MoleditPy-linux 2.4.1__py3-none-any.whl

moleditpy_linux/modules/main_window_molecular_parsers.py

@@ -0,0 +1,1044 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+MoleditPy — A Python-based molecular editing software
+
+Author: Hiromichi Yokoyama
+License: GPL-3.0 license
+Repo: https://github.com/HiroYokoyama/python_molecular_editor
+DOI: 10.5281/zenodo.17268532
+"""
+
+
+"""
+main_window_molecular_parsers.py
+MainWindow (main_window.py) から分離されたモジュール
+機能クラス: MainWindowMolecularParsers
+"""
+
+
+import io
+import os
+import contextlib
+import traceback
+import logging
+
+
+# RDKit imports (explicit to satisfy flake8 and used features)
+from rdkit import Chem
+from rdkit.Chem import AllChem, Descriptors, rdMolTransforms, rdGeometry
+try:
+    pass
+except Exception:
+    pass
+
+# PyQt6 Modules
+from PyQt6.QtWidgets import (
+    QVBoxLayout, QHBoxLayout,
+    QPushButton, QDialog, QFileDialog, QLabel, QLineEdit, QInputDialog, QDialogButtonBox
+)
+
+
+
+from PyQt6.QtCore import (
+    QPointF, QTimer
+)
+
+
+# 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
+        logging.warning("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
+except Exception:
+    # Fallback to absolute imports for script-style execution
+    from modules.constants import VERSION
+
+
+# --- クラス定義 ---
+class MainWindowMolecularParsers(object):
+    """ main_window.py から分離された機能クラス """
+
+
+    def load_mol_file(self, file_path=None):
+        if not self.check_unsaved_changes():
+                return  # ユーザーがキャンセルした場合は何もしない
+        if not file_path:
+            file_path, _ = QFileDialog.getOpenFileName(self, "Import MOL File", "", "Chemical Files (*.mol *.sdf);;All Files (*)")
+            if not file_path: 
+                return
+
+        try:
+            self.dragged_atom_info = None
+            # If this is a single-record .mol file, read & fix the counts line
+            # before parsing. For multi-record .sdf files, keep using SDMolSupplier.
+            _, ext = os.path.splitext(file_path)
+            ext = ext.lower() if ext else ''
+            if ext == '.mol':
+                # Read file text, fix CTAB counts line if needed, then parse
+                with open(file_path, 'r', encoding='utf-8', errors='replace') as fh:
+                    raw = fh.read()
+                fixed_block = self.fix_mol_block(raw)
+                mol = Chem.MolFromMolBlock(fixed_block, sanitize=True, removeHs=False)
+                if mol is None:
+                    raise ValueError("Failed to read molecule from .mol file after fixing counts line.")
+            else:
+                suppl = Chem.SDMolSupplier(file_path, removeHs=False)
+                mol = next(suppl, None)
+                if mol is None:
+                    raise ValueError("Failed to read molecule from file.")
