MoleditPy-linux 2.4.1__py3-none-any.whl

moleditpy_linux/modules/main_window_dialog_manager.py

@@ -0,0 +1,460 @@
+#!/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_dialog_manager.py
+MainWindow (main_window.py) から分離されたモジュール
+機能クラス: MainWindowDialogManager
+"""
+
+
+import os
+import json 
+
+
+# RDKit imports (explicit to satisfy flake8 and used features)
+try:
+    pass
+except Exception:
+    pass
+
+# PyQt6 Modules
+from PyQt6.QtWidgets import (
+    QMessageBox, 
+    QInputDialog
+)
+
+
+
+from PyQt6.QtCore import (
+    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 .user_template_dialog import UserTemplateDialog
+    from .about_dialog import AboutDialog
+    from .translation_dialog import TranslationDialog
+    from .mirror_dialog import MirrorDialog
+    from .move_group_dialog import MoveGroupDialog
+    from .align_plane_dialog import AlignPlaneDialog
+    from .planarize_dialog import PlanarizeDialog
+    from .alignment_dialog import AlignmentDialog
+    from .periodic_table_dialog import PeriodicTableDialog
+    from .analysis_window import AnalysisWindow
+    from .bond_length_dialog import BondLengthDialog
+    from .angle_dialog import AngleDialog
+    from .dihedral_dialog import DihedralDialog
+    from .constrained_optimization_dialog import ConstrainedOptimizationDialog
+except Exception:
+    # Fallback to absolute imports for script-style execution
+    from modules.constants import VERSION
+    from modules.user_template_dialog import UserTemplateDialog
+    from modules.about_dialog import AboutDialog
+    from modules.translation_dialog import TranslationDialog
+    from modules.mirror_dialog import MirrorDialog
+    from modules.move_group_dialog import MoveGroupDialog
+    from modules.align_plane_dialog import AlignPlaneDialog
+    from modules.planarize_dialog import PlanarizeDialog
+    from modules.alignment_dialog import AlignmentDialog
+    from modules.periodic_table_dialog import PeriodicTableDialog
+    from modules.analysis_window import AnalysisWindow
+    from modules.bond_length_dialog import BondLengthDialog
+    from modules.angle_dialog import AngleDialog
+    from modules.dihedral_dialog import DihedralDialog
+    from modules.constrained_optimization_dialog import ConstrainedOptimizationDialog
+
+
+# --- クラス定義 ---
+class MainWindowDialogManager(object):
+    """ main_window.py から分離された機能クラス """
+
+
+    def show_about_dialog(self):
+        """Show the custom About dialog with Easter egg functionality"""
+        dialog = AboutDialog(self, self)
+        dialog.exec()
+
+
+
+    def open_periodic_table_dialog(self):
+        dialog=PeriodicTableDialog(self); dialog.element_selected.connect(self.set_atom_from_periodic_table)
+        checked_action=self.tool_group.checkedAction()
+        if checked_action: self.tool_group.setExclusive(False); checked_action.setChecked(False); self.tool_group.setExclusive(True)
+        dialog.exec()
+
+
+
+    def open_analysis_window(self):
+        if self.current_mol:
+            dialog = AnalysisWindow(self.current_mol, self, is_xyz_derived=self.is_xyz_derived)
+            dialog.exec()
+        else:
+            self.statusBar().showMessage("Please generate a 3D structure first to show analysis.")
+
+
+
+    def open_template_dialog(self):
+        """テンプレートダイアログを開く"""
+        dialog = UserTemplateDialog(self, self)
+        dialog.exec()
+    
+
+
+    def open_template_dialog_and_activate(self):
+        """テンプレートダイアログを開き、テンプレートがメイン画面で使用できるようにする"""
+        # 既存のダイアログがあるかチェック
+        if hasattr(self, '_template_dialog') and self._template_dialog and not self._template_dialog.isHidden():
+            # 既存のダイアログを前面に表示
+            self._template_dialog.raise_()
+            self._template_dialog.activateWindow()
+            return
+        
+        # 新しいダイアログを作成
+        self._template_dialog = UserTemplateDialog(self, self)
+        self._template_dialog.show()  # モードレスで表示
+        
+        # ダイアログが閉じられた後、テンプレートが選択されていればアクティブ化
+        def on_dialog_finished():
+            if hasattr(self._template_dialog, 'selected_template') and self._template_dialog.selected_template:
+                template_name = self._template_dialog.selected_template.get('name', 'user_template')
+                mode_name = f"template_user_{template_name}"
+                
+                # Store template data for the scene to use
+                self.scene.user_template_data = self._template_dialog.selected_template
+                self.set_mode(mode_name)
+                
+                # Update status
+                self.statusBar().showMessage(f"Template mode: {template_name}")
+        
+        self._template_dialog.finished.connect(on_dialog_finished)
+    
+
+
+    def save_2d_as_template(self):
+        """現在の2D構造をテンプレートとして保存"""
+        if not self.data.atoms:
+            QMessageBox.warning(self, "Warning", "No structure to save as template.")
