MoleditPy-linux 2.4.1__py3-none-any.whl

moleditpy_linux/modules/angle_dialog.py

@@ -0,0 +1,440 @@
+#!/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, QHBoxLayout, QPushButton, QLineEdit, QWidget, QRadioButton
+)
+
+try:
+    from .dialog3_d_picking_mixin import Dialog3DPickingMixin
+except Exception:
+    from modules.dialog3_d_picking_mixin import Dialog3DPickingMixin
+
+from PyQt6.QtCore import Qt
+from PyQt6.QtWidgets import QMessageBox
+import numpy as np
+
+
+class AngleDialog(Dialog3DPickingMixin, QDialog):
+    def __init__(self, mol, main_window, preselected_atoms=None, parent=None):
+        QDialog.__init__(self, parent)
+        Dialog3DPickingMixin.__init__(self)
+        self.mol = mol
+        self.main_window = main_window
+        self.atom1_idx = None
+        self.atom2_idx = None  # vertex atom
+        self.atom3_idx = None
+        
+        # 事前選択された原子を設定
+        if preselected_atoms and len(preselected_atoms) >= 3:
+            self.atom1_idx = preselected_atoms[0]
+            self.atom2_idx = preselected_atoms[1]  # vertex
+            self.atom3_idx = preselected_atoms[2]
+        
+        self.init_ui()
+    
+    def init_ui(self):
+        self.setWindowTitle("Adjust Angle")
+        self.setModal(False)  # モードレスにしてクリックを阻害しない
+  # 常に前面表示
+        layout = QVBoxLayout(self)
+        
+        # Instructions
+        instruction_label = QLabel("Click three atoms in order: first-vertex-third. The angle around the vertex atom will be adjusted.")
+        instruction_label.setWordWrap(True)
+        layout.addWidget(instruction_label)
+        
+        # Selected atoms display
+        self.selection_label = QLabel("No atoms selected")
+        layout.addWidget(self.selection_label)
+        
+        # Current angle display
+        self.angle_label = QLabel("")
+        layout.addWidget(self.angle_label)
+        
+        # New angle input
+        angle_layout = QHBoxLayout()
+        angle_layout.addWidget(QLabel("New angle (degrees):"))
+        self.angle_input = QLineEdit()
+        self.angle_input.setPlaceholderText("109.5")
+        angle_layout.addWidget(self.angle_input)
+        layout.addLayout(angle_layout)
+        
+        # Movement options
+        group_box = QWidget()
+        group_layout = QVBoxLayout(group_box)
+        group_layout.addWidget(QLabel("Rotation Options:"))
+        
+        self.rotate_group_radio = QRadioButton("Atom 1,2: Fixed, Atom 3: Rotate connected group")
+        self.rotate_group_radio.setChecked(True)
+        group_layout.addWidget(self.rotate_group_radio)
+
+        self.rotate_atom_radio = QRadioButton("Atom 1,2: Fixed, Atom 3: Rotate atom only")
+        group_layout.addWidget(self.rotate_atom_radio)
+        
+        self.both_groups_radio = QRadioButton("Vertex fixed: Both arms rotate equally")
+        group_layout.addWidget(self.both_groups_radio)
+    
+        
+        layout.addWidget(group_box)
+        
+        # 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()
+        
+        self.apply_button = QPushButton("Apply")
+        self.apply_button.clicked.connect(self.apply_changes)
+        self.apply_button.setEnabled(False)
+        button_layout.addWidget(self.apply_button)
+        
+        close_button = QPushButton("Close")
+        close_button.clicked.connect(self.reject)
+        button_layout.addWidget(close_button)
+        
+        layout.addLayout(button_layout)
+        
+        # Connect to main window's picker for AngleDialog
+        self.picker_connection = None
+        self.enable_picking()
+        
+        # 事前選択された原子がある場合は初期表示を更新
+        if self.atom1_idx is not None:
+            self.show_atom_labels()
+            self.update_display()
+    
+    def on_atom_picked(self, atom_idx):
+        """原子がピックされたときの処理"""
+        if self.atom1_idx is None:
+            self.atom1_idx = atom_idx
+        elif self.atom2_idx is None:
+            self.atom2_idx = atom_idx
+        elif self.atom3_idx is None:
+            self.atom3_idx = atom_idx
+        else:
+            # Reset and start over
+            self.atom1_idx = atom_idx
+            self.atom2_idx = None
+            self.atom3_idx = None
+        
+        # 原子ラベルを表示
+        self.show_atom_labels()
+        self.update_display()
+    
+    def keyPressEvent(self, event):
+        """キーボードイベントを処理"""
+        if event.key() == Qt.Key.Key_Return or event.key() == Qt.Key.Key_Enter:
+            if self.apply_button.isEnabled():
