MoleditPy-linux 2.4.1__py3-none-any.whl

moleditpy_linux/modules/main_window_project_io.py

@@ -0,0 +1,434 @@
+#!/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_project_io.py
+MainWindow (main_window.py) から分離されたモジュール
+機能クラス: MainWindowProjectIo
+"""
+
+
+import pickle
+import os
+import json 
+import traceback
+
+
+# RDKit imports (explicit to satisfy flake8 and used features)
+try:
+    pass
+except Exception:
+    pass
+
+# PyQt6 Modules
+from PyQt6.QtWidgets import (
+    QFileDialog, QMessageBox
+)
+
+
+
+from PyQt6.QtCore import (
+    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
+        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`)
+    pass
+except Exception:
+    # Fallback to absolute imports for script-style execution
+    pass
+
+
+# --- クラス定義 ---
+class MainWindowProjectIo(object):
+    """ main_window.py から分離された機能クラス """
+
+
+    def save_project(self):
+        """上書き保存（Ctrl+S）- デフォルトでPMEPRJ形式"""
+        if not self.data.atoms and not self.current_mol: 
+            self.statusBar().showMessage("Error: Nothing to save.")
+            return
+        # 非ネイティブ形式（.mol, .sdf, .xyz など）は上書き保存せず、必ず「名前を付けて保存」にする
+        native_exts = ['.pmeprj', '.pmeraw']
+        if self.current_file_path and any(self.current_file_path.lower().endswith(ext) for ext in native_exts):
+            # 既存のPMEPRJ/PMERAWファイルの場合は上書き保存
+            try:
+                if self.current_file_path.lower().endswith('.pmeraw'):
+                    # 既存のPMERAWファイルの場合はPMERAW形式で保存
+                    save_data = self.get_current_state()
+                    with open(self.current_file_path, 'wb') as f: 
+                        pickle.dump(save_data, f)
+                else:
+                    # PMEPRJ形式で保存
+                    json_data = self.create_json_data()
+                    with open(self.current_file_path, 'w', encoding='utf-8') as f: 
+                        json.dump(json_data, f, indent=2, ensure_ascii=False)
+                
+                # 保存成功時に状態をリセット
+                self.has_unsaved_changes = False
+                self.update_window_title()
+                
+                self.statusBar().showMessage(f"Project saved to {self.current_file_path}")
+                
+            except (OSError, IOError) as e:
+                self.statusBar().showMessage(f"File I/O error: {e}")
+            except (pickle.PicklingError, TypeError, ValueError) as e:
+                self.statusBar().showMessage(f"Data serialization error: {e}")
+            except Exception as e: 
+                self.statusBar().showMessage(f"Error saving project file: {e}")
+                
+                traceback.print_exc()
+        else:
+            # MOL/SDF/XYZなどは上書き保存せず、必ず「名前を付けて保存」にする
+            self.save_project_as()
+
+
+
+    def save_project_as(self):
+        """名前を付けて保存（Ctrl+Shift+S）- デフォルトでPMEPRJ形式"""
+        if not self.data.atoms and not self.current_mol: 
+            self.statusBar().showMessage("Error: Nothing to save.")
+            return
+            
+        try:
+            # Determine a sensible default filename based on current file (strip extension)
+            default_name = "untitled"
+            try:
+                if self.current_file_path:
+                    base = os.path.basename(self.current_file_path)
+                    default_name = os.path.splitext(base)[0]
+            except Exception:
+                default_name = "untitled"
+
+            # Prefer the directory of the currently opened file as default
+            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 Project As", default_path, 
+                "PME Project Files (*.pmeprj);;All Files (*)", 
+            )
+            if not file_path:
+                return
+                
+            if not file_path.lower().endswith('.pmeprj'): 
+                file_path += '.pmeprj'
+            
+            # JSONデータを保存
+            json_data = self.create_json_data()
+            with open(file_path, 'w', encoding='utf-8') as f: 
+                json.dump(json_data, f, indent=2, ensure_ascii=False)
+            
+            # 保存成功時に状態をリセット
+            self.has_unsaved_changes = False
+            # Replace current file with the newly saved file so subsequent saves go to this path
+            self.current_file_path = file_path
+            self.update_window_title()
+            # Mark this state as the last saved state for undo tracking
+            try:
+                self._saved_state = copy.deepcopy(self.get_current_state())
+            except Exception:
+                pass
+            
+            self.statusBar().showMessage(f"Project saved to {file_path}")
+            
+        except (OSError, IOError) as e:
+            self.statusBar().showMessage(f"File I/O error: {e}")
+        except pickle.PicklingError as e:
+            self.statusBar().showMessage(f"Data serialization error: {e}")
+        except Exception as e: 
+            self.statusBar().showMessage(f"Error saving project file: {e}")
+            
+            traceback.print_exc()
+
+
+
+    def save_raw_data(self):
+        if not self.data.atoms and not self.current_mol: 
+            self.statusBar().showMessage("Error: Nothing to save.")
