepath}: {e}")
             return False
     
     def update_template_grid(self):
@@ -253,7 +254,7 @@ class UserTemplateDialog(QDialog):
             if view and not rect.isEmpty():
                 view.fitInView(rect, Qt.AspectRatioMode.KeepAspectRatio)
         except Exception as e:
-            print(f"Warning: Failed to fit preview view: {e}")
+            logging.warning(f"Warning: Failed to fit preview view: {e}")
     
     def draw_template_preview(self, scene, template_data, view_size=None):
         """テンプレートプレビューを描画 - fitInView縮小率に基づく動的スケーリング"""
@@ -303,7 +304,7 @@ class UserTemplateDialog(QDialog):
                 scale_factor = 4.0
             
             # Debug info (can be removed in production)
-            # print(f"Mol size: {mol_size:.1f}, Fit scale: {fit_scale:.3f}, Scale factor: {scale_factor:.2f}")
+            # logging.debug(f"Mol size: {mol_size:.1f}, Fit scale: {fit_scale:.3f}, Scale factor: {scale_factor:.2f}")
         else:
             scale_factor = 1.0
         
@@ -481,7 +482,7 @@ class UserTemplateDialog(QDialog):
             except Exception:
                 pass
         except Exception as e:
-            print(f"Warning: Failed to switch main window to template mode: {e}")
+            logging.warning(f"Warning: Failed to switch main window to template mode: {e}")
     
     def use_template(self, template_data):
         """テンプレートを使用（エディタに適用）"""
@@ -518,7 +519,7 @@ class UserTemplateDialog(QDialog):
                 # Mark selected and keep dialog open
                 self.selected_template = template_data
             except Exception as e:
-                print(f"Warning: Failed to switch main window to template mode: {e}")
+                logging.warning(f"Warning: Failed to switch main window to template mode: {e}")
 
             # Don't close dialog - keep it open for easy template switching
             # self.accept()