MoleditPy 1.15.1__py3-none-any.whl → 1.16.0__py3-none-any.whl

moleditpy/modules/move_group_dialog.py

@@ -0,0 +1,586 @@
+from PyQt6.QtWidgets import (
+    QDialog, QVBoxLayout, QLabel, QGridLayout, QHBoxLayout, QPushButton, QLineEdit, QMessageBox
+)
+from PyQt6.QtCore import Qt, QEvent
+import numpy as np
+import pyvista as pv
+from rdkit import Chem
+try:
+    from .constants import VDW_RADII
+except Exception:
+    from modules.constants import VDW_RADII
+
+try:
+    from .dialog3_d_picking_mixin import Dialog3DPickingMixin
+except Exception:
+    from modules.dialog3_d_picking_mixin import Dialog3DPickingMixin
+
+class MoveGroupDialog(Dialog3DPickingMixin, QDialog):
+    """結合している分子グループを選択して並行移動・回転するダイアログ"""
+    
+    def __init__(self, mol, main_window, parent=None):
+        QDialog.__init__(self, parent)
+        Dialog3DPickingMixin.__init__(self)
+        self.mol = mol
+        self.main_window = main_window
+        self.selected_atoms = set()
+        self.group_atoms = set()  # 選択原子に結合している全原子
+        self.init_ui()
+    
+    def init_ui(self):
+        self.setWindowTitle("Move Group")
+        self.setModal(False)
+        self.setWindowFlags(Qt.WindowType.Window | Qt.WindowType.WindowStaysOnTopHint)
+        self.resize(300,400)  # ウィンドウサイズを設定
+        layout = QVBoxLayout(self)
+        
+        # ドラッグ状態管理
+        self.is_dragging_group = False
+        self.drag_start_pos = None
+        self.mouse_moved_during_drag = False  # ドラッグ中にマウスが動いたかを追跡
+        
+        # Instructions
+        instruction_label = QLabel("Click an atom in the 3D view to select its connected molecule group.\n"
+                                   "Left-drag: Move the group\n"
+                                   "Right-drag: Rotate the group around its center")
+        instruction_label.setWordWrap(True)
+        layout.addWidget(instruction_label)
+        
+        # Selected group display
+        self.selection_label = QLabel("No group selected")
+        layout.addWidget(self.selection_label)
+        
+        # Translation controls
+        trans_group = QLabel("Translation (Å):")
+        trans_group.setStyleSheet("font-weight: bold;")
+        layout.addWidget(trans_group)
+        
+        trans_layout = QGridLayout()
+        self.x_trans_input = QLineEdit("0.0")
+        self.y_trans_input = QLineEdit("0.0")
+        self.z_trans_input = QLineEdit("0.0")
+        
+        # Enterキーでapply_translationを実行
+        self.x_trans_input.returnPressed.connect(self.apply_translation)
+        self.y_trans_input.returnPressed.connect(self.apply_translation)
+        self.z_trans_input.returnPressed.connect(self.apply_translation)
+        
+        trans_layout.addWidget(QLabel("X:"), 0, 0)
+        trans_layout.addWidget(self.x_trans_input, 0, 1)
+        trans_layout.addWidget(QLabel("Y:"), 1, 0)
+        trans_layout.addWidget(self.y_trans_input, 1, 1)
+        trans_layout.addWidget(QLabel("Z:"), 2, 0)
+        trans_layout.addWidget(self.z_trans_input, 2, 1)
+        
+        trans_button_layout = QHBoxLayout()
+        reset_trans_button = QPushButton("Reset")
+        reset_trans_button.clicked.connect(self.reset_translation_inputs)
+        trans_button_layout.addWidget(reset_trans_button)
+        
+        apply_trans_button = QPushButton("Apply Translation")
+        apply_trans_button.clicked.connect(self.apply_translation)
+        trans_button_layout.addWidget(apply_trans_button)
+        
+        trans_layout.addLayout(trans_button_layout, 3, 0, 1, 2)
+        
+        layout.addLayout(trans_layout)
+        
+        layout.addSpacing(10)
+        
+        # Rotation controls
+        rot_group = QLabel("Rotation (degrees):")
+        rot_group.setStyleSheet("font-weight: bold;")
+        layout.addWidget(rot_group)
+        
+        rot_layout = QGridLayout()
+        self.x_rot_input = QLineEdit("0.0")
+        self.y_rot_input = QLineEdit("0.0")
+        self.z_rot_input = QLineEdit("0.0")
+        
+        # Enterキーでapply_rotationを実行
+        self.x_rot_input.returnPressed.connect(self.apply_rotation)
+        self.y_rot_input.returnPressed.connect(self.apply_rotation)
+        self.z_rot_input.returnPressed.connect(self.apply_rotation)
+        
+        rot_layout.addWidget(QLabel("Around X:"), 0, 0)