+            return
+        
+        # Get template name
+        name, ok = QInputDialog.getText(self, "Save Template", "Enter template name:")
+        if not ok or not name.strip():
+            return
+        
+        name = name.strip()
+        
+        try:
+            # Template directory
+            template_dir = os.path.join(self.settings_dir, 'user-templates')
+            if not os.path.exists(template_dir):
+                os.makedirs(template_dir)
+            
+            # Convert current structure to template format
+            atoms_data = []
+            bonds_data = []
+            
+            # Convert atoms
+            for atom_id, atom_info in self.data.atoms.items():
+                pos = atom_info['pos']
+                atoms_data.append({
+                    'id': atom_id,
+                    'symbol': atom_info['symbol'],
+                    'x': pos.x(),
+                    'y': pos.y(),
+                    'charge': atom_info.get('charge', 0),
+                    'radical': atom_info.get('radical', 0)
+                })
+            
+            # Convert bonds
+            for (atom1_id, atom2_id), bond_info in self.data.bonds.items():
+                bonds_data.append({
+                    'atom1': atom1_id,
+                    'atom2': atom2_id,
+                    'order': bond_info['order'],
+                    'stereo': bond_info.get('stereo', 0)
+                })
+            
+            # Create template data
+            template_data = {
+                'format': "PME Template",
+                'version': "1.0",
+                'application': "MoleditPy",
+                'application_version': VERSION,
+                'name': name,
+                'created': str(QDateTime.currentDateTime().toString()),
+                'atoms': atoms_data,
+                'bonds': bonds_data
+            }
+            
+            # Save to file
+            filename = f"{name.replace(' ', '_')}.pmetmplt"
+            filepath = os.path.join(template_dir, filename)
+            
+            if os.path.exists(filepath):
+                reply = QMessageBox.question(
+                    self, "Overwrite Template",
+                    f"Template '{name}' already exists. Overwrite?",
+                    QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No
+                )
+                if reply != QMessageBox.StandardButton.Yes:
+                    return
+            
+            with open(filepath, 'w', encoding='utf-8') as f:
+                json.dump(template_data, f, indent=2, ensure_ascii=False)
+            
+            # Mark as saved (no unsaved changes for this operation)
+            self.has_unsaved_changes = False
+            self.update_window_title()
+            
+            QMessageBox.information(self, "Success", f"Template '{name}' saved successfully.")
+            
+        except Exception as e:
+            QMessageBox.critical(self, "Error", f"Failed to save template: {str(e)}")
+
+
+
+    def open_translation_dialog(self):
+        """平行移動ダイアログを開く"""
+        # 測定モードを無効化
+        if self.measurement_mode:
+            self.measurement_action.setChecked(False)
+            self.toggle_measurement_mode(False)
+        
+        dialog = TranslationDialog(self.current_mol, self, parent=self)
+        self.active_3d_dialogs.append(dialog)  # 参照を保持
+        dialog.show()  # execではなくshowを使用してモードレス表示
+        dialog.accepted.connect(lambda: self.statusBar().showMessage("Translation applied."))
+        dialog.accepted.connect(self.push_undo_state)
+        dialog.finished.connect(lambda: self.remove_dialog_from_list(dialog))  # ダイアログが閉じられた時にリストから削除
+    
+
+
+    def open_move_group_dialog(self):
+        """Move Groupダイアログを開く"""
+        # 測定モードを無効化
+        if self.measurement_mode:
+            self.measurement_action.setChecked(False)
+            self.toggle_measurement_mode(False)
+        
+        dialog = MoveGroupDialog(self.current_mol, self, parent=self)
+        self.active_3d_dialogs.append(dialog)
+        dialog.show()
+        dialog.accepted.connect(lambda: self.statusBar().showMessage("Group transformation applied."))