+                self.apply_changes()
+            event.accept()
+        else:
+            super().keyPressEvent(event)
+    
+    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()
+        super().closeEvent(event)
+    
+    def reject(self):
+        """キャンセル時の処理"""
+        self.clear_atom_labels()
+        self.disable_picking()
+        super().reject()
+    
+    def accept(self):
+        """OK時の処理"""
+        self.clear_atom_labels()
+        self.disable_picking()
+        super().accept()
+    
+    def clear_selection(self):
+        """選択をクリア"""
+        self.atom1_idx = None
+        self.atom2_idx = None  # vertex atom
+        self.atom3_idx = None
+        self.clear_selection_labels()
+        self.update_display()
+    
+    def show_atom_labels(self):
+        """選択された原子にラベルを表示"""
+        # 既存のラベルをクリア
+        self.clear_atom_labels()
+        
+        # 新しいラベルを表示
+        if not hasattr(self, 'selection_labels'):
+            self.selection_labels = []
+        
+        selected_atoms = [self.atom1_idx, self.atom2_idx, self.atom3_idx]
+        labels = ["1st", "2nd (vertex)", "3rd"]
+        colors = ["yellow", "yellow", "yellow"]  # 全て黄色に統一
+        
+        for i, atom_idx in enumerate(selected_atoms):
+            if atom_idx is not None:
+                pos = self.main_window.atom_positions_3d[atom_idx]
+                label_text = f"{labels[i]}"
+                
+                # ラベルを追加
+                label_actor = self.main_window.plotter.add_point_labels(
+                    [pos], [label_text], 
+                    point_size=20, 
+                    font_size=12,
+                    text_color=colors[i],
+                    always_visible=True
+                )
+                self.selection_labels.append(label_actor)
+    
+    def clear_atom_labels(self):
+        """原子ラベルをクリア"""
+        if hasattr(self, 'selection_labels'):
+            for label_actor in self.selection_labels:
+                try:
+                    self.main_window.plotter.remove_actor(label_actor)
+                except Exception:
+                    pass
+            self.selection_labels = []
+    
+    def clear_selection_labels(self):
+        """選択ラベルをクリア"""
+        if hasattr(self, 'selection_labels'):
+            for label_actor in self.selection_labels:
+                try:
+                    self.main_window.plotter.remove_actor(label_actor)
+                except Exception:
+                    pass
+            self.selection_labels = []
+    
+    def add_selection_label(self, atom_idx, label_text):
+        """選択された原子にラベルを追加"""
+        if not hasattr(self, 'selection_labels'):
+            self.selection_labels = []
+        
+        # 原子の位置を取得
+        pos = self.main_window.atom_positions_3d[atom_idx]
+        
+        # ラベルを追加
+        label_actor = self.main_window.plotter.add_point_labels(
+            [pos], [label_text], 
+            point_size=20, 
+            font_size=12,
+            text_color='yellow',
+            always_visible=True
+        )
+        self.selection_labels.append(label_actor)
+    
+    def update_display(self):
+        """表示を更新"""
+        # 既存のラベルをクリア
+        self.clear_selection_labels()
+        
+        if self.atom1_idx is None:
+            self.selection_label.setText("No atoms selected")
+            self.angle_label.setText("")
+            self.apply_button.setEnabled(False)
+            # Clear angle input when no selection
+            try:
+                self.angle_input.clear()
+            except Exception:
+                pass
+        elif self.atom2_idx is None:
+            symbol1 = self.mol.GetAtomWithIdx(self.atom1_idx).GetSymbol()
+            self.selection_label.setText(f"First atom: {symbol1} (index {self.atom1_idx})")
+            self.angle_label.setText("")
+            self.apply_button.setEnabled(False)
+            # ラベル追加
+            self.add_selection_label(self.atom1_idx, "1")
+            # Clear angle input while selection is incomplete
+            try:
+                self.angle_input.clear()
+            except Exception:
+                pass
+        elif self.atom3_idx is None:
+            symbol1 = self.mol.GetAtomWithIdx(self.atom1_idx).GetSymbol()
+            symbol2 = self.mol.GetAtomWithIdx(self.atom2_idx).GetSymbol()
+            self.selection_label.setText(f"Selected: {symbol1}({self.atom1_idx}) - {symbol2}({self.atom2_idx}) - ?")