+
+            Chem.Kekulize(mol)
+
+            self.restore_ui_for_editing()
+            self.clear_2d_editor(push_to_undo=False)
+            self.current_mol = None
+            self.plotter.clear()
+            self.analysis_action.setEnabled(False)
+            
+            # 1. 座標がなければ2D座標を生成する
+            if mol.GetNumConformers() == 0: 
+                AllChem.Compute2DCoords(mol)
+            
+            # 2. 座標の有無にかかわらず、常に立体化学を割り当て、2D表示用にくさび結合を設定する
+            # これにより、3D座標を持つMOLファイルからでも正しく2Dの立体表現が生成される
+            AllChem.AssignStereochemistry(mol, cleanIt=True, force=True)
+            conf = mol.GetConformer()
+            AllChem.WedgeMolBonds(mol, conf)
+
+            conf = mol.GetConformer()
+
+            SCALE_FACTOR = 50.0
+            
+            view_center = self.view_2d.mapToScene(self.view_2d.viewport().rect().center())
+
+            positions = [conf.GetAtomPosition(i) for i in range(mol.GetNumAtoms())]
+            if positions:
+                mol_center_x = sum(p.x for p in positions) / len(positions)
+                mol_center_y = sum(p.y for p in positions) / len(positions)
+            else:
+                mol_center_x, mol_center_y = 0.0, 0.0
+
+            rdkit_idx_to_my_id = {}
+            for i in range(mol.GetNumAtoms()):
+                atom = mol.GetAtomWithIdx(i)
+                pos = conf.GetAtomPosition(i)
+                charge = atom.GetFormalCharge()
+                
+                relative_x = pos.x - mol_center_x
+                relative_y = pos.y - mol_center_y
+                
+                scene_x = (relative_x * SCALE_FACTOR) + view_center.x()
+                scene_y = (-relative_y * SCALE_FACTOR) + view_center.y()
+                
+                atom_id = self.scene.create_atom(atom.GetSymbol(), QPointF(scene_x, scene_y), charge=charge)
+                rdkit_idx_to_my_id[i] = atom_id
+                        
+            for bond in mol.GetBonds():
+                b_idx,e_idx=bond.GetBeginAtomIdx(),bond.GetEndAtomIdx()
+                b_type = bond.GetBondTypeAsDouble(); b_dir = bond.GetBondDir()
+                stereo = 0
+                # Check for single bond Wedge/Dash
+                if b_dir == Chem.BondDir.BEGINWEDGE:
+                    stereo = 1
+                elif b_dir == Chem.BondDir.BEGINDASH:
+                    stereo = 2
+                # ADDED: Check for double bond E/Z stereochemistry
+                if bond.GetBondType() == Chem.BondType.DOUBLE:
+                    if bond.GetStereo() == Chem.BondStereo.STEREOZ:
+                        stereo = 3 # Z
+                    elif bond.GetStereo() == Chem.BondStereo.STEREOE:
+                        stereo = 4 # E
+
+                a1_id, a2_id = rdkit_idx_to_my_id[b_idx], rdkit_idx_to_my_id[e_idx]
+                a1_item,a2_item=self.data.atoms[a1_id]['item'],self.data.atoms[a2_id]['item']
+
+                self.scene.create_bond(a1_item, a2_item, bond_order=int(b_type), bond_stereo=stereo)
+
+            self.statusBar().showMessage(f"Successfully loaded {file_path}")
+            self.reset_undo_stack()
+            # NEWファイル扱い: ファイルパスをクリアし未保存状態はFalse（変更なければ保存警告なし）
+            self.current_file_path = file_path
+            self.has_unsaved_changes = False
+            self.update_window_title()
+            QTimer.singleShot(0, self.fit_to_view)
+            
+        except FileNotFoundError:
+            self.statusBar().showMessage(f"File not found: {file_path}")
+        except ValueError as e:
+            self.statusBar().showMessage(f"Invalid MOL file format: {e}")
+        except Exception as e: 
+            self.statusBar().showMessage(f"Error loading file: {e}")
+            
+            traceback.print_exc()
+    
+
+
+    def load_xyz_file(self, file_path):
+        """XYZファイルを読み込んでRDKitのMolオブジェクトを作成する"""
+        
+        if not self.check_unsaved_changes():
+            return  # ユーザーがキャンセルした場合は何もしない
+
+        try:
+            # We will attempt one silent load with default charge=0 (no dialog).
+            # If RDKit emits chemistry warnings (for example "Explicit valence ..."),
+            # prompt the user once for an overall charge and retry. Only one retry is allowed.