+        dialog.accepted.connect(self.push_undo_state)
+        dialog.finished.connect(lambda: self.remove_dialog_from_list(dialog))
+    
+
+
+    def open_align_plane_dialog(self, plane):
+        """alignダイアログを開く"""
+        # 事前選択された原子を取得（測定モード無効化前に）
+        preselected_atoms = []
+        if hasattr(self, 'selected_atoms_3d') and self.selected_atoms_3d:
+            preselected_atoms = list(self.selected_atoms_3d)
+        elif hasattr(self, 'selected_atoms_for_measurement') and self.selected_atoms_for_measurement:
+            preselected_atoms = list(self.selected_atoms_for_measurement)
+        
+        # 測定モードを無効化
+        if self.measurement_mode:
+            self.measurement_action.setChecked(False)
+            self.toggle_measurement_mode(False)
+        
+        dialog = AlignPlaneDialog(self.current_mol, self, plane, preselected_atoms, parent=self)
+        self.active_3d_dialogs.append(dialog)  # 参照を保持
+        dialog.show()  # execではなくshowを使用してモードレス表示
+        dialog.accepted.connect(lambda: self.statusBar().showMessage(f"Atoms alignd to {plane.upper()} plane."))
+        dialog.accepted.connect(self.push_undo_state)
+        dialog.finished.connect(lambda: self.remove_dialog_from_list(dialog))  # ダイアログが閉じられた時にリストから削除
+        
+
+
+    def open_planarize_dialog(self, plane=None):
+        """選択原子群を最適平面へ投影するダイアログを開く"""
+        # 事前選択された原子を取得（測定モード無効化前に）
+        preselected_atoms = []
+        if hasattr(self, 'selected_atoms_3d') and self.selected_atoms_3d:
+            preselected_atoms = list(self.selected_atoms_3d)
+        elif hasattr(self, 'selected_atoms_for_measurement') and self.selected_atoms_for_measurement:
+            preselected_atoms = list(self.selected_atoms_for_measurement)
+
+        # 測定モードを無効化
+        if self.measurement_mode:
+            self.measurement_action.setChecked(False)
+            self.toggle_measurement_mode(False)
+
+        dialog = PlanarizeDialog(self.current_mol, self, preselected_atoms, parent=self)
+        self.active_3d_dialogs.append(dialog)
+        dialog.show()
+        dialog.accepted.connect(lambda: self.statusBar().showMessage("Selection planarized to best-fit plane."))
+        dialog.accepted.connect(self.push_undo_state)
+        dialog.finished.connect(lambda: self.remove_dialog_from_list(dialog))
+    
+
+
+    def open_alignment_dialog(self, axis):
+        """アライメントダイアログを開く"""
+        # 事前選択された原子を取得（測定モード無効化前に）
+        preselected_atoms = []
+        if hasattr(self, 'selected_atoms_3d') and self.selected_atoms_3d:
+            preselected_atoms = list(self.selected_atoms_3d)
+        elif hasattr(self, 'selected_atoms_for_measurement') and self.selected_atoms_for_measurement:
+            preselected_atoms = list(self.selected_atoms_for_measurement)
+        
+        # 測定モードを無効化
+        if self.measurement_mode:
+            self.measurement_action.setChecked(False)
+            self.toggle_measurement_mode(False)
+        
+        dialog = AlignmentDialog(self.current_mol, self, axis, preselected_atoms, parent=self)
+        self.active_3d_dialogs.append(dialog)  # 参照を保持
+        dialog.show()  # execではなくshowを使用してモードレス表示
+        dialog.accepted.connect(lambda: self.statusBar().showMessage(f"Atoms aligned to {axis.upper()}-axis."))
+        dialog.accepted.connect(self.push_undo_state)
+        dialog.finished.connect(lambda: self.remove_dialog_from_list(dialog))  # ダイアログが閉じられた時にリストから削除
+    
+
+
+    def open_bond_length_dialog(self):
+        """結合長変換ダイアログを開く"""
+        # 事前選択された原子を取得（測定モード無効化前に）
+        preselected_atoms = []
+        if hasattr(self, 'selected_atoms_3d') and self.selected_atoms_3d:
+            preselected_atoms = list(self.selected_atoms_3d)
+        elif hasattr(self, 'selected_atoms_for_measurement') and self.selected_atoms_for_measurement:
+            preselected_atoms = list(self.selected_atoms_for_measurement)
+        
+        # 測定モードを無効化
+        if self.measurement_mode:
+            self.measurement_action.setChecked(False)
+            self.toggle_measurement_mode(False)
+        
+        dialog = BondLengthDialog(self.current_mol, self, preselected_atoms, parent=self)
+        self.active_3d_dialogs.append(dialog)  # 参照を保持
+        dialog.show()  # execではなくshowを使用してモードレス表示
+        dialog.accepted.connect(lambda: self.statusBar().showMessage("Bond length adjusted."))
