MoleditPy 1.15.1__py3-none-any.whl → 1.16.0__py3-none-any.whl

moleditpy/modules/main_window_app_state.py

@@ -0,0 +1,747 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+main_window_app_state.py
+MainWindow (main_window.py) から分離されたモジュール
+機能クラス: MainWindowAppState
+"""
+
+
+import numpy as np
+import copy
+import os
+import base64
+
+
+# RDKit imports (explicit to satisfy flake8 and used features)
+from rdkit import Chem
+from rdkit.Chem import Descriptors, rdMolDescriptors
+try:
+    pass
+except Exception:
+    pass
+
+# PyQt6 Modules
+from PyQt6.QtWidgets import (
+    QMessageBox
+)
+
+
+
+from PyQt6.QtCore import (
+    Qt, QPointF, QDateTime
+)
+
+
+# Use centralized Open Babel availability from package-level __init__
+# Use per-package modules availability (local __init__).
+try:
+    from . import OBABEL_AVAILABLE
+except Exception:
+    from modules import OBABEL_AVAILABLE
+# Only import pybel on demand — `moleditpy` itself doesn't expose `pybel`.
+if OBABEL_AVAILABLE:
+    try:
+        from openbabel import pybel
+    except Exception:
+        # 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.")
+else:
+    pybel = None
+    
+# Optional SIP helper: on some PyQt6 builds sip.isdeleted is available and
+# allows safely detecting C++ wrapper objects that have been deleted. Import
+# it once at module import time and expose a small, robust wrapper so callers
+# can avoid re-importing sip repeatedly and so we centralize exception
+# handling (this reduces crash risk during teardown and deletion operations).
+try:
+    import sip as _sip  # type: ignore
+    _sip_isdeleted = getattr(_sip, 'isdeleted', None)
+except Exception:
+    _sip = None
+    _sip_isdeleted = None
+
+try:
+    # package relative imports (preferred when running as `python -m moleditpy`)
+    from .constants import VERSION
+    from .atom_item import AtomItem
+    from .bond_item import BondItem
+except Exception:
+    # Fallback to absolute imports for script-style execution
+    from modules.constants import VERSION
+    from modules.atom_item import AtomItem
+    from modules.bond_item import BondItem
+
+
+# --- クラス定義 ---
+class MainWindowAppState(object):
+    """ main_window.py から分離された機能クラス """
+
+    def __init__(self):
+        """
+        クラスの初期化
+        BoundFeature経由で呼ばれるため、'self' には MainWindow インスタンスが渡されます。
+        """
+        self.DEBUG_UNDO = False
+
+
+
+    def get_current_state(self):
+        atoms = {atom_id: {'symbol': data['symbol'],
+                           'pos': (data['item'].pos().x(), data['item'].pos().y()),
+                           'charge': data.get('charge', 0),
+                           'radical': data.get('radical', 0)} 
+                 for atom_id, data in self.data.atoms.items()}
+        bonds = {key: {'order': data['order'], 'stereo': data.get('stereo', 0)} for key, data in self.data.bonds.items()}
+        state = {'atoms': atoms, 'bonds': bonds, '_next_atom_id': self.data._next_atom_id}
+
+        state['version'] = VERSION 
+        
+        if self.current_mol: state['mol_3d'] = self.current_mol.ToBinary()
+
+        state['is_3d_viewer_mode'] = not self.is_2d_editable
+
+        json_safe_constraints = []
+        try:
+            for const in self.constraints_3d:
+                # (Type, (Idx...), Value, Force) -> [Type, [Idx...], Value, Force]
+                if len(const) == 4:
+                    json_safe_constraints.append([const[0], list(const[1]), const[2], const[3]])
+                else:
+                    # 後方互換性: 3要素の場合はデフォルトForceを追加
+                    json_safe_constraints.append([const[0], list(const[1]), const[2], 1.0e5])
+        except Exception:
+            pass # 失敗したら空リスト
+        state['constraints_3d'] = json_safe_constraints
+            
+        return state
+
+
+
+    def set_state_from_data(self, state_data):
+        self.dragged_atom_info = None
+        self.clear_2d_editor(push_to_undo=False)
+        
+        loaded_data = copy.deepcopy(state_data)
+
+        # ファイルのバージョンを取得（存在しない場合は '0.0.0' とする）
+        file_version_str = loaded_data.get('version', '0.0.0')
+
+        try:
+            app_version_parts = tuple(map(int, VERSION.split('.')))