+        rot_layout.addWidget(self.x_rot_input, 0, 1)
+        rot_layout.addWidget(QLabel("Around Y:"), 1, 0)
+        rot_layout.addWidget(self.y_rot_input, 1, 1)
+        rot_layout.addWidget(QLabel("Around Z:"), 2, 0)
+        rot_layout.addWidget(self.z_rot_input, 2, 1)
+        
+        rot_button_layout = QHBoxLayout()
+        reset_rot_button = QPushButton("Reset")
+        reset_rot_button.clicked.connect(self.reset_rotation_inputs)
+        rot_button_layout.addWidget(reset_rot_button)
+        
+        apply_rot_button = QPushButton("Apply Rotation")
+        apply_rot_button.clicked.connect(self.apply_rotation)
+        rot_button_layout.addWidget(apply_rot_button)
+        
+        rot_layout.addLayout(rot_button_layout, 3, 0, 1, 2)
+        
+        layout.addLayout(rot_layout)
+        
+        # Buttons
+        button_layout = QHBoxLayout()
+        self.clear_button = QPushButton("Clear Selection")
+        self.clear_button.clicked.connect(self.clear_selection)
+        button_layout.addWidget(self.clear_button)
+        
+        button_layout.addStretch()
+        
+        close_button = QPushButton("Close")
+        close_button.clicked.connect(self.reject)
+        button_layout.addWidget(close_button)
+        
+        layout.addLayout(button_layout)
+        
+        # Enable picking to handle atom selection
+        self.enable_picking()
+    
+    def eventFilter(self, obj, event):
+        """3Dビューでのマウスイベント処理 - グループが選択されている場合はCustomInteractorStyleに任せる"""
+        if obj == self.main_window.plotter.interactor:
+            # ダブルクリック/トリプルクリックで状態が混乱するのを防ぐ
+            if event.type() == QEvent.Type.MouseButtonDblClick:
+                # ダブルクリックは無視し、状態をリセット
+                self.is_dragging_group = False
+                self.drag_start_pos = None
+                self.mouse_moved_during_drag = False
+                self.potential_drag = False
+                if hasattr(self, 'clicked_atom_for_toggle'):
+                    delattr(self, 'clicked_atom_for_toggle')
+                return False
+            
+            if event.type() == QEvent.Type.MouseButtonPress and event.button() == Qt.MouseButton.LeftButton:
+                # 前回の状態をクリーンアップ（トリプルクリック対策）
+                self.is_dragging_group = False
+                self.potential_drag = False
+                if hasattr(self, 'clicked_atom_for_toggle'):
+                    delattr(self, 'clicked_atom_for_toggle')
+                # グループが既に選択されている場合は、CustomInteractorStyleに処理を任せる
+                if self.group_atoms:
+                    return False
+                
+                # マウスプレス時の処理
+                # マウスプレス時の処理
+                try:
+                    interactor = self.main_window.plotter.interactor
+                    click_pos = interactor.GetEventPosition()
+                    
+                    # まずピッキングしてどの原子がクリックされたか確認
+                    picker = self.main_window.plotter.picker
+                    picker.Pick(click_pos[0], click_pos[1], 0, self.main_window.plotter.renderer)
+                    
+                    clicked_atom_idx = None
+                    if picker.GetActor() is self.main_window.atom_actor:
+                        picked_position = np.array(picker.GetPickPosition())
+                        distances = np.linalg.norm(self.main_window.atom_positions_3d - picked_position, axis=1)
+                        closest_atom_idx = np.argmin(distances)
+                        
+                        # 閾値チェック
+                        if 0 <= closest_atom_idx < self.mol.GetNumAtoms():
+                            atom = self.mol.GetAtomWithIdx(int(closest_atom_idx))
+                            if atom:
+                                atomic_num = atom.GetAtomicNum()
+                                pt = Chem.GetPeriodicTable()
+                                vdw_radius = pt.GetRvdw(atomic_num)
+                                click_threshold = vdw_radius * 1.5
+                                
+                                if distances[closest_atom_idx] < click_threshold:
+                                    clicked_atom_idx = int(closest_atom_idx)
+                    
+                    
+                    # クリックされた原子の処理
+                    if clicked_atom_idx is not None:
+                        if self.group_atoms and clicked_atom_idx in self.group_atoms:
+                            # 既存のグループ内の原子 - ドラッグ準備（まだドラッグとは確定しない）
+                            self.is_dragging_group = False  # まだドラッグ中ではない
+                            self.drag_start_pos = click_pos
+                            self.drag_atom_idx = clicked_atom_idx
+                            self.mouse_moved_during_drag = False
+                            self.potential_drag = True  # ドラッグの可能性がある
+                            self.clicked_atom_for_toggle = clicked_atom_idx  # トグル用に保存
+                            # イベントを消費せず、カメラ操作を許可（閾値超えたらドラッグ開始）
+                            return False
+                        else:
+                            # グループ外の原子 - 新しいグループを選択
+                            # 親クラス（Mixin）のon_atom_pickedを手動で呼ぶ
+                            self.on_atom_picked(clicked_atom_idx)
+                            return True
+                    else:
+                        # 原子以外をクリック
+                        # グループがあっても通常のカメラ操作を許可
+                        return False
+                    
+                except Exception as e:
+                    print(f"Error in mouse press: {e}")
+                    return False
+            
+            elif event.type() == QEvent.Type.MouseMove:
+                # マウス移動時の処理
+                if getattr(self, 'potential_drag', False) and self.drag_start_pos and not self.is_dragging_group:
+                    # potential_drag状態：閾値チェック
+                    try:
+                        interactor = self.main_window.plotter.interactor
+                        current_pos = interactor.GetEventPosition()
+                        dx = current_pos[0] - self.drag_start_pos[0]
+                        dy = current_pos[1] - self.drag_start_pos[1]
+                        
+                        # 閾値を超えたらドラッグ開始
+                        drag_threshold = 5  # ピクセル
+                        if abs(dx) > drag_threshold or abs(dy) > drag_threshold:
+                            # ドラッグ開始を確定
+                            self.is_dragging_group = True
+                            self.potential_drag = False
+                            try:
+                                self.main_window.plotter.setCursor(Qt.CursorShape.ClosedHandCursor)
+                            except Exception:
+                                pass
+                    except Exception:
+                        pass
+                    
+                    # 閾値以下の場合はカメラ操作を許可
+                    if not self.is_dragging_group:
+                        return False
+                
+                if self.is_dragging_group and self.drag_start_pos:
+                    # ドラッグモード中 - 移動距離を記録するのみ（リアルタイム更新なし）
+                    try:
+                        interactor = self.main_window.plotter.interactor
+                        current_pos = interactor.GetEventPosition()
+                        
+                        dx = current_pos[0] - self.drag_start_pos[0]
+                        dy = current_pos[1] - self.drag_start_pos[1]
+                        
+                        if abs(dx) > 2 or abs(dy) > 2:
+                            self.mouse_moved_during_drag = True
+                    except Exception:
+                        pass
+                    
+                    # ドラッグ中はイベントを消費してカメラ回転を防ぐ
+                    return True
+                
+                # ホバー処理（ドラッグ中でない場合）
+                if self.group_atoms:
+                    try:
+                        interactor = self.main_window.plotter.interactor
+                        current_pos = interactor.GetEventPosition()
+                        picker = self.main_window.plotter.picker
+                        picker.Pick(current_pos[0], current_pos[1], 0, self.main_window.plotter.renderer)
+                        
+                        if picker.GetActor() is self.main_window.atom_actor:
+                            picked_position = np.array(picker.GetPickPosition())
+                            distances = np.linalg.norm(self.main_window.atom_positions_3d - picked_position, axis=1)
+                            closest_atom_idx = np.argmin(distances)
+                            
+                            if closest_atom_idx in self.group_atoms:
+                                self.main_window.plotter.setCursor(Qt.CursorShape.OpenHandCursor)
+                            else:
+                                self.main_window.plotter.setCursor(Qt.CursorShape.ArrowCursor)
+                        else:
+                            self.main_window.plotter.setCursor(Qt.CursorShape.ArrowCursor)
+                    except Exception:
+                        pass
+                
+                # ドラッグ中でない場合はカメラ回転を許可
+                return False
+            
+            elif event.type() == QEvent.Type.MouseButtonRelease and event.button() == Qt.MouseButton.LeftButton:
+                # マウスリリース時の処理
+                if getattr(self, 'potential_drag', False) or (self.is_dragging_group and self.drag_start_pos):
+                    try:
+                        if self.is_dragging_group and self.mouse_moved_during_drag:
+                            # ドラッグが実行された - CustomInteractorStyleに任せる（何もしない）
+                            pass
+                        else:
+                            # マウスが閾値以下の移動 = 単なるクリック
+                            # グループ内の原子をクリックした場合は選択/解除をトグル
+                            if hasattr(self, 'clicked_atom_for_toggle'):
+                                clicked_atom = self.clicked_atom_for_toggle
+                                delattr(self, 'clicked_atom_for_toggle')
+                                # ドラッグ状態をリセットしてからトグル処理
+                                self.is_dragging_group = False
+                                self.drag_start_pos = None
+                                self.mouse_moved_during_drag = False
+                                self.potential_drag = False
+                                if hasattr(self, 'last_drag_positions'):
+                                    delattr(self, 'last_drag_positions')
+                                # トグル処理を実行
+                                self.on_atom_picked(clicked_atom)
+                                try:
+                                    self.main_window.plotter.setCursor(Qt.CursorShape.ArrowCursor)
+                                except Exception:
+                                    pass
+                                return True
+                        
+                    except Exception:
+                        pass
+                    finally:
+                        # ドラッグ状態をリセット
+                        self.is_dragging_group = False
+                        self.drag_start_pos = None
+                        self.mouse_moved_during_drag = False
+                        self.potential_drag = False
+                        # 保存していた位置情報をクリア
+                        if hasattr(self, 'last_drag_positions'):
+                            delattr(self, 'last_drag_positions')
+                        try:
+                            self.main_window.plotter.setCursor(Qt.CursorShape.ArrowCursor)
+                        except Exception:
+                            pass
+                    
+                    return True  # イベントを消費
+                
+                # ドラッグ中でない場合は通常のリリース処理
+                return False
+        
+        # その他のイベントは親クラスに渡す
+        return False
+    
+    def on_atom_picked(self, atom_idx):
+        """原子がピックされたときに、その原子が属する連結成分全体を選択（複数グループ対応）"""
+        # ドラッグ中は選択を変更しない（ただしリリース時のトグルは許可）
+        if getattr(self, 'is_dragging_group', False):
+            return
+        
+        # BFS/DFSで連結成分を探索
+        visited = set()
+        queue = [atom_idx]
+        visited.add(atom_idx)
+        
+        while queue:
+            current_idx = queue.pop(0)
+            for bond_idx in range(self.mol.GetNumBonds()):
+                bond = self.mol.GetBondWithIdx(bond_idx)
+                begin_idx = bond.GetBeginAtomIdx()
+                end_idx = bond.GetEndAtomIdx()
+                
+                if begin_idx == current_idx and end_idx not in visited:
+                    visited.add(end_idx)
+                    queue.append(end_idx)
+                elif end_idx == current_idx and begin_idx not in visited:
+                    visited.add(begin_idx)
+                    queue.append(begin_idx)
+        
+        # 新しいグループとして追加または解除
+        if visited.issubset(self.group_atoms):
+            # すでに選択されている - 解除
+            self.group_atoms -= visited
+        else:
+            # 新しいグループを追加