+        dialog.accepted.connect(self.push_undo_state)
+        dialog.finished.connect(lambda: self.remove_dialog_from_list(dialog))  # ダイアログが閉じられた時にリストから削除
+    
+
+
+    def open_angle_dialog(self):
+        """角度変換ダイアログを開く"""
+        # 事前選択された原子を取得（測定モード無効化前に）
+        preselected_atoms = []
+        if hasattr(self, 'selected_atoms_3d') and self.selected_atoms_3d:
+            preselected_atoms = list(self.selected_atoms_3d)
+        elif hasattr(self, 'selected_atoms_for_measurement') and self.selected_atoms_for_measurement:
+            preselected_atoms = list(self.selected_atoms_for_measurement)
+        
+        # 測定モードを無効化
+        if self.measurement_mode:
+            self.measurement_action.setChecked(False)
+            self.toggle_measurement_mode(False)
+        
+        dialog = AngleDialog(self.current_mol, self, preselected_atoms, parent=self)
+        self.active_3d_dialogs.append(dialog)  # 参照を保持
+        dialog.show()  # execではなくshowを使用してモードレス表示
+        dialog.accepted.connect(lambda: self.statusBar().showMessage("Angle adjusted."))
+        dialog.accepted.connect(self.push_undo_state)
+        dialog.finished.connect(lambda: self.remove_dialog_from_list(dialog))  # ダイアログが閉じられた時にリストから削除
+    
+
+
+    def open_dihedral_dialog(self):
+        """二面角変換ダイアログを開く"""
+        # 事前選択された原子を取得（測定モード無効化前に）
+        preselected_atoms = []
+        if hasattr(self, 'selected_atoms_3d') and self.selected_atoms_3d:
+            preselected_atoms = list(self.selected_atoms_3d)
+        elif hasattr(self, 'selected_atoms_for_measurement') and self.selected_atoms_for_measurement:
+            preselected_atoms = list(self.selected_atoms_for_measurement)
+        
+        # 測定モードを無効化
+        if self.measurement_mode:
+            self.measurement_action.setChecked(False)
+            self.toggle_measurement_mode(False)
+        
+        dialog = DihedralDialog(self.current_mol, self, preselected_atoms, parent=self)
+        self.active_3d_dialogs.append(dialog)  # 参照を保持
+        dialog.show()  # execではなくshowを使用してモードレス表示
+        dialog.accepted.connect(lambda: self.statusBar().showMessage("Dihedral angle adjusted."))
+        dialog.accepted.connect(self.push_undo_state)
+        dialog.finished.connect(lambda: self.remove_dialog_from_list(dialog))  # ダイアログが閉じられた時にリストから削除
+    
+
+
+    def open_mirror_dialog(self):
+        """ミラー機能ダイアログを開く"""
+        if not self.current_mol:
+            self.statusBar().showMessage("No 3D molecule loaded.")
+            return
+        
+        # 測定モードを無効化
+        if self.measurement_mode:
+            self.measurement_action.setChecked(False)
+            self.toggle_measurement_mode(False)
+        
+        dialog = MirrorDialog(self.current_mol, self)
+        dialog.exec()  # モーダルダイアログとして表示
+
+
+
+    def open_constrained_optimization_dialog(self):
+        """制約付き最適化ダイアログを開く"""
+        if not self.current_mol:
+            self.statusBar().showMessage("No 3D molecule loaded.")
+            return
+        
+        # 測定モードを無効化
+        if self.measurement_mode:
+            self.measurement_action.setChecked(False)
+            self.toggle_measurement_mode(False)
+        
+        dialog = ConstrainedOptimizationDialog(self.current_mol, self, parent=self)
+        self.active_3d_dialogs.append(dialog)  # 参照を保持
+        dialog.show()  # モードレス表示
+        dialog.finished.connect(lambda: self.remove_dialog_from_list(dialog))
+