MoleditPy-linux 2.2.4__py3-none-any.whl

moleditpy_linux/modules/custom_qt_interactor.py

@@ -0,0 +1,59 @@
+#!/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 pyvistaqt import QtInteractor
+
+
+class CustomQtInteractor(QtInteractor):
+    def __init__(self, parent=None, main_window=None, **kwargs):
+        super().__init__(parent, **kwargs)
+        self.main_window = main_window
+        # Track recent clicks so we can detect and swallow triple-clicks
+        # Triple-clicks are not a distinct Qt event on all platforms, so we
+        # implement a small timing-based counter here and accept the event
+        # when 3 rapid clicks are detected to prevent them from reaching
+        # the VTK interactor and causing unexpected behaviour in the 3D view.
+        self._last_click_time = 0.0
+        self._click_count = 0
+
+    def wheelEvent(self, event):
+        """
+        マウスホイールイベントをオーバーライドする。
+        """
+        # 最初に親クラスのイベントを呼び、通常のズーム処理を実行させる
+        super().wheelEvent(event)
+        
+        # ズーム処理の完了後、2Dビューにフォーカスを強制的に戻す
+        if self.main_window and hasattr(self.main_window, 'view_2d'):
+            self.main_window.view_2d.setFocus()
+
+    def mouseReleaseEvent(self, event):
+        """
+        Qtのマウスリリースイベントをオーバーライドし、
+        3Dビューでの全ての操作完了後に2Dビューへフォーカスを戻す。
+        """
+        super().mouseReleaseEvent(event) # 親クラスのイベントを先に処理
+        if self.main_window and hasattr(self.main_window, 'view_2d'):
+            self.main_window.view_2d.setFocus()
+
+    def mouseDoubleClickEvent(self, event):
+        """Ignore mouse double-clicks on the 3D widget to avoid accidental actions.
+
+        Swallow the double-click event so it doesn't trigger selection, editing,
+        or camera jumps. We intentionally do not call the superclass handler.
+        """
+        try:
+            # Accept the event to mark it handled and prevent further processing.
+            event.accept()
+        except Exception:
+            # If event doesn't support accept for some reason, just return.
+            return

moleditpy_linux/modules/dialog3_d_picking_mixin.py

@@ -0,0 +1,108 @@
+#!/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.QtCore import Qt, QEvent
+import numpy as np
+try:
+    from .constants import pt
+except Exception:
+    from modules.constants import pt
+
+
+class Dialog3DPickingMixin:
+    """3D原子選択のための共通機能を提供するMixin"""
+    
+    def __init__(self):
+        """Mixinの初期化"""
+        self.picking_enabled = False
+    
+    def eventFilter(self, obj, event):
+        """3Dビューでのマウスクリックをキャプチャする（元の3D editロジックを正確に再現）"""
+        if (obj == self.main_window.plotter.interactor and 
+            event.type() == QEvent.Type.MouseButtonPress and 
+            event.button() == Qt.MouseButton.LeftButton):
+            
+            try:
+                # VTKイベント座標を取得（元のロジックと同じ）
+                interactor = self.main_window.plotter.interactor
+                click_pos = interactor.GetEventPosition()
+                picker = self.main_window.plotter.picker
+                picker.Pick(click_pos[0], click_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)
+
+                    # 範囲チェックを追加
+                    if 0 <= closest_atom_idx < self.mol.GetNumAtoms():
+                        # クリック閾値チェック（元のロジックと同じ）
+                        atom = self.mol.GetAtomWithIdx(int(closest_atom_idx))
+                        if atom:
+                            atomic_num = atom.GetAtomicNum()
+                            vdw_radius = pt.GetRvdw(atomic_num)
+                            click_threshold = vdw_radius * 1.5
+
+                            if distances[closest_atom_idx] < click_threshold:
+                                # We handled the pick (atom clicked) -> consume the event so
+                                # other UI elements (including the VTK interactor observers)
+                                # don't also process it. Set a flag on the main window so
+                                # the VTK-based handlers can ignore the same logical click
+                                # when it arrives via the VTK event pipeline.
