MoleditPy-linux 2.4.1__py3-none-any.whl

moleditpy_linux/modules/main_window_view_loaders.py

@@ -0,0 +1,355 @@
+#!/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_view_loaders.py
+MainWindow (main_window.py) から分離されたモジュール
+機能クラス: MainWindowViewLoaders
+"""
+
+
+import os
+import traceback
+
+
+# RDKit imports (explicit to satisfy flake8 and used features)
+from rdkit import Chem
+from rdkit.Chem import AllChem
+try:
+    pass
+except Exception:
+    pass
+
+# PyQt6 Modules
+from PyQt6.QtWidgets import (
+    QFileDialog
+)
+
+
+
+
+
+# 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
+except Exception:
+    # Fallback to absolute imports for script-style execution
+    from modules.constants import VERSION
+
+# --- クラス定義 ---
+class MainWindowViewLoaders(object):
+    """ main_window.py から分離された機能クラス """
+
+    def load_xyz_for_3d_viewing(self, file_path=None):
+        """XYZファイルを読み込んで3Dビューアで表示する"""
+        if not file_path:
+            file_path, _ = QFileDialog.getOpenFileName(self, "Load 3D XYZ (View Only)", "", "XYZ Files (*.xyz);;All Files (*)")
+            if not file_path:
+                return
+
+        try:
+            mol = self.load_xyz_file(file_path)
+            if mol is None:
+                raise ValueError("Failed to create molecule from XYZ file.")
+            if mol.GetNumConformers() == 0:
+                raise ValueError("XYZ file has no 3D coordinates.")
+
+            # 2Dエディタをクリア
+            self.clear_2d_editor(push_to_undo=False)
+            
+            # 3D構造をセットして描画
+            # Set the molecule. If bonds were determined (mol has bonds),
+            # treat this the same as loading a MOL file: clear the XYZ-derived
+            # flag and enable 3D optimization. Only mark as XYZ-derived and
+            # disable 3D optimization when the molecule has no bond information.
+            self.current_mol = mol
+
+            # XYZファイル読み込み時はマッピングをクリア（2D構造がないため）
+            self.atom_id_to_rdkit_idx_map = {}
+
+            # If the loader marked the molecule as produced under skip_chemistry_checks,
+            # always treat it as XYZ-derived and disable optimization. Otherwise
+            # fall back to the existing behavior based on bond presence.
+            skip_flag = False
+            try:
+                # Prefer RDKit int prop
+                skip_flag = bool(self.current_mol.GetIntProp("_xyz_skip_checks"))
+            except Exception:
+                try:
+                    skip_flag = bool(getattr(self.current_mol, '_xyz_skip_checks', False))
+                except Exception:
+                    skip_flag = False
+
+            if skip_flag:
+                self.is_xyz_derived = True
+                if hasattr(self, 'optimize_3d_button'):
+                    try:
+                        self.optimize_3d_button.setEnabled(False)
+                    except Exception:
+                        pass
+            else:
+                try:
+                    has_bonds = (self.current_mol.GetNumBonds() > 0)
+                except Exception:
+                    has_bonds = False
+
+                if has_bonds:
+                    self.is_xyz_derived = False
+                    if hasattr(self, 'optimize_3d_button'):
+                        try:
+                            # Only enable optimize if the molecule is not considered XYZ-derived
+                            if not getattr(self, 'is_xyz_derived', False):
+                                self.optimize_3d_button.setEnabled(True)
+                            else:
+                                self.optimize_3d_button.setEnabled(False)
+                        except Exception:
+                            pass
+                else:
+                    self.is_xyz_derived = True
+                    if hasattr(self, 'optimize_3d_button'):
+                        try:
+                            self.optimize_3d_button.setEnabled(False)
+                        except Exception:
+                            pass
+
+            self.draw_molecule_3d(self.current_mol)
+            self.plotter.reset_camera()
+
+            # UIを3Dビューアモードに設定
+            self._enter_3d_viewer_ui_mode()
+
+            # 3D関連機能を統一的に有効化
+            self._enable_3d_features(True)
+            
+            # メニューテキストと状態を更新
+            self.update_atom_id_menu_text()
+            self.update_atom_id_menu_state()
+            
+            self.statusBar().showMessage(f"3D Viewer Mode: Loaded {os.path.basename(file_path)}")
+            self.reset_undo_stack()
+            # XYZファイル名をcurrent_file_pathにセットし、未保存状態はFalse
+            self.current_file_path = file_path
+            self.has_unsaved_changes = False
+            self.update_window_title()
+
+        except FileNotFoundError:
+            self.statusBar().showMessage(f"File not found: {file_path}")
+            self.restore_ui_for_editing()
+        except ValueError as e:
+            self.statusBar().showMessage(f"Invalid XYZ file: {e}")
+            self.restore_ui_for_editing()
+        except Exception as e:
+            self.statusBar().showMessage(f"Error loading XYZ file: {e}")
+            self.restore_ui_for_editing()
+            
+            traceback.print_exc()
+
+
+
+    def save_3d_as_mol(self):
+        if not self.current_mol:
+            self.statusBar().showMessage("Error: Please generate a 3D structure first.")