+            file_version_parts = tuple(map(int, file_version_str.split('.')))
+
+            # ファイルのバージョンがアプリケーションのバージョンより新しい場合に警告
+            if file_version_parts > app_version_parts:
+                QMessageBox.warning(
+                    self,
+                    "Version Mismatch",
+                    f"The file you are opening was saved with a newer version of MoleditPy (ver. {file_version_str}).\n\n"
+                    f"Your current version is {VERSION}.\n\n"
+                    "Some features may not load or work correctly."
+                )
+        except (ValueError, AttributeError):
+            pass
+
+        raw_atoms = loaded_data.get('atoms', {})
+        raw_bonds = loaded_data.get('bonds', {})
+
+        # 制約データの復元 (pmeraw)
+        try:
+            loaded_constraints = loaded_data.get("constraints_3d", [])
+            # pmerawもJSON互換形式 [Type, [Idx...], Value, Force] で保存されている想定
+            self.constraints_3d = []
+            for const in loaded_constraints:
+                if isinstance(const, list):
+                    if len(const) == 4:
+                        # [Type, [Idx...], Value, Force] -> (Type, (Idx...), Value, Force)
+                        self.constraints_3d.append((const[0], tuple(const[1]), const[2], const[3]))
+                    elif len(const) == 3:
+                        # 後方互換性: [Type, [Idx...], Value] -> (Type, (Idx...), Value, 1.0e5)
+                        self.constraints_3d.append((const[0], tuple(const[1]), const[2], 1.0e5))
+        except Exception:
+            self.constraints_3d = [] # 読み込み失敗時はリセット
+
+        for atom_id, data in raw_atoms.items():
+            pos = QPointF(data['pos'][0], data['pos'][1])
+            charge = data.get('charge', 0)
+            radical = data.get('radical', 0)  # <-- ラジカル情報を取得
+            # AtomItem生成時にradicalを渡す
+            atom_item = AtomItem(atom_id, data['symbol'], pos, charge=charge, radical=radical)
+            # self.data.atomsにもradical情報を格納する
+            self.data.atoms[atom_id] = {'symbol': data['symbol'], 'pos': pos, 'item': atom_item, 'charge': charge, 'radical': radical}
+            self.scene.addItem(atom_item)
+        
+        self.data._next_atom_id = loaded_data.get('_next_atom_id', max(self.data.atoms.keys()) + 1 if self.data.atoms else 0)
+
+        for key_tuple, data in raw_bonds.items():
+            id1, id2 = key_tuple
+            if id1 in self.data.atoms and id2 in self.data.atoms:
+                atom1_item = self.data.atoms[id1]['item']; atom2_item = self.data.atoms[id2]['item']
+                bond_item = BondItem(atom1_item, atom2_item, data.get('order', 1), data.get('stereo', 0))
+                self.data.bonds[key_tuple] = {'order': data.get('order', 1), 'stereo': data.get('stereo', 0), 'item': bond_item}
+                atom1_item.bonds.append(bond_item); atom2_item.bonds.append(bond_item)
+                self.scene.addItem(bond_item)
+
+        for atom_data in self.data.atoms.values():
+            if atom_data['item']: atom_data['item'].update_style()
+        self.scene.update()
+
+        if 'mol_3d' in loaded_data and loaded_data['mol_3d'] is not None:
+            try:
+                self.current_mol = Chem.Mol(loaded_data['mol_3d'])
+                # デバッグ：3D構造が有効かチェック
+                if self.current_mol and self.current_mol.GetNumAtoms() > 0:
+                    self.draw_molecule_3d(self.current_mol)
+                    self.plotter.reset_camera()
+                    # 3D関連機能を統一的に有効化
+                    self._enable_3d_features(True)
+                    
+                    # 3D原子情報ホバー表示を再設定
+                    self.setup_3d_hover()
+                else:
+                    # 無効な3D構造の場合
+                    self.current_mol = None
+                    self.plotter.clear()
+                    # 3D関連機能を統一的に無効化
+                    self._enable_3d_features(False)
+            except Exception as e:
+                self.statusBar().showMessage(f"Could not load 3D model from project: {e}")
+                self.current_mol = None
+                # 3D関連機能を統一的に無効化
+                self._enable_3d_features(False)
+        else:
+            self.current_mol = None; self.plotter.clear(); self.analysis_action.setEnabled(False)
+            self.optimize_3d_button.setEnabled(False)
+            # 3D関連機能を統一的に無効化
+            self._enable_3d_features(False)
+
+        self.update_implicit_hydrogens()
+        self.update_chiral_labels()
+
+        if loaded_data.get('is_3d_viewer_mode', False):
+            self._enter_3d_viewer_ui_mode()
+            self.statusBar().showMessage("Project loaded in 3D Viewer Mode.")