+                                try:
+                                    self.main_window._picking_consumed = True
+                                except Exception:
+                                    pass
+                                self.on_atom_picked(int(closest_atom_idx))
+                                return True
+                
+                # 原子以外をクリックした場合は選択をクリア（Measurementモードと同じロジック）
+                if hasattr(self, 'clear_selection'):
+                    self.clear_selection()
+                # We did not actually pick an atom; do NOT consume the event here so
+                # the interactor and CustomInteractorStyle can handle camera rotation
+                # and other behaviors. Returning False (or calling the base
+                # implementation) allows normal processing to continue.
+                return False
+                    
+            except Exception as e:
+                print(f"Error in eventFilter: {e}")
+                # On exception, don't swallow the event either — let the normal
+                # event pipeline continue so the UI remains responsive.
+                return False
+
+        return super().eventFilter(obj, event)
+    
+    def enable_picking(self):
+        """3Dビューでの原子選択を有効にする"""
+        self.main_window.plotter.interactor.installEventFilter(self)
+        self.picking_enabled = True
+        # Ensure the main window flag exists
+        try:
+            self.main_window._picking_consumed = False
+        except Exception:
+            pass
+    
+    def disable_picking(self):
+        """3Dビューでの原子選択を無効にする"""
+        if hasattr(self, 'picking_enabled') and self.picking_enabled:
+            self.main_window.plotter.interactor.removeEventFilter(self)
+            self.picking_enabled = False
+        try:
+            # Clear any leftover flag when picking is disabled
+            if hasattr(self.main_window, '_picking_consumed'):
+                self.main_window._picking_consumed = False
+        except Exception:
+            pass
+    
+    def try_alternative_picking(self, x, y):
+        """代替のピッキング方法（使用しない）"""

moleditpy_linux/modules/dihedral_dialog.py

@@ -0,0 +1,443 @@
+#!/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
+import numpy as np
+from PyQt6.QtWidgets import QMessageBox
+
+
+class DihedralDialog(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  # central bond start
+        self.atom3_idx = None  # central bond end
+        self.atom4_idx = None
+        
+        # 事前選択された原子を設定
+        if preselected_atoms and len(preselected_atoms) >= 4:
+            self.atom1_idx = preselected_atoms[0]
+            self.atom2_idx = preselected_atoms[1]  # central bond start
+            self.atom3_idx = preselected_atoms[2]  # central bond end
+            self.atom4_idx = preselected_atoms[3]
+        
+        self.init_ui()
+    
+    def init_ui(self):
+        self.setWindowTitle("Adjust Dihedral Angle")
+        self.setModal(False)  # モードレスにしてクリックを阻害しない
+        self.setWindowFlags(Qt.WindowType.Window | Qt.WindowType.WindowStaysOnTopHint)  # 常に前面表示
+        layout = QVBoxLayout(self)
+        
+        # Instructions
+        instruction_label = QLabel("Click four atoms in order to define a dihedral angle. The rotation will be around the bond between the 2nd and 3rd atoms.")