+            self.angle_label.setText("")
+            self.apply_button.setEnabled(False)
+            # ラベル追加
+            self.add_selection_label(self.atom1_idx, "1")
+            self.add_selection_label(self.atom2_idx, "2(vertex)")
+            # Clear angle input while selection is incomplete
+            try:
+                self.angle_input.clear()
+            except Exception:
+                pass
+        else:
+            symbol1 = self.mol.GetAtomWithIdx(self.atom1_idx).GetSymbol()
+            symbol2 = self.mol.GetAtomWithIdx(self.atom2_idx).GetSymbol()
+            symbol3 = self.mol.GetAtomWithIdx(self.atom3_idx).GetSymbol()
+            self.selection_label.setText(f"Angle: {symbol1}({self.atom1_idx}) - {symbol2}({self.atom2_idx}) - {symbol3}({self.atom3_idx})")
+            
+            # Calculate current angle
+            current_angle = self.calculate_angle()
+            self.angle_label.setText(f"Current angle: {current_angle:.2f}°")
+            self.apply_button.setEnabled(True)
+            # Update angle input box with current angle
+            try:
+                self.angle_input.setText(f"{current_angle:.2f}")
+            except Exception:
+                pass
+            # ラベル追加
+            self.add_selection_label(self.atom1_idx, "1")
+            self.add_selection_label(self.atom2_idx, "2(vertex)")
+            self.add_selection_label(self.atom3_idx, "3")
+    
+    def calculate_angle(self):
+        """現在の角度を計算"""
+        conf = self.mol.GetConformer()
+        pos1 = np.array(conf.GetAtomPosition(self.atom1_idx))
+        pos2 = np.array(conf.GetAtomPosition(self.atom2_idx))  # vertex
+        pos3 = np.array(conf.GetAtomPosition(self.atom3_idx))
+        
+        vec1 = pos1 - pos2
+        vec2 = pos3 - pos2
+        
+        cos_angle = np.dot(vec1, vec2) / (np.linalg.norm(vec1) * np.linalg.norm(vec2))
+        cos_angle = np.clip(cos_angle, -1.0, 1.0)
+        angle_rad = np.arccos(cos_angle)
+        return np.degrees(angle_rad)
+    
+    def apply_changes(self):
+        """変更を適用"""
+        if self.atom1_idx is None or self.atom2_idx is None or self.atom3_idx is None:
+            return
+        
+        try:
+            new_angle = float(self.angle_input.text())
+            if new_angle < 0 or new_angle >= 360:
+                QMessageBox.warning(self, "Invalid Input", "Angle must be between 0 and 360 degrees.")
+                return
+        except ValueError:
+            QMessageBox.warning(self, "Invalid Input", "Please enter a valid number.")