+
+
+            # Helper: prompt for charge once when needed
+            # Returns a tuple: (charge_value_or_0, accepted:bool, skip_chemistry:bool)
+            def prompt_for_charge():
+                try:
+                    # Create a custom dialog so we can provide a "Skip chemistry" button
+                    dialog = QDialog(self)
+                    dialog.setWindowTitle("Import XYZ Charge")
+                    layout = QVBoxLayout(dialog)
+
+                    label = QLabel("Enter total molecular charge:")
+                    line_edit = QLineEdit(dialog)
+                    line_edit.setText("")
+
+                    # Standard OK/Cancel buttons
+                    btn_box = QDialogButtonBox(QDialogButtonBox.Ok | QDialogButtonBox.Cancel, parent=dialog)
+
+                    # Additional Skip chemistry button
+                    skip_btn = QPushButton("Skip chemistry", dialog)
+
+                    # Horizontal layout for buttons
+                    hl = QHBoxLayout()
+                    hl.addWidget(btn_box)
+                    hl.addWidget(skip_btn)
+
+                    layout.addWidget(label)
+                    layout.addWidget(line_edit)
+                    layout.addLayout(hl)
+
+                    result = {"accepted": False, "skip": False}
+
+                    def on_ok():
+                        result["accepted"] = True
+                        dialog.accept()
+
+                    def on_cancel():
+                        dialog.reject()
+
+                    def on_skip():
+                        # Mark skip and accept so caller can proceed with skip behavior
+                        result["skip"] = True
+                        dialog.accept()
+
+                    try:
+                        btn_box.button(QDialogButtonBox.Ok).clicked.connect(on_ok)
+                        btn_box.button(QDialogButtonBox.Cancel).clicked.connect(on_cancel)
+                    except Exception:
+                        # Fallback if button lookup fails
+                        btn_box.accepted.connect(on_ok)
+                        btn_box.rejected.connect(on_cancel)
+
+                    skip_btn.clicked.connect(on_skip)
+
+                    # Execute dialog modally
+                    if dialog.exec_() != QDialog.Accepted:
+                        return None, False, False
+
+                    if result["skip"]:
+                        # User chose to skip chemistry checks; return skip flag
+                        return 0, True, True
+
+                    if not result["accepted"]:
+                        return None, False, False
+
+                    charge_text = line_edit.text()
+                except Exception:
+                    # On any dialog creation error, fall back to simple input dialog
+                    try:
+                        charge_text, ok = QInputDialog.getText(self, "Import XYZ Charge", "Enter total molecular charge:", text="0")
+                    except Exception:
+                        return 0, True, False
+                    if not ok:
+                        return None, False, False
+                    try:
+                        return int(str(charge_text).strip()), True, False
+                    except Exception:
+                        try:
+                            return int(float(str(charge_text).strip())), True, False
+                        except Exception:
+                            return 0, True, False
+
+                if charge_text is None:
+                    return None, False, False
+
+                try:
+                    return int(str(charge_text).strip()), True, False
+                except Exception:
+                    try:
+                        return int(float(str(charge_text).strip())), True, False
+                    except Exception:
+                        return 0, True, False
+
+            with open(file_path, 'r', encoding='utf-8') as f:
+                lines = f.readlines()
+            
+            # 空行とコメント行を除去（但し、先頭2行は保持）
+            non_empty_lines = []
+            for i, line in enumerate(lines):
+                stripped = line.strip()
+                if i < 2:  # 最初の2行は原子数とコメント行なので保持
+                    non_empty_lines.append(stripped)
+                elif stripped and not stripped.startswith('#'):  # 空行とコメント行をスキップ
+                    non_empty_lines.append(stripped)
+            
+            if len(non_empty_lines) < 2:
+                raise ValueError("XYZ file format error: too few lines")
+            
+            # 原子数を読み取り
+            try:
+                num_atoms = int(non_empty_lines[0])
+            except ValueError:
+                raise ValueError("XYZ file format error: invalid atom count")
+            
+            if num_atoms <= 0:
+                raise ValueError("XYZ file format error: atom count must be positive")
+            
+            # コメント行（2行目）
+            comment = non_empty_lines[1] if len(non_empty_lines) > 1 else ""
+            
+            # 原子データを読み取り
+            atoms_data = []
+            data_lines = non_empty_lines[2:]
+            
+            if len(data_lines) < num_atoms:
+                raise ValueError(f"XYZ file format error: expected {num_atoms} atom lines, found {len(data_lines)}")
+            