+        else:
+            self.restore_ui_for_editing()
+            # 3D分子がある場合は、2Dエディタモードでも3D編集機能を有効化
+            if self.current_mol and self.current_mol.GetNumAtoms() > 0:
+                self._enable_3d_edit_actions(True)
+        
+        # undo/redo後に測定ラベルの位置を更新
+        self.update_2d_measurement_labels()
+        
+
+
+
+    def push_undo_state(self):
+        if self._is_restoring_state:
+            return
+            
+        current_state_for_comparison = {
+            'atoms': {k: (v['symbol'], v['item'].pos().x(), v['item'].pos().y(), v.get('charge', 0), v.get('radical', 0)) for k, v in self.data.atoms.items()},
+            'bonds': {k: (v['order'], v.get('stereo', 0)) for k, v in self.data.bonds.items()},
+            '_next_atom_id': self.data._next_atom_id,
+            'mol_3d': self.current_mol.ToBinary() if self.current_mol else None
+        }
+        
+        last_state_for_comparison = None
+        if self.undo_stack:
+            last_state = self.undo_stack[-1]
+            last_atoms = last_state.get('atoms', {})
+            last_bonds = last_state.get('bonds', {})
+            last_state_for_comparison = {
+                'atoms': {k: (v['symbol'], v['pos'][0], v['pos'][1], v.get('charge', 0), v.get('radical', 0)) for k, v in last_atoms.items()},
+                'bonds': {k: (v['order'], v.get('stereo', 0)) for k, v in last_bonds.items()},
+                '_next_atom_id': last_state.get('_next_atom_id'),
+                'mol_3d': last_state.get('mol_3d', None)
+            }
+
+        if not last_state_for_comparison or current_state_for_comparison != last_state_for_comparison:
+            # Deepcopy state to ensure saved states are immutable and not affected
+            # by later modifications to objects referenced from the state.
+            state = copy.deepcopy(self.get_current_state())
+            self.undo_stack.append(state)
+            if getattr(self, 'DEBUG_UNDO', False):
+                try:
+                    print(f"DEBUG_UNDO: push_undo_state -> new stack size: {len(self.undo_stack)}")
+                except Exception:
+                    pass
+            self.redo_stack.clear()
+            # 初期化完了後のみ変更があったことを記録
+            if self.initialization_complete:
+                self.has_unsaved_changes = True
+                self.update_window_title()
+        
+        self.update_implicit_hydrogens()
+        self.update_realtime_info()
+        self.update_undo_redo_actions()
+
+
+
+    def update_window_title(self):
+        """ウィンドウタイトルを更新（保存状態を反映）"""
+        base_title = f"MoleditPy Ver. {VERSION}"
+        if self.current_file_path:
+            filename = os.path.basename(self.current_file_path)
+            title = f"{filename} - {base_title}"
+            if self.has_unsaved_changes:
+                title = f"*{title}"
+        else:
+            # Untitledファイルとして扱う
+            title = f"Untitled - {base_title}"
+            if self.has_unsaved_changes:
+                title = f"*{title}"
+        self.setWindowTitle(title)
+
+
+
+    def check_unsaved_changes(self):
+        """未保存の変更があるかチェックし、警告ダイアログを表示"""
+        if not self.has_unsaved_changes:
+            return True  # 保存済みまたは変更なし
+        
+        if not self.data.atoms and self.current_mol is None:
+            return True  # 空のドキュメント
+        
+        reply = QMessageBox.question(
+            self,
+            "Unsaved Changes",
+            "You have unsaved changes. Do you want to save them?",
+            QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No | QMessageBox.StandardButton.Cancel,
+            QMessageBox.StandardButton.Yes
+        )
+        
+        if reply == QMessageBox.StandardButton.Yes:
+            # 拡張子がPMEPRJでなければ「名前を付けて保存」
+            file_path = self.current_file_path
+            if not file_path or not file_path.lower().endswith('.pmeprj'):
+                self.save_project_as()
+            else:
+                self.save_project()
+            return not self.has_unsaved_changes  # 保存に成功した場合のみTrueを返す
+        elif reply == QMessageBox.StandardButton.No:
+            return True  # 保存せずに続行
+        else:
+            return False  # キャンセル
+
+
+
+    def reset_undo_stack(self):
+        self.undo_stack.clear()
+        self.redo_stack.clear()
+        self.push_undo_state()
+        if getattr(self, 'DEBUG_UNDO', False):
+            try:
+                print(f"DEBUG_UNDO: reset_undo_stack -> undo={len(self.undo_stack)} redo={len(self.redo_stack)}")