+            return
+            
+        try:
+            save_data = self.get_current_state()
+            # default filename based on current file
+            default_name = "untitled"
+            try:
+                if self.current_file_path:
+                    base = os.path.basename(self.current_file_path)
+                    default_name = os.path.splitext(base)[0]
+            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 Project File", default_path, "Project Files (*.pmeraw);;All Files (*)")
+            if not file_path:
+                return
+                
+            if not file_path.lower().endswith('.pmeraw'): 
+                file_path += '.pmeraw'
+                
+            with open(file_path, 'wb') as f: 
+                pickle.dump(save_data, f)
+            
+            # 保存成功時に状態をリセット
+            self.has_unsaved_changes = False
+            # Update current file to the newly saved raw file
+            self.current_file_path = file_path
+            self.update_window_title()
+            try:
+                self._saved_state = copy.deepcopy(self.get_current_state())
+            except Exception:
+                pass
+            
+            self.statusBar().showMessage(f"Project saved to {file_path}")
+            
+        except (OSError, IOError) as e:
+            self.statusBar().showMessage(f"File I/O error: {e}")
+        except pickle.PicklingError as e:
+            self.statusBar().showMessage(f"Data serialization error: {e}")
+        except Exception as e: 
+            self.statusBar().showMessage(f"Error saving project file: {e}")
+            
+            traceback.print_exc()
+
+
+
+
+    def load_raw_data(self, file_path=None):
+        if not file_path:
+            file_path, _ = QFileDialog.getOpenFileName(self, "Open Project File", "", "Project Files (*.pmeraw);;All Files (*)")
+            if not file_path: 
+                return
+        
+        try:
+            with open(file_path, 'rb') as f: 
+                loaded_data = pickle.load(f)
+            self.restore_ui_for_editing()
+            self.set_state_from_data(loaded_data)
+            
+            # ファイル読み込み時に状態をリセット
+            self.reset_undo_stack()
+            self.has_unsaved_changes = False
+            self.current_file_path = file_path
+            self.update_window_title()
+            try:
+                self._saved_state= copy.deepcopy(self.et_current_state())
+            except Exception:
+                pass
+         
+            self.statusBar.showMessage(f"Project loaded from {file_path}")
+            
+            QTimer.singleShot(0, self.fit_to_view)
+            
+        except FileNotFoundError:
+            self.statusBar().showMessage(f"File not found: {file_path}")
+        except (OSError, IOError) as e:
+            self.statusBar().showMessage(f"File I/O error: {e}")
+        except pickle.UnpicklingError as e:
+            self.statusBar().showMessage(f"Invalid project file format: {e}")
+        except Exception as e: 
+            self.statusBar().showMessage(f"Error loading project file: {e}")
+            
+            traceback.print_exc()
+
+
+
+    def save_as_json(self):
+        """PMEJSONファイル形式で保存 (3D MOL情報含む)"""
+        if not self.data.atoms and not self.current_mol: 
+            self.statusBar().showMessage("Error: Nothing to save.")