+            for i, line in enumerate(data_lines[:num_atoms]):
+                parts = line.split()
+                if len(parts) < 4:
+                    raise ValueError(f"XYZ file format error: invalid atom data at line {i+3}")
+                
+                symbol = parts[0].strip()
+                
+                # 元素記号の妥当性をチェック
+                try:
+                    # RDKitで認識される元素かどうかをチェック
+                    test_atom = Chem.Atom(symbol)
+                except Exception:
+                    # 認識されない場合、最初の文字を大文字にして再試行
+                    symbol = symbol.capitalize()
+                    try:
+                        test_atom = Chem.Atom(symbol)
+                    except Exception:
+                        # If user requested to skip chemistry checks, coerce unknown symbols to C
+                        if self.settings.get('skip_chemistry_checks', False):
+                            symbol = 'C'
+                        else:
+                            raise ValueError(f"Unrecognized element symbol: {parts[0]} at line {i+3}")
+                
+                try:
+                    x, y, z = float(parts[1]), float(parts[2]), float(parts[3])
+                except ValueError:
+                    raise ValueError(f"XYZ file format error: invalid coordinates at line {i+3}")
+                
+                atoms_data.append((symbol, x, y, z))
+            
+            if len(atoms_data) == 0:
+                raise ValueError("XYZ file format error: no atoms found")
+            
+            # RDKitのMolオブジェクトを作成
+            mol = Chem.RWMol()
+            
+            # 原子を追加
+            for i, (symbol, x, y, z) in enumerate(atoms_data):
+                atom = Chem.Atom(symbol)
+                # XYZファイルでの原子のUniqueID（0ベースのインデックス）を保存
+                atom.SetIntProp("xyz_unique_id", i)
+                mol.AddAtom(atom)
+            
+            # 3D座標を設定
+            conf = Chem.Conformer(len(atoms_data))
+            for i, (symbol, x, y, z) in enumerate(atoms_data):
+                conf.SetAtomPosition(i, rdGeometry.Point3D(x, y, z))
+            mol.AddConformer(conf)
+            # If user requested to skip chemistry checks, bypass RDKit's
+            # DetermineBonds/sanitization flow entirely and use only the
+            # distance-based bond estimation. Treat the resulting molecule
+            # as "XYZ-derived" (disable 3D optimization) and return it.
+            try:
+                skip_checks = bool(self.settings.get('skip_chemistry_checks', False))
+            except Exception:
+                skip_checks = False
+
+            if skip_checks:
+                used_rd_determine = False
+                try:
+                    # Use the conservative distance-based heuristic to add bonds
+                    self.estimate_bonds_from_distances(mol)
+                except Exception:
+                    # Non-fatal: continue even if distance-based estimation fails
+                    pass
+
+                # Finalize and return a plain Mol object
+                try:
+                    candidate_mol = mol.GetMol()
+                except Exception:
+                    try:
+                        candidate_mol = Chem.Mol(mol)
+                    except Exception:
+                        candidate_mol = None
+
+                if candidate_mol is None:
+                    raise ValueError("Failed to create valid molecule object when skip_chemistry_checks=True")
+
+                # Attach a default charge property
+                try:
+                    candidate_mol.SetIntProp("_xyz_charge", 0)
+                except Exception:
+                    try:
+                        candidate_mol._xyz_charge = 0
+                    except Exception:
+                        pass
+
+                # Mark that this molecule was produced via the skip-chemistry path
+                try:
+                    candidate_mol.SetIntProp("_xyz_skip_checks", 1)
+                except Exception:
+                    try:
+                        candidate_mol._xyz_skip_checks = True
+                    except Exception:
+                        pass
+
+                # Set UI flags consistently: mark as XYZ-derived and disable optimize
+                try:
+                    self.current_mol = candidate_mol
+                    self.is_xyz_derived = True
+                    if hasattr(self, 'optimize_3d_button'):
+                        try:
+                            self.optimize_3d_button.setEnabled(False)
+                        except Exception:
+                            pass
+                except Exception:
+                    pass
+
+                # Store atom data for later analysis and return
+                candidate_mol._xyz_atom_data = atoms_data
+                return candidate_mol
+            # We'll attempt silently first with charge=0 and only prompt the user
+            # for a charge when the RDKit processing block fails (raises an
+            # exception). If the user provides a charge, retry; allow repeated
+            # prompts until the user cancels. This preserves the previous
+            # fallback behaviors (skip_chemistry_checks, distance-based bond
+            # estimation) and property attachments.