+            except Exception:
+                pass
+
+
+
+    def undo(self):
+        if len(self.undo_stack) > 1:
+            self.redo_stack.append(self.undo_stack.pop())
+            state = self.undo_stack[-1]
+            self._is_restoring_state = True
+            try:
+                self.set_state_from_data(state)
+            finally:
+                self._is_restoring_state = False
+
+            
+            # Undo後に3D構造の状態に基づいてメニューを再評価
+            if self.current_mol and self.current_mol.GetNumAtoms() > 0:
+                # 3D構造がある場合は3D編集機能を有効化
+                self._enable_3d_edit_actions(True)
+            else:
+                # 3D構造がない場合は3D編集機能を無効化
+                self._enable_3d_edit_actions(False)
+                    
+        if getattr(self, 'DEBUG_UNDO', False):
+            try:
+                print(f"DEBUG_UNDO: undo -> undo_stack size: {len(self.undo_stack)}, redo_stack size: {len(self.redo_stack)}")
+            except Exception:
+                pass
+        self.update_undo_redo_actions()
+        self.update_realtime_info()
+        self.view_2d.setFocus() 
+
+
+
+    def redo(self):
+        if self.redo_stack:
+            state = self.redo_stack.pop()
+            self.undo_stack.append(state)
+            self._is_restoring_state = True
+            try:
+                self.set_state_from_data(state)
+            finally:
+                self._is_restoring_state = False
+            
+            # Redo後に3D構造の状態に基づいてメニューを再評価
+            if self.current_mol and self.current_mol.GetNumAtoms() > 0:
+                # 3D構造がある場合は3D編集機能を有効化
+                self._enable_3d_edit_actions(True)
+            else:
+                # 3D構造がない場合は3D編集機能を無効化
+                self._enable_3d_edit_actions(False)
+                    
+        if getattr(self, 'DEBUG_UNDO', False):
+            try:
+                print(f"DEBUG_UNDO: redo -> undo_stack size: {len(self.undo_stack)}, redo_stack size: {len(self.redo_stack)}")
+            except Exception:
+                pass
+        self.update_undo_redo_actions()
+        self.update_realtime_info()
+        self.view_2d.setFocus() 
+        
+
+
+    def update_undo_redo_actions(self):
+        self.undo_action.setEnabled(len(self.undo_stack) > 1)
+        self.redo_action.setEnabled(len(self.redo_stack) > 0)
+
+
+
+    def update_realtime_info(self):
+        """ステータスバーの右側に現在の分子情報を表示する"""
+        if not self.data.atoms:
+            self.formula_label.setText("")  # 原子がなければ右側のラベルをクリア
+            return
+
+        try:
+            mol = self.data.to_rdkit_mol()
+            if mol:
+                # 水素原子を明示的に追加した分子オブジェクトを生成
+                mol_with_hs = Chem.AddHs(mol)
+                mol_formula = rdMolDescriptors.CalcMolFormula(mol)
+                # 水素を含む分子オブジェクトから原子数を取得
+                num_atoms = mol_with_hs.GetNumAtoms()
+                # 右側のラベルのテキストを更新
+                self.formula_label.setText(f"Formula: {mol_formula}   |   Atoms: {num_atoms}")
+        except Exception:
+            # 計算に失敗してもアプリは継続
+            self.formula_label.setText("Invalid structure")
+
+
+
+    def create_json_data(self):
+        """現在の状態をPMEJSON形式のデータに変換"""
+        # 基本的なメタデータ
+        json_data = {
+            "format": "PME Project",
+            "version": "1.0",
+            "application": "MoleditPy",
+            "application_version": VERSION,
+            "created": str(QDateTime.currentDateTime().toString(Qt.DateFormat.ISODate)),
+            "is_3d_viewer_mode": not self.is_2d_editable
+        }
+        
+        # 2D構造データ
+        if self.data.atoms:
+            atoms_2d = []
+            for atom_id, data in self.data.atoms.items():
+                pos = data['item'].pos()
+                atom_data = {
+                    "id": atom_id,
+                    "symbol": data['symbol'],
+                    "x": pos.x(),
+                    "y": pos.y(),
+                    "charge": data.get('charge', 0),
+                    "radical": data.get('radical', 0)
+                }
+                atoms_2d.append(atom_data)
+            
+            bonds_2d = []
+            for (atom1_id, atom2_id), bond_data in self.data.bonds.items():
+                bond_info = {
+                    "atom1": atom1_id,
+                    "atom2": atom2_id,
+                    "order": bond_data['order'],
+                    "stereo": bond_data.get('stereo', 0)