+            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)
+                    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 MOL File", default_path, "MOL Files (*.mol);;All Files (*)")
+            if not file_path:
+                return
+                
+            if not file_path.lower().endswith('.mol'):
+                file_path += '.mol'
+
+            mol_to_save = Chem.Mol(self.current_mol)
+
+            if mol_to_save.HasProp("_2D"):
+                mol_to_save.ClearProp("_2D")
+
+            mol_block = Chem.MolToMolBlock(mol_to_save, includeStereo=True)
+            lines = mol_block.split('\n')
+            if len(lines) > 1 and 'RDKit' in lines[1]:
+                lines[1] = '  MoleditPy Ver. ' + VERSION + '  3D'
+            modified_mol_block = '\n'.join(lines)
+            
+            with open(file_path, 'w', encoding='utf-8') as f:
+                f.write(modified_mol_block)
+            self.statusBar().showMessage(f"3D 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 3D MOL file: {e}")
+            
+            traceback.print_exc()
+
+
+
+    def load_mol_file_for_3d_viewing(self, file_path=None):
+        """MOL/SDFファイルを3Dビューアーで開く"""
+        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, "Open MOL/SDF File", "", 
+                "MOL/SDF Files (*.mol *.sdf);;All Files (*)"
+            )
+            if not file_path:
+                return
+        
+        try:
+            
+            # Determine extension early and handle .mol specially by reading the
+            # raw block and running it through fix_mol_block before parsing.
+            _, ext = os.path.splitext(file_path)
+            ext = ext.lower() if ext else ''
+
+            if ext == '.sdf':
+                suppl = Chem.SDMolSupplier(file_path, removeHs=False)
+                mol = next(suppl, None)
+
+            elif ext == '.mol':
+                # Read the file contents and attempt to fix malformed counts lines
+                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 parsing the fixed block fails, fall back to RDKit's file reader
+                # as a last resort (keeps behavior conservative).
+                if mol is None:
+                    try:
+                        mol = Chem.MolFromMolFile(file_path, removeHs=False)
+                    except Exception:
+                        mol = None
+
+                if mol is None:
+                    self.statusBar().showMessage(f"Failed to load molecule from {file_path}")
+                    return
+
+            else:
+                # Default: let RDKit try to read the file (most common case)
+                if file_path.lower().endswith('.sdf'):
+                    suppl = Chem.SDMolSupplier(file_path, removeHs=False)
+                    mol = next(suppl, None)
+                else:
+                    mol = Chem.MolFromMolFile(file_path, removeHs=False)
+
+                if mol is None:
+                    self.statusBar().showMessage(f"Failed to load molecule from {file_path}")
+                    return
+
+            # 3D座標がない場合は2Dから3D変換（最適化なし）
+            if mol.GetNumConformers() == 0:
+                self.statusBar().showMessage("No 3D coordinates found. Converting to 3D...")
+                try:
+                    try:
+                        AllChem.EmbedMolecule(mol)
+                        # 最適化は実行しない
+                        # 3D変換直後にUndoスタックに積む
+                        self.current_mol = mol
+                        self.push_undo_state()
+                    except Exception:
+                        # If skipping chemistry checks, allow molecule to be displayed without 3D embedding
+                        if self.settings.get('skip_chemistry_checks', False):
+                            self.statusBar().showMessage("Warning: failed to generate 3D coordinates but skip_chemistry_checks is enabled; continuing.")
+                            # Keep mol as-is (may lack conformer); downstream code checks for conformers
+                        else:
+                            raise
+                except Exception:
+                    self.statusBar().showMessage("Failed to generate 3D coordinates")
+                    return
+            
+            # Clear XYZ markers on the newly loaded MOL/SDF so Optimize 3D is
+            # correctly enabled when appropriate.