+            self.group_atoms |= visited
+        
+        self.selected_atoms.add(atom_idx)
+        self.show_atom_labels()
+        self.update_display()
+    
+    def update_display(self):
+        if not self.group_atoms:
+            self.selection_label.setText("No group selected")
+        else:
+            atom_info = []
+            for atom_idx in sorted(self.group_atoms):
+                symbol = self.mol.GetAtomWithIdx(atom_idx).GetSymbol()
+                atom_info.append(f"{symbol}({atom_idx})")
+            
+            self.selection_label.setText(f"Selected group: {len(self.group_atoms)} atoms - {', '.join(atom_info[:5])}{' ...' if len(atom_info) > 5 else ''}")
+    
+    def show_atom_labels(self):
+        """選択されたグループの原子をハイライト表示（Ctrlクリックと同じスタイル）"""
+        self.clear_atom_labels()
+        
+        if not self.group_atoms:
+            return
+        
+        # 選択された原子のインデックスリストを作成
+        selected_indices = list(self.group_atoms)
+        
+        # 選択された原子の位置を取得
+        selected_positions = self.main_window.atom_positions_3d[selected_indices]
+        
+        # 原子の半径を少し大きくしてハイライト表示
+        selected_radii = np.array([VDW_RADII.get(
+            self.mol.GetAtomWithIdx(i).GetSymbol(), 0.4) * 1.3 
+            for i in selected_indices])
+        
+        # ハイライト用のデータセットを作成
+        highlight_source = pv.PolyData(selected_positions)
+        highlight_source['radii'] = selected_radii
+        
+        # 黄色の半透明球でハイライト
+        highlight_glyphs = highlight_source.glyph(
+            scale='radii', 
+            geom=pv.Sphere(radius=1.0, theta_resolution=16, phi_resolution=16), 
+            orient=False
+        )
+        
+        # ハイライトアクターを追加して保存（ピッキング不可に設定）
+        self.highlight_actor = self.main_window.plotter.add_mesh(
+            highlight_glyphs, 
+            color='yellow', 
+            opacity=0.3, 
+            name='move_group_highlight',
+            pickable=False  # ピッキングを無効化
+        )
+        
+        self.main_window.plotter.render()
+    
+    def clear_atom_labels(self):
+        """原子ハイライトをクリア"""
+        try:
+            self.main_window.plotter.remove_actor('move_group_highlight')
+        except Exception:
+            pass
+        
+        if hasattr(self, 'highlight_actor'):
+            try:
+                self.main_window.plotter.remove_actor(self.highlight_actor)
+            except Exception:
+                pass
+            self.highlight_actor = None
+        
+        try:
+            self.main_window.plotter.render()
+        except Exception:
+            pass
+    
+    def reset_translation_inputs(self):
+        """Translation入力フィールドをリセット"""
+        self.x_trans_input.setText("0.0")
+        self.y_trans_input.setText("0.0")
+        self.z_trans_input.setText("0.0")
+    
+    def apply_translation(self):
+        """選択したグループを並行移動"""
+        if not self.group_atoms:
+            QMessageBox.warning(self, "Warning", "Please select a group first.")
+            return
+        
+        try:
+            dx = float(self.x_trans_input.text())
+            dy = float(self.y_trans_input.text())
+            dz = float(self.z_trans_input.text())
+        except ValueError:
+            QMessageBox.warning(self, "Warning", "Please enter valid translation values.")
+            return
+        
+        translation_vector = np.array([dx, dy, dz])
+        
+        conf = self.mol.GetConformer()
+        for atom_idx in self.group_atoms:
+            atom_pos = np.array(conf.GetAtomPosition(atom_idx))
+            new_pos = atom_pos + translation_vector
+            conf.SetAtomPosition(atom_idx, new_pos.tolist())
+            self.main_window.atom_positions_3d[atom_idx] = new_pos
+        
+        self.main_window.draw_molecule_3d(self.mol)
+        self.main_window.update_chiral_labels()
+        self.show_atom_labels()  # ラベルを再描画
+        self.main_window.push_undo_state()
+    
+    def reset_rotation_inputs(self):
+        """Rotation入力フィールドをリセット"""
+        self.x_rot_input.setText("0.0")
+        self.y_rot_input.setText("0.0")
+        self.z_rot_input.setText("0.0")
+    
+    def apply_rotation(self):
+        """選択したグループを回転"""
+        if not self.group_atoms:
+            QMessageBox.warning(self, "Warning", "Please select a group first.")