+                }
+                bonds_2d.append(bond_info)
+            
+            json_data["2d_structure"] = {
+                "atoms": atoms_2d,
+                "bonds": bonds_2d,
+                "next_atom_id": self.data._next_atom_id
+            }
+        
+        # 3D分子データ
+        if self.current_mol and self.current_mol.GetNumConformers() > 0:
+            try:
+                # MOLデータをBase64エンコードで保存（バイナリデータの安全な保存）
+                mol_binary = self.current_mol.ToBinary()
+                mol_base64 = base64.b64encode(mol_binary).decode('ascii')
+                
+                # 3D座標を抽出
+                atoms_3d = []
+                if self.current_mol.GetNumConformers() > 0:
+                    conf = self.current_mol.GetConformer()
+                    for i in range(self.current_mol.GetNumAtoms()):
+                        atom = self.current_mol.GetAtomWithIdx(i)
+                        pos = conf.GetAtomPosition(i)
+
+                        # Try to preserve original editor atom ID (if present) so it can be
+                        # restored when loading PMEPRJ files. RDKit atom properties may
+                        # contain _original_atom_id when the molecule was created from
+                        # the editor's 2D structure.
+                        original_id = None
+                        try:
+                            if atom.HasProp("_original_atom_id"):
+                                original_id = atom.GetIntProp("_original_atom_id")
+                        except Exception:
+                            original_id = None
+
+                        atom_3d = {
+                            "index": i,
+                            "symbol": atom.GetSymbol(),
+                            "atomic_number": atom.GetAtomicNum(),
+                            "x": pos.x,
+                            "y": pos.y,
+                            "z": pos.z,
+                            "formal_charge": atom.GetFormalCharge(),
+                            "num_explicit_hs": atom.GetNumExplicitHs(),
+                            "num_implicit_hs": atom.GetNumImplicitHs(),
+                            # include original editor atom id when available for round-trip
+                            "original_id": original_id
+                        }
+                        atoms_3d.append(atom_3d)
+                
+                # 結合情報を抽出
+                bonds_3d = []
+                for bond in self.current_mol.GetBonds():
+                    bond_3d = {
+                        "atom1": bond.GetBeginAtomIdx(),
+                        "atom2": bond.GetEndAtomIdx(),
+                        "order": int(bond.GetBondType()),
+                        "is_aromatic": bond.GetIsAromatic(),
+                        "stereo": int(bond.GetStereo())
+                    }
+                    bonds_3d.append(bond_3d)
+                
+                # constraints_3dをJSON互換形式に変換
+                json_safe_constraints = []
+                try:
+                    for const in self.constraints_3d:
+                        if len(const) == 4:
+                            json_safe_constraints.append([const[0], list(const[1]), const[2], const[3]])
+                        else:
+                            json_safe_constraints.append([const[0], list(const[1]), const[2], 1.0e5])
+                except Exception:
+                    json_safe_constraints = []
+                
+                json_data["3d_structure"] = {
+                    "mol_binary_base64": mol_base64,
+                    "atoms": atoms_3d,
+                    "bonds": bonds_3d,
+                    "num_conformers": self.current_mol.GetNumConformers(),
+                    "constraints_3d": json_safe_constraints
+                }
+                
+                # 分子の基本情報
+                json_data["molecular_info"] = {
+                    "num_atoms": self.current_mol.GetNumAtoms(),
+                    "num_bonds": self.current_mol.GetNumBonds(),
+                    "molecular_weight": Descriptors.MolWt(self.current_mol),
+                    "formula": rdMolDescriptors.CalcMolFormula(self.current_mol)
+                }
+                
+                # SMILESとInChI（可能であれば）
+                try:
+                    json_data["identifiers"] = {
+                        "smiles": Chem.MolToSmiles(self.current_mol),