+        instruction_label.setWordWrap(True)
+        layout.addWidget(instruction_label)
+        
+        # Selected atoms display
+        self.selection_label = QLabel("No atoms selected")
+        layout.addWidget(self.selection_label)
+        
+        # Current dihedral angle display
+        self.dihedral_label = QLabel("")
+        layout.addWidget(self.dihedral_label)
+        
+        # New dihedral angle input
+        dihedral_layout = QHBoxLayout()
+        dihedral_layout.addWidget(QLabel("New dihedral angle (degrees):"))
+        self.dihedral_input = QLineEdit()
+        self.dihedral_input.setPlaceholderText("180.0")
+        dihedral_layout.addWidget(self.dihedral_input)
+        layout.addLayout(dihedral_layout)
+        
+        # Movement options
+        group_box = QWidget()
+        group_layout = QVBoxLayout(group_box)
+        group_layout.addWidget(QLabel("Move:"))
+        
+        self.move_group_radio = QRadioButton("Atom 1,2,3: Fixed, Atom 4 group: Rotate")
+        self.move_group_radio.setChecked(True)
+        group_layout.addWidget(self.move_group_radio)
+        
+        self.move_atom_radio = QRadioButton("Atom 1,2,3: Fixed, Atom 4: Rotate atom only")
+        group_layout.addWidget(self.move_atom_radio)
+        
+        self.both_groups_radio = QRadioButton("Central bond fixed: Both groups 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 DihedralDialog
+        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
+        elif self.atom4_idx is None:
+            self.atom4_idx = atom_idx
+        else:
+            # Reset and start over
+            self.atom1_idx = atom_idx
+            self.atom2_idx = None
+            self.atom3_idx = None
+            self.atom4_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  # central bond start
+        self.atom3_idx = None  # central bond end
+        self.atom4_idx = None
+        self.clear_atom_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, self.atom4_idx]
+        labels = ["1st", "2nd (bond start)", "3rd (bond end)", "4th"]
+        colors = ["yellow", "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 update_display(self):
+        """表示を更新"""
+        selected_count = sum(x is not None for x in [self.atom1_idx, self.atom2_idx, self.atom3_idx, self.atom4_idx])
+        
+        if selected_count == 0:
+            self.selection_label.setText("No atoms selected")
+            self.dihedral_label.setText("")
+            self.apply_button.setEnabled(False)
+            # Clear dihedral input when no selection
+            try:
+                self.dihedral_input.clear()
+            except Exception:
+                pass
+        elif selected_count < 4:
+            selected_atoms = [self.atom1_idx, self.atom2_idx, self.atom3_idx, self.atom4_idx]
+            
+            display_parts = []
+            for atom_idx in selected_atoms:
+                if atom_idx is not None:
+                    symbol = self.mol.GetAtomWithIdx(atom_idx).GetSymbol()
+                    display_parts.append(f"{symbol}({atom_idx})")
+                else:
+                    display_parts.append("?")
+            
+            self.selection_label.setText(" - ".join(display_parts))
+            self.dihedral_label.setText("")
+            self.apply_button.setEnabled(False)
+            # Clear dihedral input while selection is incomplete
+            try:
+                self.dihedral_input.clear()
+            except Exception:
+                pass
+        else:
+            selected_atoms = [self.atom1_idx, self.atom2_idx, self.atom3_idx, self.atom4_idx]
+            
+            display_parts = []
+            for atom_idx in selected_atoms:
+                symbol = self.mol.GetAtomWithIdx(atom_idx).GetSymbol()
+                display_parts.append(f"{symbol}({atom_idx})")
+            
+            self.selection_label.setText(" - ".join(display_parts))
+            
+            # Calculate current dihedral angle
+            current_dihedral = self.calculate_dihedral()
+            self.dihedral_label.setText(f"Current dihedral: {current_dihedral:.2f}°")
+            self.apply_button.setEnabled(True)
+            # Update dihedral input box with current dihedral
+            try:
+                self.dihedral_input.setText(f"{current_dihedral:.2f}")
+            except Exception:
+                pass
+    
+    def calculate_dihedral(self):
+        """現在の二面角を計算（正しい公式を使用）"""
+        conf = self.mol.GetConformer()
+        pos1 = np.array(conf.GetAtomPosition(self.atom1_idx))
+        pos2 = np.array(conf.GetAtomPosition(self.atom2_idx))
+        pos3 = np.array(conf.GetAtomPosition(self.atom3_idx))
+        pos4 = np.array(conf.GetAtomPosition(self.atom4_idx))
+        
+        # Vectors between consecutive atoms
+        v1 = pos2 - pos1  # 1->2
+        v2 = pos3 - pos2  # 2->3 (central bond)
+        v3 = pos4 - pos3  # 3->4
+        
+        # Normalize the central bond vector
+        v2_norm = v2 / np.linalg.norm(v2)
+        
+        # Calculate plane normal vectors
+        n1 = np.cross(v1, v2)  # Normal to plane 1-2-3
+        n2 = np.cross(v2, v3)  # Normal to plane 2-3-4
+        
+        # Normalize the normal vectors
+        n1_norm = np.linalg.norm(n1)
+        n2_norm = np.linalg.norm(n2)
+        
+        if n1_norm == 0 or n2_norm == 0:
+            return 0.0  # Atoms are collinear
+        
+        n1 = n1 / n1_norm
+        n2 = n2 / n2_norm
+        
+        # Calculate the cosine of the dihedral angle
+        cos_angle = np.dot(n1, n2)
+        cos_angle = np.clip(cos_angle, -1.0, 1.0)
+        
+        # Calculate the sine for proper sign determination
+        sin_angle = np.dot(np.cross(n1, n2), v2_norm)
+        
+        # Calculate the dihedral angle with correct sign
+        angle_rad = np.arctan2(sin_angle, cos_angle)
+        return np.degrees(angle_rad)
+    
+    def apply_changes(self):
+        """変更を適用"""
+        if any(idx is None for idx in [self.atom1_idx, self.atom2_idx, self.atom3_idx, self.atom4_idx]):
+            return
+        
+        try:
+            new_dihedral = float(self.dihedral_input.text())
+            if new_dihedral < -180 or new_dihedral > 180:
+                QMessageBox.warning(self, "Invalid Input", "Dihedral angle must be between -180 and 180 degrees.")