+            used_rd_determine = False
+            final_mol = None
+
+            # First, try silently with charge=0. If that raises an exception we
+            # will enter a loop prompting the user for a charge and retrying as
+            # long as the user provides values. If the user cancels, return None.
+            def _process_with_charge(charge_val):
+                """Inner helper: attempt to build/finalize molecule with given charge.
+
+                Returns the finalized RDKit Mol on success. May raise exceptions
+                which will be propagated to the caller.
+                """
+                nonlocal used_rd_determine
+                # Capture RDKit stderr while we run the processing to avoid
+                # spamming the console. We won't treat warnings specially here;
+                # only exceptions will trigger a prompt/retry. We also want to
+                # distinguish failures originating from DetermineBonds so the
+                # outer logic can decide whether to prompt the user repeatedly
+                # for different charge values.
+                buf = io.StringIO()
+                determine_failed = False
+                with contextlib.redirect_stderr(buf):
+                    # Try DetermineBonds if available
+                    try:
+                        from rdkit.Chem import rdDetermineBonds
+                        try:
+                            try:
+                                mol_candidate = Chem.RWMol(Chem.Mol(mol))
+                            except Exception:
+                                mol_candidate = Chem.RWMol(mol)
+
+                            # This call may raise. If it does, mark determine_failed
+                            # so the caller can prompt for a different charge.
+                            rdDetermineBonds.DetermineBonds(mol_candidate, charge=charge_val)
+                            mol_to_finalize = mol_candidate
+                            used_rd_determine = True
+                        except Exception:
+                            # DetermineBonds failed for this charge value. We
+                            # should allow the caller to prompt for another
+                            # charge (or cancel). Mark the flag and re-raise a
+                            # dedicated exception to be handled by the outer
+                            # loop.
+                            determine_failed = True
+                            used_rd_determine = False
+                            mol_to_finalize = mol
+                            # Raise a sentinel exception to indicate DetermineBonds failure
+                            raise RuntimeError("DetermineBondsFailed")
+                    except RuntimeError:
+                        # Propagate our sentinel so outer code can catch it.
+                        raise
+                    except Exception:
+                        # rdDetermineBonds not available or import failed; use
+                        # distance-based fallback below.
+                        used_rd_determine = False
+                        mol_to_finalize = mol
+
+                    if not used_rd_determine:
+                        # distance-based fallback
+                        self.estimate_bonds_from_distances(mol_to_finalize)
+
+                    # Finalize molecule
+                    try:
+                        candidate_mol = mol_to_finalize.GetMol()
+                    except Exception:
+                        candidate_mol = None
+
+                    if candidate_mol is None:
+                        # Try salvage path
+                        try:
+                            candidate_mol = mol.GetMol()
+                        except Exception:
+                            candidate_mol = None
+
+                    if candidate_mol is None:
+                        raise ValueError("Failed to create valid molecule object")
+
+                    # Attach charge property if possible
+                    try:
+                        try:
+                            candidate_mol.SetIntProp("_xyz_charge", int(charge_val))
+                        except Exception:
+                            try:
+                                candidate_mol._xyz_charge = int(charge_val)
+                            except Exception:
+                                pass
+                    except Exception:
+                        pass
+
+                    # Preserve whether the user requested skip_chemistry_checks
+                    try:
+                        if bool(self.settings.get('skip_chemistry_checks', False)):
+                            try:
+                                candidate_mol.SetIntProp("_xyz_skip_checks", 1)
+                            except Exception:
+                                try:
+                                    candidate_mol._xyz_skip_checks = True
+                                except Exception:
+                                    pass
+                    except Exception:
+                        pass
+
+                    # Run chemistry checks which may emit warnings to stderr
+                    self._apply_chem_check_and_set_flags(candidate_mol, source_desc='XYZ')
+
+                    # Accept the candidate
+                    return candidate_mol
+
+            # Decide whether to silently try charge=0 first, or prompt user first.
