MoleditPy 2.2.0a0__py3-none-any.whl → 2.2.0a1__py3-none-any.whl

moleditpy/plugins/Optimization/conf_search.py

@@ -0,0 +1,224 @@
+from PyQt6.QtWidgets import (
+    QDialog, QVBoxLayout, QHBoxLayout, QTableWidget, 
+    QTableWidgetItem, QPushButton, QMessageBox, QLabel, QHeaderView, QAbstractItemView,
+    QApplication, QComboBox
+)
+from PyQt6.QtCore import Qt
+from rdkit import Chem
+from rdkit.Chem import AllChem
+import copy
+
+PLUGIN_NAME = "Conformational Search"
+__version__="2025.12.25"
+__author__="HiroYokoyama"
+
+class ConformerSearchDialog(QDialog):
+    def __init__(self, main_window, parent=None):
+        super().__init__(parent)
+        self.main_window = main_window
+        self.setWindowTitle("Conformational Search & Preview")
+        self.resize(400, 500)
+        
+        # メインウィンドウの分子への参照
+        self.target_mol = getattr(main_window, "current_mol", None)
+        
+        # 計算用の一時的な分子（オリジナルを汚染しないため）
+        self.temp_mol = None
+        # 生成された配座データのリスト [(Energy, ConformerID), ...]
+        self.conformer_data = []
+
+        self.init_ui()
+
+    def init_ui(self):
+        layout = QVBoxLayout(self)
+
+        # 説明ラベル
+        self.lbl_info = QLabel("Click 'Run Search' to generate conformers.\nSelect a row to preview.")
+        layout.addWidget(self.lbl_info)
+
+        # Force Field Selection
+        hbox_ff = QHBoxLayout()
+        hbox_ff.addWidget(QLabel("Force Field:"))
+        self.combo_ff = QComboBox()
+        self.combo_ff.addItems(["MMFF94", "UFF"])
+        hbox_ff.addWidget(self.combo_ff)
+        hbox_ff.addStretch()
+        layout.addLayout(hbox_ff)
+        
+        # Set default based on main window setting
+        default_method = getattr(self.main_window, "optimization_method", "MMFF_RDKIT")
+        if default_method:
+            default_method = default_method.upper()
+            if "UFF" in default_method:
+                self.combo_ff.setCurrentText("UFF")
+            else:
+                self.combo_ff.setCurrentText("MMFF94")
+
+        # 結果表示用テーブル
+        self.table = QTableWidget()
+        self.table.setColumnCount(2)
+        self.table.setHorizontalHeaderLabels(["Rank", "Energy (kcal/mol)"])
+        self.table.horizontalHeader().setSectionResizeMode(QHeaderView.ResizeMode.Stretch)
+        self.table.setSelectionBehavior(QAbstractItemView.SelectionBehavior.SelectRows)
+        self.table.setSelectionMode(QAbstractItemView.SelectionMode.SingleSelection)
+        self.table.itemClicked.connect(self.preview_conformer)
+        layout.addWidget(self.table)
+
+        # ボタンエリア
+        btn_layout = QHBoxLayout()
+        self.btn_run = QPushButton("Run Search")
+        self.btn_run.clicked.connect(self.run_search)
+        
+        self.btn_close = QPushButton("Close")
+        self.btn_close.clicked.connect(self.accept) # 閉じる（現在のプレビュー状態で確定）
+
+        btn_layout.addWidget(self.btn_run)
+        btn_layout.addWidget(self.btn_close)
+        layout.addLayout(btn_layout)
+
+    def accept(self):
+        # Push undo state when closing the dialog (confirming the selection)
+        if hasattr(self.main_window, "push_undo_state"):
+            self.main_window.push_undo_state()
+        super().accept()
+
+    def run_search(self):
+        if not self.target_mol:
+            return
+
+        self.btn_run.setEnabled(False)
+        self.lbl_info.setText("Running conformational search... please wait.")
+        QApplication.processEvents()
+
+        try:
+            # 計算用に分子を複製（水素が付加されていることを推奨）
+            mol_calc = copy.deepcopy(self.target_mol)
+            
+            # 1. 配座生成 (ETKDGv3)
+            params = AllChem.ETKDGv3()
+            params.useSmallRingTorsions = True
+            cids = AllChem.EmbedMultipleConfs(mol_calc, numConfs=30, params=params)
+
+            if not cids:
+                QMessageBox.warning(self, PLUGIN_NAME, "Failed to generate conformers.")
+                self.lbl_info.setText("Failed.")
