MoleditPy-linux 1.16.1a2__py3-none-any.whl → 1.16.2__py3-none-any.whl

{moleditpy-linux → moleditpy_linux}/modules/constants.py

@@ -4,7 +4,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '1.16.1a2'
+VERSION = '1.16.2'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy-linux → moleditpy_linux}/modules/main_window_main_init.py

@@ -79,6 +79,8 @@ def detect_system_theme():
 
         # macOS: 'defaults read -g AppleInterfaceStyle'
         if platform.system() == 'Darwin':
+            return 'light'
+            '''
             try:
                 # 'defaults read ...' が成功すればダークモード
                 p = subprocess.run(
@@ -94,6 +96,7 @@ def detect_system_theme():
             except Exception:
                 # その他のエラー
                 pass
+            '''
 
         # Linux / GNOME: try color-scheme gsetting; fallback to gtk-theme detection
         if platform.system() == 'Linux':
@@ -494,11 +497,10 @@ class MainWindowMainInit(object):
         def _icon_foreground_color():
             """Return a QColor for icon foreground.
 
-            NOTE: this application inverts the usual foreground mapping so icons
-            will be the *opposite* color to the background (i.e., black on dark
-            backgrounds, white on light backgrounds). This intentionally reverses
-            the previous behavior so button icons don't blend into the 3D-view
-            background. Priority: explicit setting in 'icon_foreground' -> OS
+            NOTE: choose icon foreground to contrast against the background
+            (i.e., white on dark backgrounds, black on light backgrounds). This
+            matches common conventions. Priority: explicit setting in
+            'icon_foreground' -> OS theme preference -> configured 3D
             theme preference -> configured 3D background -> application palette.
             """
             try:
@@ -513,9 +515,9 @@ class MainWindowMainInit(object):
             # 1) Prefer the system/OS dark-mode preference if available.
             try:
                 os_pref = detect_system_dark_mode()
-                # Invert the color so in dark-pref OS we return black, in light we return white
+                # Standard mapping: dark -> white, light -> black
                 if os_pref is not None:
-                    return QColor('#000000') if os_pref else QColor('#FFFFFF')
+                    return QColor('#FFFFFF') if os_pref else QColor('#000000')
             except Exception:
                 pass
 
@@ -527,8 +529,8 @@ class MainWindowMainInit(object):
                     bg = QColor(bg_hex)
                     if bg.isValid():
                         lum = 0.2126 * bg.redF() + 0.7152 * bg.greenF() + 0.0722 * bg.blueF()
-                        # Inverted: return black on dark (lum<0.5), white on light
-                        return QColor('#000000') if lum < 0.5 else QColor('#FFFFFF')
+                        # Return white on dark (lum<0.5), black on light
+                        return QColor('#FFFFFF') if lum < 0.5 else QColor('#000000')
             except Exception:
                 pass
 
@@ -537,8 +539,8 @@ class MainWindowMainInit(object):
                 # palette.window() returns a QBrush; call color()
                 window_bg = pal.window().color()
                 lum = 0.2126 * window_bg.redF() + 0.7152 * window_bg.greenF() + 0.0722 * window_bg.blueF()
-                # Inverted mapping for palette fallback
-                return QColor('#000000') if lum < 0.5 else QColor('#FFFFFF')
+                # Palette-based mapping: white on dark palette background
+                return QColor('#FFFFFF') if lum < 0.5 else QColor('#000000')
             except Exception:
                 return QColor('#000000')
 
@@ -1577,6 +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 → 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 → 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 → 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 ---
@@ -210,6 +217,26 @@ class SettingsDialog(QDialog):
         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:", 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
+
         # Add Other tab to the tab widget
         self.tab_widget.addTab(self.other_widget, "Other")
 
@@ -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

{moleditpy_linux-1.16.1a2.dist-info → moleditpy_linux-1.16.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 1.16.1a2
+Version: 1.16.2
 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

moleditpy_linux-1.16.2.dist-info/RECORD

@@ -0,0 +1,54 @@
+moleditpy_linux/__init__.py,sha256=QCzpw3P5V_CwDtN4itK4hT9J99JgsH4gmpTfvuus6p8,46
+moleditpy_linux/__main__.py,sha256=az0UrbFsuprbQYycF_bSUXxb0F20DuLvYxrZl1-X5EU,831
+moleditpy_linux/main.py,sha256=cEZJuCL0HrLPUYvuwPSxgUkaDykVb573A-3qVvjF9RM,1180
+moleditpy_linux/modules/__init__.py,sha256=DIO4nzCCnpeYLjFqzHxcRYqbECtWWMEGQ_-sb03jirs,1127
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