+            always_ask = bool(self.settings.get('always_ask_charge', False))
+
+            try:
+                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
+
+                            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)
+                                    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.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:
+                                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
+                        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:
+                            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
+                # back to salvaging or prompting depending on settings.
+                salvaged = None
+                try:
+                    salvaged = mol.GetMol()
+                except Exception:
+                    salvaged = None
+
+                try:
+                    skip_checks = bool(self.settings.get('skip_chemistry_checks', False))
+                except Exception:
+                    skip_checks = False
+
+                if skip_checks and salvaged is not None:
+                    final_mol = salvaged
+                else:
+                    # Repeatedly prompt until the user cancels or processing
+                    # succeeds.
+                    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:
+                                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
+                        except RuntimeError:
+                            # DetermineBonds failed for this charge -> let the
+                            # user try another
+                            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:
+                            try:
+                                self.statusBar().showMessage(f"Retry failed: {e_prompt}")
+                            except Exception:
+                                pass
+                            continue
+
+            # If we have a finalized molecule, apply the same UI flags and return
+            if final_mol is not None:
+                mol = final_mol
+                try:
+                    self.current_mol = mol
+
+                    self.is_xyz_derived = not used_rd_determine
+                    if hasattr(self, 'optimize_3d_button'):
+                        try:
+                            has_bonds = mol.GetNumBonds() > 0
+                            # Respect the XYZ-derived flag: if the molecule is XYZ-derived,
+                            # keep Optimize disabled regardless of bond detection.
+                            if getattr(self, 'is_xyz_derived', False):
+                                self.optimize_3d_button.setEnabled(False)
+                            else:
+                                self.optimize_3d_button.setEnabled(bool(has_bonds))
+                        except Exception:
+                            pass
+                except Exception:
+                    pass
+
+                # Store original atom data for analysis
+                mol._xyz_atom_data = atoms_data
+                return mol
+            
+            # 元のXYZ原子データを分子オブジェクトに保存（分析用）
+            mol._xyz_atom_data = atoms_data
+            
+            return mol
+            
+        except (OSError, IOError) as e:
+            raise ValueError(f"File I/O error: {e}")
+        except Exception as e:
+            if "XYZ file format error" in str(e) or "Unrecognized element" in str(e):
+                raise e
+            else:
+                raise ValueError(f"Error parsing XYZ file: {e}")
+
+
+
+    def estimate_bonds_from_distances(self, mol):
+        """原子間距離に基づいて結合を推定する"""
+        
+        # 一般的な共有結合半径（Ångström）- より正確な値
+        covalent_radii = {
+            'H': 0.31, 'He': 0.28, 'Li': 1.28, 'Be': 0.96, 'B': 0.84, 'C': 0.76,
+            'N': 0.75, 'O': 0.73, 'F': 0.71, 'Ne': 0.58, 'Na': 1.66, 'Mg': 1.41,
+            'Al': 1.21, 'Si': 1.11, 'P': 1.07, 'S': 1.05, 'Cl': 1.02, 'Ar': 1.06,