+            return
+        
+        try:
+            rx = float(self.x_rot_input.text())
+            ry = float(self.y_rot_input.text())
+            rz = float(self.z_rot_input.text())
+        except ValueError:
+            QMessageBox.warning(self, "Warning", "Please enter valid rotation values.")
+            return
+        
+        # 度をラジアンに変換
+        rx_rad = np.radians(rx)
+        ry_rad = np.radians(ry)
+        rz_rad = np.radians(rz)
+        
+        # グループの重心を計算
+        conf = self.mol.GetConformer()
+        positions = []
+        for atom_idx in self.group_atoms:
+            pos = conf.GetAtomPosition(atom_idx)
+            positions.append([pos.x, pos.y, pos.z])
+        centroid = np.mean(positions, axis=0)
+        
+        # 回転行列を作成
+        # X軸周り
+        Rx = np.array([
+            [1, 0, 0],
+            [0, np.cos(rx_rad), -np.sin(rx_rad)],
+            [0, np.sin(rx_rad), np.cos(rx_rad)]
+        ])
+        # Y軸周り
+        Ry = np.array([
+            [np.cos(ry_rad), 0, np.sin(ry_rad)],
+            [0, 1, 0],
+            [-np.sin(ry_rad), 0, np.cos(ry_rad)]
+        ])
+        # Z軸周り
+        Rz = np.array([
+            [np.cos(rz_rad), -np.sin(rz_rad), 0],
+            [np.sin(rz_rad), np.cos(rz_rad), 0],
+            [0, 0, 1]
+        ])
+        
+        # 合成回転行列 (Z * Y * X)
+        R = Rz @ Ry @ Rx
+        
+        # 各原子を回転
+        for atom_idx in self.group_atoms:
+            atom_pos = np.array(conf.GetAtomPosition(atom_idx))
+            # 重心を原点に移動
+            centered_pos = atom_pos - centroid
+            # 回転
+            rotated_pos = R @ centered_pos
+            # 重心を元に戻す
+            new_pos = rotated_pos + centroid
+            conf.SetAtomPosition(atom_idx, new_pos.tolist())
+            self.main_window.atom_positions_3d[atom_idx] = new_pos
+        
+        self.main_window.draw_molecule_3d(self.mol)
+        self.main_window.update_chiral_labels()
+        self.show_atom_labels()  # ラベルを再描画
+        self.main_window.push_undo_state()
+    
+    def clear_selection(self):
+        """選択をクリア"""
+        self.selected_atoms.clear()
+        self.group_atoms.clear()
+        self.clear_atom_labels()
+        self.update_display()
+        # ドラッグ関連のフラグもリセット
+        self.is_dragging_group = False
+        self.drag_start_pos = None
+        if hasattr(self, 'last_drag_positions'):
+            delattr(self, 'last_drag_positions')
+    
+    def closeEvent(self, event):
+        """ダイアログが閉じられる時の処理"""
+        self.clear_atom_labels()
+        self.disable_picking()
+        try:
+            self.main_window.draw_molecule_3d(self.mol)
+        except Exception:
+            pass
+        super().closeEvent(event)
+    
+    def reject(self):
+        """キャンセル時の処理"""
+        self.clear_atom_labels()
+        self.disable_picking()
+        try:
+            self.main_window.draw_molecule_3d(self.mol)
+        except Exception:
+            pass
+        super().reject()

moleditpy/modules/periodic_table_dialog.py

@@ -0,0 +1,72 @@
+from PyQt6.QtWidgets import QDialog, QGridLayout, QPushButton
+from PyQt6.QtGui import QColor
+try:
+    from .constants import CPK_COLORS
+except Exception:
+    from modules.constants import CPK_COLORS
+
+from PyQt6.QtCore import pyqtSignal
+
+class PeriodicTableDialog(QDialog):