+            return
+            
+        try:
+            # default filename based on current file
+            default_name = "untitled"
+            try:
+                if self.current_file_path:
+                    base = os.path.basename(self.current_file_path)
+                    default_name = os.path.splitext(base)[0]
+            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 as PME Project", default_path, 
+                "PME Project Files (*.pmeprj);;All Files (*)", 
+            )
+            if not file_path:
+                return
+                
+            if not file_path.lower().endswith('.pmeprj'): 
+                file_path += '.pmeprj'
+            
+            # JSONデータを作成
+            json_data = self.create_json_data()
+            
+            # JSON形式で保存（美しい整形付き）
+            with open(file_path, 'w', encoding='utf-8') as f: 
+                json.dump(json_data, f, indent=2, ensure_ascii=False)
+            
+            # 保存成功時に状態をリセット
+            self.has_unsaved_changes = False
+            # Replace current file with the newly saved PME Project
+            self.current_file_path = file_path
+            self.update_window_title()
+            
+            self.statusBar().showMessage(f"PME Project saved to {file_path}")
+            
+        except (OSError, IOError) as e:
+            self.statusBar().showMessage(f"File I/O error: {e}")
+        except (TypeError, ValueError) as e:
+            self.statusBar().showMessage(f"JSON serialization error: {e}")
+        except Exception as e: 
+            self.statusBar().showMessage(f"Error saving PME Project file: {e}")
+            
+            traceback.print_exc()
+
+
+
+    def load_json_data(self, file_path=None):
+        """PME Projectファイル形式を読み込み"""
+        if not file_path:
+            file_path, _ = QFileDialog.getOpenFileName(
+                self, "Open PME Project File", "", 
+                "PME Project Files (*.pmeprj);;All Files (*)", 
+            )
+            if not file_path: 
+                return
+        
+        try:
+            with open(file_path, 'r', encoding='utf-8') as f: 
+                json_data = json.load(f)
+            
+            # フォーマット検証
+            if json_data.get("format") != "PME Project":
+                QMessageBox.warning(
+                    self, "Invalid Format", 
+                    "This file is not a valid PME Project format."
+                )
+                return
+            
+            # バージョン確認
+            file_version = json_data.get("version", "1.0")
+            if file_version != "1.0":
+                QMessageBox.information(
+                    self, "Version Notice", 
+                    f"This file was created with PME Project version {file_version}.\n"
+                    "Loading will be attempted but some features may not work correctly."
+                )
+            
+            self.restore_ui_for_editing()
+            self.load_from_json_data(json_data)
+            # ファイル読み込み時に状態をリセット
+            self.reset_undo_stack()
+            self.has_unsaved_changes = False
+            self.current_file_path = file_path
+            self.update_window_title()
+            
+            self.statusBar().showMessage(f"PME Project loaded from {file_path}")
+            
+            QTimer.singleShot(0, self.fit_to_view)
+            
+        except FileNotFoundError:
+            self.statusBar().showMessage(f"File not found: {file_path}")
+        except json.JSONDecodeError as e:
+            self.statusBar().showMessage(f"Invalid JSON format: {e}")
+        except (OSError, IOError) as e:
+            self.statusBar().showMessage(f"File I/O error: {e}")
+        except Exception as e: 
+            self.statusBar().showMessage(f"Error loading PME Project file: {e}")
+            
+            traceback.print_exc()
+
+
+
+    def open_project_file(self, file_path=None):
+        """プロジェクトファイルを開く（.pmeprjと.pmerawの両方に対応）"""
+        # Check for unsaved changes before opening a new project file.
+        # Previously this function opened .pmeprj/.pmeraw without prompting the
+        # user to save current unsaved work. Ensure we honor the global
+        # unsaved-change check like other loaders (SMILES/MOL/etc.).
+        if not self.check_unsaved_changes():
+            return
+        if not file_path:
+            file_path, _ = QFileDialog.getOpenFileName(
+                self, "Open Project File", "", 
+                "PME Project Files (*.pmeprj);;PME Raw Files (*.pmeraw);;All Files (*)", 
+            )
+            if not file_path: 
+                return
+        
+        # 拡張子に応じて適切な読み込み関数を呼び出し
+        if file_path.lower().endswith('.pmeprj'):
+            self.load_json_data(file_path)
+        elif file_path.lower().endswith('.pmeraw'):
+            self.load_raw_data(file_path)
+        else:
+            # 拡張子不明の場合はJSONとして試行
+            try:
+                self.load_json_data(file_path)
+            except Exception:
+                try:
+                    self.load_raw_data(file_path)
+                except Exception:
+                    self.statusBar().showMessage("Error: Unable to determine file format.")
+