+                        "canonical_smiles": Chem.MolToSmiles(self.current_mol, canonical=True)
+                    }
+                    
+                    # InChI生成を試行
+                    try:
+                        inchi = Chem.MolToInchi(self.current_mol)
+                        inchi_key = Chem.MolToInchiKey(self.current_mol)
+                        json_data["identifiers"]["inchi"] = inchi
+                        json_data["identifiers"]["inchi_key"] = inchi_key
+                    except:
+                        pass  # InChI生成に失敗した場合は無視
+                        
+                except Exception as e:
+                    print(f"Warning: Could not generate molecular identifiers: {e}")
+                    
+            except Exception as e:
+                print(f"Warning: Could not process 3D molecular data: {e}")
+        else:
+            # 3D情報がない場合の記録
+            json_data["3d_structure"] = None
+            json_data["note"] = "No 3D structure available. Generate 3D coordinates first."
+
+        # Record the last-successful optimization method (if any)
+        # This is a convenience field so saved projects remember which
+        # optimizer variant was last used (e.g. "MMFF94s", "MMFF94", "UFF").
+        try:
+            json_data["last_successful_optimization_method"] = getattr(self, 'last_successful_optimization_method', None)
+        except Exception:
+            json_data["last_successful_optimization_method"] = None
+        
+        return json_data
+
+
+
+    def load_from_json_data(self, json_data):
+        """JSONデータから状態を復元"""
+        self.dragged_atom_info = None
+        self.clear_2d_editor(push_to_undo=False)
+        self._enable_3d_edit_actions(False)
+        self._enable_3d_features(False)
+
+        # 3Dビューアーモードの設定
+        is_3d_mode = json_data.get("is_3d_viewer_mode", False)
+        # Restore last successful optimization method if present in file
+        try:
+            self.last_successful_optimization_method = json_data.get("last_successful_optimization_method", None)
+        except Exception:
+            self.last_successful_optimization_method = None
+
+
+        # 2D構造データの復元
+        if "2d_structure" in json_data:
+            structure_2d = json_data["2d_structure"]
+            atoms_2d = structure_2d.get("atoms", [])
+            bonds_2d = structure_2d.get("bonds", [])
+
+            # 原子の復元
+            for atom_data in atoms_2d:
+                atom_id = atom_data["id"]
+                symbol = atom_data["symbol"]
+                pos = QPointF(atom_data["x"], atom_data["y"])
+                charge = atom_data.get("charge", 0)
+                radical = atom_data.get("radical", 0)
+
+                atom_item = AtomItem(atom_id, symbol, pos, charge=charge, radical=radical)
+                self.data.atoms[atom_id] = {
+                    'symbol': symbol,
+                    'pos': pos,
+                    'item': atom_item,
+                    'charge': charge,
+                    'radical': radical
+                }
+                self.scene.addItem(atom_item)
+
+            # next_atom_idの復元
+            self.data._next_atom_id = structure_2d.get(
+                "next_atom_id",
+                max([atom["id"] for atom in atoms_2d]) + 1 if atoms_2d else 0
+            )
+
+            # 結合の復元
+            for bond_data in bonds_2d:
+                atom1_id = bond_data["atom1"]
+                atom2_id = bond_data["atom2"]
+
+                if atom1_id in self.data.atoms and atom2_id in self.data.atoms:
+                    atom1_item = self.data.atoms[atom1_id]['item']
+                    atom2_item = self.data.atoms[atom2_id]['item']
+
+                    bond_order = bond_data["order"]
+                    stereo = bond_data.get("stereo", 0)
+
+                    bond_item = BondItem(atom1_item, atom2_item, bond_order, stereo=stereo)
+                    # 原子の結合リストに追加（重要：炭素原子の可視性判定で使用）
+                    atom1_item.bonds.append(bond_item)
+                    atom2_item.bonds.append(bond_item)
+
+                    self.data.bonds[(atom1_id, atom2_id)] = {
+                        'order': bond_order,
+                        'item': bond_item,
+                        'stereo': stereo
+                    }
+                    self.scene.addItem(bond_item)
+
+            # --- ここで全AtomItemのスタイルを更新（炭素原子の可視性を正しく反映） ---
+            for atom in self.data.atoms.values():
+                atom['item'].update_style()