+            'K': 2.03, 'Ca': 1.76, 'Sc': 1.70, 'Ti': 1.60, 'V': 1.53, 'Cr': 1.39,
+            'Mn': 1.39, 'Fe': 1.32, 'Co': 1.26, 'Ni': 1.24, 'Cu': 1.32, 'Zn': 1.22,
+            'Ga': 1.22, 'Ge': 1.20, 'As': 1.19, 'Se': 1.20, 'Br': 1.14, 'Kr': 1.16,
+            'Rb': 2.20, 'Sr': 1.95, 'Y': 1.90, 'Zr': 1.75, 'Nb': 1.64, 'Mo': 1.54,
+            'Tc': 1.47, 'Ru': 1.46, 'Rh': 1.42, 'Pd': 1.39, 'Ag': 1.45, 'Cd': 1.44,
+            'In': 1.42, 'Sn': 1.39, 'Sb': 1.39, 'Te': 1.38, 'I': 1.33, 'Xe': 1.40
+        }
+        
+        conf = mol.GetConformer()
+        num_atoms = mol.GetNumAtoms()
+        
+        # 追加された結合をトラッキング
+        bonds_added = []
+        
+        for i in range(num_atoms):
+            for j in range(i + 1, num_atoms):
+                atom_i = mol.GetAtomWithIdx(i)
+                atom_j = mol.GetAtomWithIdx(j)
+                
+                # 原子間距離を計算
+                distance = rdMolTransforms.GetBondLength(conf, i, j)
+                
+                # 期待される結合距離を計算
+                symbol_i = atom_i.GetSymbol()
+                symbol_j = atom_j.GetSymbol()
+                
+                radius_i = covalent_radii.get(symbol_i, 1.0)  # デフォルト半径
+                radius_j = covalent_radii.get(symbol_j, 1.0)
+                
+                expected_bond_length = radius_i + radius_j
+                
+                # 結合タイプによる許容範囲を調整
+                # 水素結合は通常の共有結合より短い
+                if symbol_i == 'H' or symbol_j == 'H':
+                    tolerance_factor = 1.2  # 水素は結合が短くなりがち
+                else:
+                    tolerance_factor = 1.3  # 他の原子は少し余裕を持たせる
+                
+                max_bond_length = expected_bond_length * tolerance_factor
+                min_bond_length = expected_bond_length * 0.5  # 最小距離も設定
+                
+                # 距離が期待値の範囲内なら結合を追加
+                if min_bond_length <= distance <= max_bond_length:
+                    try:
+                        mol.AddBond(i, j, Chem.BondType.SINGLE)
+                        bonds_added.append((i, j, distance))
+                    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）
+        # Added bonds based on distance analysis
+        
+        return len(bonds_added)
+
+
+
+    def save_as_mol(self):
+        try:
+            mol_block = self.data.to_mol_block()
+            if not mol_block: 
+                self.statusBar().showMessage("Error: No 2D data to save.") 
+                return
+                
+            lines = mol_block.split('\n')
+            if len(lines) > 1 and 'RDKit' in lines[1]:
+                lines[1] = '  MoleditPy Ver. ' + VERSION + '  2D'
+            modified_mol_block = '\n'.join(lines)
+            
+            # default filename: based on current_file_path, append -2d for 2D mol
+            default_name = "untitled-2d"
+            try:
+                if self.current_file_path:
+                    base = os.path.basename(self.current_file_path)
+                    name = os.path.splitext(base)[0]
+                    default_name = f"{name}-2d"
+            except Exception:
+                default_name = "untitled-2d"
+
+            # prefer same directory as current file when available
+            default_path = default_name
+            try:
+                if self.current_file_path:
+                    default_path = os.path.join(os.path.dirname(self.current_file_path), default_name)
+            except Exception:
+                default_path = default_name
+
+            file_path, _ = QFileDialog.getSaveFileName(self, "Save 2D MOL File", default_path, "MOL Files (*.mol);;All Files (*)")
+            if not file_path:
+                return
+                
+            if not file_path.lower().endswith('.mol'): 
+                file_path += '.mol'
+                
+            with open(file_path, 'w', encoding='utf-8') as f: 
+                f.write(modified_mol_block)
+            self.statusBar().showMessage(f"2D data saved to {file_path}")
+            
+        except (OSError, IOError) as e:
+            self.statusBar().showMessage(f"File I/O error: {e}")
+        except UnicodeEncodeError as e:
+            self.statusBar().showMessage(f"Text encoding error: {e}")
+        except Exception as e: 
+            self.statusBar().showMessage(f"Error saving file: {e}")
+            
+            traceback.print_exc()
+            
+
+
+    def save_as_xyz(self):
+        if not self.current_mol: self.statusBar().showMessage("Error: Please generate a 3D structure first."); return
+        # default filename based on current file
+        default_name = "untitled"
+        try:
+            if self.current_file_path:
+                base = os.path.basename(self.current_file_path)
+                name = os.path.splitext(base)[0]
+                default_name = f"{name}"
+        except Exception:
+            default_name = "untitled"
+
+        # prefer same directory as current file when available
+        default_path = default_name
+        try:
+            if self.current_file_path:
+                default_path = os.path.join(os.path.dirname(self.current_file_path), default_name)
+        except Exception:
+            default_path = default_name
+
+        file_path,_=QFileDialog.getSaveFileName(self,"Save 3D XYZ File",default_path,"XYZ Files (*.xyz);;All Files (*)")
+        if file_path:
+            if not file_path.lower().endswith('.xyz'): file_path += '.xyz'
+            try:
+                conf=self.current_mol.GetConformer(); num_atoms=self.current_mol.GetNumAtoms()
+                xyz_lines=[str(num_atoms)]
+                # 電荷と多重度を計算
+                try:
+                    charge = Chem.GetFormalCharge(self.current_mol)
+                except Exception:
+                    charge = 0 # 取得失敗時は0
+                
+                try:
+                    # 全原子のラジカル電子の合計を取得
+                    num_radicals = Descriptors.NumRadicalElectrons(self.current_mol)
+                    # スピン多重度を計算 (M = N + 1, N=ラジカル電子数)
+                    multiplicity = num_radicals + 1
+                except Exception:
+                    multiplicity = 1 # 取得失敗時は 1 (singlet)
+
+                smiles=Chem.MolToSmiles(Chem.RemoveHs(self.current_mol))
+                xyz_lines.append(f"chrg = {charge}  mult = {multiplicity} | Generated by MoleditPy Ver. {VERSION}")
+                for i in range(num_atoms):
+                    pos=conf.GetAtomPosition(i); symbol=self.current_mol.GetAtomWithIdx(i).GetSymbol()
+                    xyz_lines.append(f"{symbol} {pos.x:.6f} {pos.y:.6f} {pos.z:.6f}")
+                with open(file_path,'w') as f: f.write("\n".join(xyz_lines) + "\n")
+                self.statusBar().showMessage(f"Successfully saved to {file_path}")
+            except Exception as e: self.statusBar().showMessage(f"Error saving file: {e}")
+
+
+    def fix_mol_counts_line(self, line: str) -> str:
+        """
+        Check and fix the CTAB counts line in a MOL file.
+        If the line already contains 'V3000' or 'V2000' it is left unchanged.
+        Otherwise the line is treated as V2000 and the proper 39-character
+        format (33 chars of counts + ' V2000') is returned.
+        """
+        # If already V3000 or V2000, leave as-is
+        if 'V3000' in line or 'V2000' in line:
+            return line
+
+        # Prepare prefix (first 33 characters for the 11 * I3 fields)
+        prefix = line.rstrip().ljust(33)[0:33]
+        version_str = ' V2000'
+        return prefix + version_str
+
+    def fix_mol_block(self, mol_block: str) -> str:
+        """
+        Given an entire MOL block as a string, ensure the 4th line (CTAB counts
+        line) is valid. If the file has fewer than 4 lines, return as-is.
+        """
+        lines = mol_block.splitlines()
+        if len(lines) < 4:
+            # Not a valid MOL block — return unchanged
+            return mol_block
+
+        counts_line = lines[3]
+        fixed_counts_line = self.fix_mol_counts_line(counts_line)
+        lines[3] = fixed_counts_line
+        return "\n".join(lines)
+