+    element_selected = pyqtSignal(str)
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.setWindowTitle("Select an Element")
+        layout = QGridLayout(self)
+        self.setLayout(layout)
+
+        elements = [
+            ('H',1,1), ('He',1,18),
+            ('Li',2,1), ('Be',2,2), ('B',2,13), ('C',2,14), ('N',2,15), ('O',2,16), ('F',2,17), ('Ne',2,18),
+            ('Na',3,1), ('Mg',3,2), ('Al',3,13), ('Si',3,14), ('P',3,15), ('S',3,16), ('Cl',3,17), ('Ar',3,18),
+            ('K',4,1), ('Ca',4,2), ('Sc',4,3), ('Ti',4,4), ('V',4,5), ('Cr',4,6), ('Mn',4,7), ('Fe',4,8),
+            ('Co',4,9), ('Ni',4,10), ('Cu',4,11), ('Zn',4,12), ('Ga',4,13), ('Ge',4,14), ('As',4,15), ('Se',4,16),
+            ('Br',4,17), ('Kr',4,18),
+            ('Rb',5,1), ('Sr',5,2), ('Y',5,3), ('Zr',5,4), ('Nb',5,5), ('Mo',5,6), ('Tc',5,7), ('Ru',5,8),
+            ('Rh',5,9), ('Pd',5,10), ('Ag',5,11), ('Cd',5,12), ('In',5,13), ('Sn',5,14), ('Sb',5,15), ('Te',5,16),
+            ('I',5,17), ('Xe',5,18),
+            ('Cs',6,1), ('Ba',6,2), ('Hf',6,4), ('Ta',6,5), ('W',6,6), ('Re',6,7), ('Os',6,8),
+            ('Ir',6,9), ('Pt',6,10), ('Au',6,11), ('Hg',6,12), ('Tl',6,13), ('Pb',6,14), ('Bi',6,15), ('Po',6,16),
+            ('At',6,17), ('Rn',6,18),
+            ('Fr',7,1), ('Ra',7,2), ('Rf',7,4), ('Db',7,5), ('Sg',7,6), ('Bh',7,7), ('Hs',7,8),
+            ('Mt',7,9), ('Ds',7,10), ('Rg',7,11), ('Cn',7,12), ('Nh',7,13), ('Fl',7,14), ('Mc',7,15), ('Lv',7,16),
+            ('Ts',7,17), ('Og',7,18),
+            # Lanthanides (placed on a separate row)
+            ('La',8,3), ('Ce',8,4), ('Pr',8,5), ('Nd',8,6), ('Pm',8,7), ('Sm',8,8), ('Eu',8,9), ('Gd',8,10), ('Tb',8,11),
+            ('Dy',8,12), ('Ho',8,13), ('Er',8,14), ('Tm',8,15), ('Yb',8,16), ('Lu',8,17),
+            # Actinides (separate row)
+            ('Ac',9,3), ('Th',9,4), ('Pa',9,5), ('U',9,6), ('Np',9,7), ('Pu',9,8), ('Am',9,9), ('Cm',9,10), ('Bk',9,11),
+            ('Cf',9,12), ('Es',9,13), ('Fm',9,14), ('Md',9,15), ('No',9,16), ('Lr',9,17),
+        ]
+        for symbol, row, col in elements:
+            b = QPushButton(symbol)
+            b.setFixedSize(40,40)
+
+            # Prefer saved user override (from parent.settings), otherwise use CPK_COLORS
+            try:
+                overrides = parent.settings.get('cpk_colors', {}) if parent and hasattr(parent, 'settings') else {}
+                override = overrides.get(symbol)
+            except Exception:
+                override = None
+            q_color = QColor(override) if override else CPK_COLORS.get(symbol, CPK_COLORS['DEFAULT'])
+
+            # 背景色の輝度を計算して、文字色を黒か白に決定
+            # 輝度 = (R*299 + G*587 + B*114) / 1000
+            brightness = (q_color.red() * 299 + q_color.green() * 587 + q_color.blue() * 114) / 1000
+            text_color = "white" if brightness < 128 else "black"
+
+            # ボタンのスタイルシートを設定
+            b.setStyleSheet(
+                f"background-color: {q_color.name()};"
+                f"color: {text_color};"
+                "border: 1px solid #555;"
+                "font-weight: bold;"
+            )
+
+            b.clicked.connect(self.on_button_clicked)
+            layout.addWidget(b, row, col)
+
+    def on_button_clicked(self):
+        b=self.sender()
+        self.element_selected.emit(b.text())
+        self.accept()