MoleditPy-linux 2.4.1__py3-none-any.whl

moleditpy_linux/modules/main_window_string_importers.py

@@ -0,0 +1,275 @@
+#!/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_string_importers.py
+MainWindow (main_window.py) から分離されたモジュール
+機能クラス: MainWindowStringImporters
+"""
+
+
+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 (
+    QInputDialog
+)
+
+
+
+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
+        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 MainWindowStringImporters(object):
+    """ main_window.py から分離された機能クラス """
+
+
+    def import_smiles_dialog(self):
+        """ユーザーにSMILES文字列の入力を促すダイアログを表示する"""
+        smiles, ok = QInputDialog.getText(self, "Import SMILES", "Enter SMILES string:")
+        if ok and smiles:
+            self.load_from_smiles(smiles)
+
+
+
+    def import_inchi_dialog(self):
+        """ユーザーにInChI文字列の入力を促すダイアログを表示する"""
+        inchi, ok = QInputDialog.getText(self, "Import InChI", "Enter InChI string:")
+        if ok and inchi:
+            self.load_from_inchi(inchi)
+
+
+
+    def load_from_smiles(self, smiles_string):
+        """SMILES文字列から分子を読み込み、2Dエディタに表示する"""
+        try:
+            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
+
+            cleaned_smiles = smiles_string.strip()
+            
+            mol = Chem.MolFromSmiles(cleaned_smiles)
+            if mol is None:
+                if not cleaned_smiles:
+                    raise ValueError("SMILES string was empty.")
+                raise ValueError("Invalid SMILES string.")
+
+            AllChem.Compute2DCoords(mol)
+            Chem.Kekulize(mol)
+
+            AllChem.AssignStereochemistry(mol, cleanIt=True, force=True)
+            conf = mol.GetConformer()
+            AllChem.WedgeMolBonds(mol, conf)
+
+            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)
+
+            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())]
+            mol_center_x = sum(p.x for p in positions) / len(positions) if positions else 0.0
+            mol_center_y = sum(p.y for p in positions) / len(positions) if positions else 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
+                # 単結合の立体
+                if b_dir == Chem.BondDir.BEGINWEDGE:
+                    stereo = 1 # Wedge
+                elif b_dir == Chem.BondDir.BEGINDASH:
+                    stereo = 2 # Dash
+                # 二重結合のE/Z
+                if bond.GetBondType() == Chem.BondType.DOUBLE:
+                    if bond.GetStereo() == Chem.BondStereo.STEREOZ:
+                        stereo = 3 # Z
+                    elif bond.GetStereo() == Chem.BondStereo.STEREOE:
+                        stereo = 4 # E
+
+                if b_idx in rdkit_idx_to_my_id and e_idx in rdkit_idx_to_my_id:
+                    a1_id, a2_id = rdkit_idx_to_my_id[b_idx], rdkit_idx_to_my_id[e_idx]
+                    a1_item = self.data.atoms[a1_id]['item']
+                    a2_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("Successfully loaded from SMILES.")
+            self.reset_undo_stack()
+            self.has_unsaved_changes = False
+            self.update_window_title()
+            QTimer.singleShot(0, self.fit_to_view)
+            
+        except ValueError as e:
+            self.statusBar().showMessage(f"Invalid SMILES: {e}")
+        except Exception as e:
+            self.statusBar().showMessage(f"Error loading from SMILES: {e}")
+            
+            traceback.print_exc()
+
+
+
+    def load_from_inchi(self, inchi_string):
+        """InChI文字列から分子を読み込み、2Dエディタに表示する"""
+        try:
+            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
+            cleaned_inchi = inchi_string.strip()
+            
+            mol = Chem.MolFromInchi(cleaned_inchi)
+            if mol is None:
+                if not cleaned_inchi:
+                    raise ValueError("InChI string was empty.")
+                raise ValueError("Invalid InChI string.")
+
+            AllChem.Compute2DCoords(mol)
+            Chem.Kekulize(mol)
+
+            AllChem.AssignStereochemistry(mol, cleanIt=True, force=True)
+            conf = mol.GetConformer()
+            AllChem.WedgeMolBonds(mol, conf)
+
+            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)
+
+            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())]
+            mol_center_x = sum(p.x for p in positions) / len(positions) if positions else 0.0
+            mol_center_y = sum(p.y for p in positions) / len(positions) if positions else 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
+                # 単結合の立体
+                if b_dir == Chem.BondDir.BEGINWEDGE:
+                    stereo = 1 # Wedge
+                elif b_dir == Chem.BondDir.BEGINDASH:
+                    stereo = 2 # Dash
+                # 二重結合のE/Z
+                if bond.GetBondType() == Chem.BondType.DOUBLE:
+                    if bond.GetStereo() == Chem.BondStereo.STEREOZ:
+                        stereo = 3 # Z
+                    elif bond.GetStereo() == Chem.BondStereo.STEREOE:
+                        stereo = 4 # E
+
+                if b_idx in rdkit_idx_to_my_id and e_idx in rdkit_idx_to_my_id:
+                    a1_id, a2_id = rdkit_idx_to_my_id[b_idx], rdkit_idx_to_my_id[e_idx]
+                    a1_item = self.data.atoms[a1_id]['item']
+                    a2_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("Successfully loaded from InChI.")
+            self.reset_undo_stack()
+            self.has_unsaved_changes = False
+            self.update_window_title()
+            QTimer.singleShot(0, self.fit_to_view)
+            
+        except ValueError as e:
+            self.statusBar().showMessage(f"Invalid InChI: {e}")
+        except Exception as e:
+            self.statusBar().showMessage(f"Error loading from InChI: {e}")
+            
+            traceback.print_exc()
+