+                self.btn_run.setEnabled(True)
+                return
+
+            # 2. 構造最適化とエネルギー計算
+            results = []
+            selected_ff = self.combo_ff.currentText()
+            
+            for i, cid in enumerate(cids):
+                energy = None
+                
+                if selected_ff == "MMFF94":
+                     # MMFF94 Optimize
+                    if AllChem.MMFFOptimizeMolecule(mol_calc, confId=cid) != -1:
+                         # Calculate Energy
+                         prop = AllChem.MMFFGetMoleculeProperties(mol_calc)
+                         if prop:
+                             ff = AllChem.MMFFGetMoleculeForceField(mol_calc, prop, confId=cid)
+                             if ff:
+                                 energy = ff.CalcEnergy()
+                
+                elif selected_ff == "UFF":
+                     # UFF Optimize
+                     if AllChem.UFFOptimizeMolecule(mol_calc, confId=cid) != -1:
+                         # Calculate Energy
+                         ff = AllChem.UFFGetMoleculeForceField(mol_calc, confId=cid)
+                         if ff:
+                             energy = ff.CalcEnergy()
+
+                if energy is not None:
+                    results.append((energy, cid))
+                
+                # UIの応答性を維持
+                if i % 5 == 0:
+                    QApplication.processEvents()
+
+            if not results:
+                 QMessageBox.warning(self, PLUGIN_NAME, f"Optimization failed with {selected_ff}.")
+                 self.btn_run.setEnabled(True)
+                 return
+
+            # エネルギーが低い順にソート
+            results.sort(key=lambda x: x[0])
+            
+            # データを保持
+            self.temp_mol = mol_calc
+            self.conformer_data = results
+
+            # テーブル更新
+            self.update_table()
+            self.lbl_info.setText(f"Found {len(results)} conformers ({selected_ff}).")
+
+        except Exception as e:
+            QMessageBox.critical(self, PLUGIN_NAME, f"Error during search: {str(e)}")
+            self.lbl_info.setText("Error occurred.")
+        finally:
+            self.btn_run.setEnabled(True)
+
+    def update_table(self):
+        self.table.setRowCount(0)
+        # base_energy = self.conformer_data[0][0] if self.conformer_data else 0
+
+        for rank, (energy, cid) in enumerate(self.conformer_data):
+            row_idx = self.table.rowCount()
+            self.table.insertRow(row_idx)
+            
+            # Rank
+            self.table.setItem(row_idx, 0, QTableWidgetItem(str(rank + 1)))
+            
+            # Energy
+            energy_str = f"{energy:.4f}"
+            self.table.setItem(row_idx, 1, QTableWidgetItem(energy_str))
+            
+            # 隠しデータとしてConformer IDを持たせる
+            self.table.item(row_idx, 0).setData(Qt.ItemDataRole.UserRole, cid)
+
+    def preview_conformer(self, item):
+        """リスト選択時にメインウィンドウの表示を更新"""
+        if not self.temp_mol or not self.target_mol:
+            return
+        
+        row = item.row()
+        # Rankカラム(0)にCIDを埋め込んでいるので取得
+        cid = self.table.item(row, 0).data(Qt.ItemDataRole.UserRole)
+        
+        # 選択された配座の座標を取得
+        source_conf = self.temp_mol.GetConformer(cid)
+        target_conf = self.target_mol.GetConformer() # 現在の表示用Conformer
+        
+        # 座標のコピー
+        for i in range(self.target_mol.GetNumAtoms()):
+            pos = source_conf.GetAtomPosition(i)
+            target_conf.SetAtomPosition(i, pos)
+            
+        # ビューの更新（ユーザー提供コードのロジックに従う）
+        if hasattr(self.main_window, "draw_molecule_3d"):
+            self.main_window.draw_molecule_3d(self.target_mol)
+        elif hasattr(self.main_window, "update_view"):
+            self.main_window.update_view()
+        elif hasattr(self.main_window, "gl_widget"):
+            # GLWidgetのリフレッシュ
+            getattr(self.main_window.gl_widget, "update", lambda: None)()
+
+def run(mw):
+    mol = getattr(mw, "current_mol", None)
+    if not mol:
+        QMessageBox.warning(mw, PLUGIN_NAME, "No molecule loaded.")
+        return
+        
+    # 既存のダイアログがあればアクティブにする
+    if hasattr(mw, "_conformer_search_dialog") and mw._conformer_search_dialog.isVisible():
+        mw._conformer_search_dialog.raise_()
+        mw._conformer_search_dialog.activateWindow()
+        return
+
+    dialog = ConformerSearchDialog(mw, parent=mw)
+    # 参照を保持してGCを防ぐ
+    mw._conformer_search_dialog = dialog
+    dialog.show() # モーダルではなくModeless（非ブロック）で表示
+
+# initialize removed as it only registered the menu action