+            return
+        
+        # Undo状態を保存
+        self.main_window.push_undo_state()
+        
+        # Apply the angle change
+        self.adjust_angle(new_angle)
+        
+        # キラルラベルを更新
+        self.main_window.update_chiral_labels()
+    
+    def adjust_angle(self, new_angle_deg):
+        """角度を調整（均等回転オプション付き）"""
+        conf = self.mol.GetConformer()
+        pos1 = np.array(conf.GetAtomPosition(self.atom1_idx))
+        pos2 = np.array(conf.GetAtomPosition(self.atom2_idx))  # vertex
+        pos3 = np.array(conf.GetAtomPosition(self.atom3_idx))
+        
+        vec1 = pos1 - pos2
+        vec2 = pos3 - pos2
+        
+        # Current angle
+        current_angle_rad = np.arccos(np.clip(
+            np.dot(vec1, vec2) / (np.linalg.norm(vec1) * np.linalg.norm(vec2)), -1.0, 1.0))
+        
+        # Target angle
+        target_angle_rad = np.radians(new_angle_deg)
+        
+        # Rotation axis (perpendicular to the plane containing vec1 and vec2)
+        rotation_axis = np.cross(vec1, vec2)
+        rotation_axis_norm = np.linalg.norm(rotation_axis)
+        
+        if rotation_axis_norm == 0:
+            # Vectors are parallel, cannot rotate
+            return
+        
+        rotation_axis = rotation_axis / rotation_axis_norm
+        
+        # Total rotation angle needed
+        total_rotation_angle = target_angle_rad - current_angle_rad
+        
+        # Rodrigues' rotation formula
+        def rotate_vector(v, axis, angle):
+            cos_a = np.cos(angle)
+            sin_a = np.sin(angle)
+            return v * cos_a + np.cross(axis, v) * sin_a + axis * np.dot(axis, v) * (1 - cos_a)
+        
+        if self.both_groups_radio.isChecked():
+            # Both arms rotate equally (half angle each in opposite directions)
+            half_rotation = total_rotation_angle / 2
+            
+            # Get both connected groups
+            group1_atoms = self.get_connected_group(self.atom1_idx, exclude=self.atom2_idx)
+            group3_atoms = self.get_connected_group(self.atom3_idx, exclude=self.atom2_idx)
+            
+            # Rotate group 1 by -half_rotation
+            for atom_idx in group1_atoms:
+                current_pos = np.array(conf.GetAtomPosition(atom_idx))
+                relative_pos = current_pos - pos2
+                rotated_pos = rotate_vector(relative_pos, rotation_axis, -half_rotation)
+                new_pos = pos2 + rotated_pos
+                conf.SetAtomPosition(atom_idx, new_pos.tolist())
+                self.main_window.atom_positions_3d[atom_idx] = new_pos
+            
+            # Rotate group 3 by +half_rotation
+            for atom_idx in group3_atoms:
+                current_pos = np.array(conf.GetAtomPosition(atom_idx))
+                relative_pos = current_pos - pos2
+                rotated_pos = rotate_vector(relative_pos, rotation_axis, half_rotation)
+                new_pos = pos2 + rotated_pos
+                conf.SetAtomPosition(atom_idx, new_pos.tolist())
+                self.main_window.atom_positions_3d[atom_idx] = new_pos
+                
+        elif self.rotate_atom_radio.isChecked():
+            # Move only the third atom
+            new_vec2 = rotate_vector(vec2, rotation_axis, total_rotation_angle)
+            new_pos3 = pos2 + new_vec2
+            conf.SetAtomPosition(self.atom3_idx, new_pos3.tolist())
+            self.main_window.atom_positions_3d[self.atom3_idx] = new_pos3
+        else:
+            # Rotate the connected group around atom2 (vertex) - default behavior
+            atoms_to_move = self.get_connected_group(self.atom3_idx, exclude=self.atom2_idx)
+            
+            for atom_idx in atoms_to_move:
+                current_pos = np.array(conf.GetAtomPosition(atom_idx))
+                # Transform to coordinate system centered at atom2
+                relative_pos = current_pos - pos2
+                # Rotate around the rotation axis
+                rotated_pos = rotate_vector(relative_pos, rotation_axis, total_rotation_angle)
+                # Transform back to world coordinates
+                new_pos = pos2 + rotated_pos
+                conf.SetAtomPosition(atom_idx, new_pos.tolist())
+                self.main_window.atom_positions_3d[atom_idx] = new_pos
+        
+        # Update the 3D view
+        self.main_window.draw_molecule_3d(self.mol)
+    
+    def get_connected_group(self, start_atom, exclude=None):
+        """指定された原子から連結されているグループを取得"""
+        visited = set()
+        to_visit = [start_atom]
+        
+        while to_visit:
+            current = to_visit.pop()
+            if current in visited or current == exclude:
+                continue
+            
+            visited.add(current)
+            
+            # Get neighboring atoms
+            atom = self.mol.GetAtomWithIdx(current)
+            for bond in atom.GetBonds():
+                other_idx = bond.GetOtherAtomIdx(current)
+                if other_idx not in visited and other_idx != exclude:
+                    to_visit.append(other_idx)
+        
+        return visited