+            try:
+                self._clear_xyz_flags(mol)
+            except Exception:
+                pass
+
+            # 3Dビューアーに表示
+            # Centralized chemical/sanitization handling
+            # Ensure the skip_chemistry_checks setting is respected and flags are set
+            self._apply_chem_check_and_set_flags(mol, source_desc='MOL/SDF')
+
+            self.current_mol = mol
+            self.draw_molecule_3d(mol)
+            
+            # カメラをリセット
+            self.plotter.reset_camera()
+            
+            # UIを3Dビューアーモードに設定
+            self._enter_3d_viewer_ui_mode()
+            
+            # メニューテキストと状態を更新
+            self.update_atom_id_menu_text()
+            self.update_atom_id_menu_state()
+            
+            self.statusBar().showMessage(f"Loaded {file_path} in 3D viewer")
+            
+            self.reset_undo_stack()
+            self.has_unsaved_changes = False  # ファイル読込直後は未変更扱い
+            self.current_file_path = file_path
+            self.update_window_title()
+            
+
+        except Exception as e:
+            self.statusBar().showMessage(f"Error loading MOL/SDF file: {e}")
+    

moleditpy_linux/modules/mirror_dialog.py

@@ -0,0 +1,122 @@
+#!/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
+"""
+
+from PyQt6.QtWidgets import (
+    QDialog, QVBoxLayout, QLabel, QButtonGroup, QRadioButton,
+    QHBoxLayout, QPushButton, QMessageBox
+)
+from rdkit import Chem
+
+class MirrorDialog(QDialog):
+    """分子の鏡像を作成するダイアログ"""
+    
+    def __init__(self, mol, main_window, parent=None):
+        super().__init__(parent)
+        self.mol = mol
+        self.main_window = main_window
+        self.init_ui()
+    
+    def init_ui(self):
+        self.setWindowTitle("Mirror Molecule")
+        self.setMinimumSize(300, 200)
+        
+        layout = QVBoxLayout(self)
+        
+        # 説明テキスト
+        info_label = QLabel("Select the mirror plane to create molecular mirror image:")
+        layout.addWidget(info_label)
+        
+        # ミラー平面選択のラジオボタン
+        self.plane_group = QButtonGroup(self)
+        
+        self.xy_radio = QRadioButton("XY plane (Z = 0)")
+        self.xz_radio = QRadioButton("XZ plane (Y = 0)")
+        self.yz_radio = QRadioButton("YZ plane (X = 0)")
+        
+        self.xy_radio.setChecked(True)  # デフォルト選択
+        
+        self.plane_group.addButton(self.xy_radio, 0)
+        self.plane_group.addButton(self.xz_radio, 1)
+        self.plane_group.addButton(self.yz_radio, 2)
+        
+        layout.addWidget(self.xy_radio)
+        layout.addWidget(self.xz_radio)
+        layout.addWidget(self.yz_radio)
+        
+        layout.addSpacing(20)
+        
+        # ボタン
+        button_layout = QHBoxLayout()
+        
+        apply_button = QPushButton("Apply Mirror")
+        apply_button.clicked.connect(self.apply_mirror)
+
+        close_button = QPushButton("Close")
+        close_button.clicked.connect(self.reject)
+
+        button_layout.addWidget(apply_button)
+        button_layout.addWidget(close_button)
+        
+        layout.addLayout(button_layout)
+    
+    def apply_mirror(self):
+        """選択された平面に対してミラー変換を適用"""
+        if not self.mol or self.mol.GetNumConformers() == 0:
+            QMessageBox.warning(self, "Error", "No 3D coordinates available.")
+            return
+        
+        # 選択された平面を取得
+        plane_id = self.plane_group.checkedId()
+        
+        try:
+            conf = self.mol.GetConformer()
+            
+            # 各原子の座標を変換
+            for atom_idx in range(self.mol.GetNumAtoms()):
+                pos = conf.GetAtomPosition(atom_idx)
+                
+                if plane_id == 0:  # XY平面（Z軸に対してミラー）
+                    new_pos = [pos.x, pos.y, -pos.z]
+                elif plane_id == 1:  # XZ平面（Y軸に対してミラー）
+                    new_pos = [pos.x, -pos.y, pos.z]
+                elif plane_id == 2:  # YZ平面（X軸に対してミラー）
+                    new_pos = [-pos.x, pos.y, pos.z]
+                
+                # 新しい座標を設定
+                from rdkit.Geometry import Point3D
+                conf.SetAtomPosition(atom_idx, Point3D(new_pos[0], new_pos[1], new_pos[2]))
+            
+            # 3Dビューを更新
+            self.main_window.draw_molecule_3d(self.mol)
+            
+            # ミラー変換後にキラルタグを強制的に再計算
+            try:
+                if self.mol.GetNumConformers() > 0:
+                    # 既存のキラルタグをクリア
+                    for atom in self.mol.GetAtoms():
+                        atom.SetChiralTag(Chem.rdchem.ChiralType.CHI_UNSPECIFIED)
+                    # 3D座標から新しいキラルタグを計算
+                    Chem.AssignAtomChiralTagsFromStructure(self.mol, confId=0)
+            except Exception as e:
+                print(f"Error updating chiral tags: {e}")
+            
+            # キラルラベルを更新（鏡像変換でキラリティが変わる可能性があるため）
+            self.main_window.update_chiral_labels()
+            
+            self.main_window.push_undo_state()
+            
+            plane_names = ["XY", "XZ", "YZ"]
+            self.main_window.statusBar().showMessage(f"Molecule mirrored across {plane_names[plane_id]} plane.")
+        
+
+        except Exception as e:
+            QMessageBox.critical(self, "Error", f"Failed to apply mirror transformation: {str(e)}")