+        # 3D構造データの復元
+        if "3d_structure" in json_data:
+            structure_3d = json_data["3d_structure"]
+
+            # 制約データの復元 (JSONはタプルをリストとして保存するので、タプルに再変換)
+            try:
+                loaded_constraints = structure_3d.get("constraints_3d", [])
+                self.constraints_3d = []
+                for const in loaded_constraints:
+                    if isinstance(const, list):
+                        if len(const) == 4:
+                            # [Type, [Idx...], Value, Force] -> (Type, (Idx...), Value, Force)
+                            self.constraints_3d.append((const[0], tuple(const[1]), const[2], const[3]))
+                        elif len(const) == 3:
+                            # 後方互換性: [Type, [Idx...], Value] -> (Type, (Idx...), Value, 1.0e5)
+                            self.constraints_3d.append((const[0], tuple(const[1]), const[2], 1.0e5))
+            except Exception:
+                self.constraints_3d = [] # 読み込み失敗時はリセット
+
+            try:
+                # バイナリデータの復元
+                mol_base64 = structure_3d.get("mol_binary_base64")
+                if mol_base64:
+                    mol_binary = base64.b64decode(mol_base64.encode('ascii'))
+                    self.current_mol = Chem.Mol(mol_binary)
+                    if self.current_mol:
+                        # 3D座標の設定
+                        if self.current_mol.GetNumConformers() > 0:
+                            conf = self.current_mol.GetConformer()
+                            atoms_3d = structure_3d.get("atoms", [])
+                            self.atom_positions_3d = np.zeros((len(atoms_3d), 3))
+                            for atom_data in atoms_3d:
+                                idx = atom_data["index"]
+                                if idx < len(self.atom_positions_3d):
+                                    self.atom_positions_3d[idx] = [
+                                        atom_data["x"], 
+                                        atom_data["y"], 
+                                        atom_data["z"]
+                                    ]
+                                # Restore original editor atom id into RDKit atom property
+                                try:
+                                    original_id = atom_data.get("original_id", None)
+                                    if original_id is not None and idx < self.current_mol.GetNumAtoms():
+                                        rd_atom = self.current_mol.GetAtomWithIdx(idx)
+                                        # set as int prop so other code expecting _original_atom_id works
+                                        rd_atom.SetIntProp("_original_atom_id", int(original_id))
+                                except Exception:
+                                    pass
+                            # Build mapping from original 2D atom IDs to RDKit indices so
+                            # 3D picks can be synchronized back to 2D AtomItems.
+                            try:
+                                self.create_atom_id_mapping()
+                                # update menu and UI states that depend on original IDs
+                                try:
+                                    self.update_atom_id_menu_text()
+                                    self.update_atom_id_menu_state()
+                                except Exception:
+                                    pass
+                            except Exception:
+                                # non-fatal if mapping creation fails
+                                pass
+
+                        # 3D分子があれば必ず3D表示
+                        self.draw_molecule_3d(self.current_mol)
+                        # ViewerモードならUIも切り替え
+                        if is_3d_mode:
+                            self._enter_3d_viewer_ui_mode()
+                        else:
+                            self.is_2d_editable = True
+                        self.plotter.reset_camera()
+
+                        # 成功的に3D分子が復元されたので、3D関連UIを有効にする
+                        try:
+                            self._enable_3d_edit_actions(True)
+                            self._enable_3d_features(True)
+                        except Exception:
+                            pass
+                            
+            except Exception as e:
+                print(f"Warning: Could not restore 3D molecular data: {e}")
+                self.current_mol = None
+