+                return
+        except ValueError:
+            QMessageBox.warning(self, "Invalid Input", "Please enter a valid number.")
+            return
+        
+        # Apply the dihedral angle change
+        self.adjust_dihedral(new_dihedral)
+        
+        # キラルラベルを更新
+        self.main_window.update_chiral_labels()
+
+        # Undo状態を保存
+        self.main_window.push_undo_state()
+    
+    def adjust_dihedral(self, new_dihedral_deg):
+        """二面角を調整（改善されたアルゴリズム）"""
+        conf = self.mol.GetConformer()
+        pos1 = np.array(conf.GetAtomPosition(self.atom1_idx))
+        pos2 = np.array(conf.GetAtomPosition(self.atom2_idx))
+        pos3 = np.array(conf.GetAtomPosition(self.atom3_idx))
+        pos4 = np.array(conf.GetAtomPosition(self.atom4_idx))
+        
+        # Current dihedral angle
+        current_dihedral = self.calculate_dihedral()
+        
+        # Calculate rotation angle needed
+        rotation_angle_deg = new_dihedral_deg - current_dihedral
+        
+        # Handle angle wrapping for shortest rotation
+        if rotation_angle_deg > 180:
+            rotation_angle_deg -= 360
+        elif rotation_angle_deg < -180:
+            rotation_angle_deg += 360
+        
+        rotation_angle_rad = np.radians(rotation_angle_deg)
+        
+        # Skip if no rotation needed
+        if abs(rotation_angle_rad) < 1e-6:
+            return
+        
+        # Rotation axis is the bond between atom2 and atom3
+        rotation_axis = pos3 - pos2
+        axis_length = np.linalg.norm(rotation_axis)
+        
+        if axis_length == 0:
+            return  # Atoms are at the same position
+        
+        rotation_axis = rotation_axis / axis_length
+        
+        # Rodrigues' rotation formula implementation
+        def rotate_point_around_axis(point, axis_point, axis_direction, angle):
+            """Rotate a point around an axis using Rodrigues' formula"""
+            # Translate point so axis passes through origin
+            translated_point = point - axis_point
+            
+            # Apply Rodrigues' rotation formula
+            cos_a = np.cos(angle)
+            sin_a = np.sin(angle)
+            
+            rotated = (translated_point * cos_a + 
+                      np.cross(axis_direction, translated_point) * sin_a + 
+                      axis_direction * np.dot(axis_direction, translated_point) * (1 - cos_a))
+            
+            # Translate back to original coordinate system
+            return rotated + axis_point
+        
+        if self.both_groups_radio.isChecked():
+            # Both groups rotate equally around the central bond (half angle each in opposite directions)
+            half_rotation = rotation_angle_rad / 2
+            
+            # Get both connected groups
+            group1_atoms = self.get_connected_group(self.atom2_idx, exclude=self.atom3_idx)
+            group4_atoms = self.get_connected_group(self.atom3_idx, exclude=self.atom2_idx)
+            
+            # Rotate group1 (atom1 side) by -half_rotation
+            for atom_idx in group1_atoms:
+                current_pos = np.array(conf.GetAtomPosition(atom_idx))
+                new_pos = rotate_point_around_axis(current_pos, pos2, rotation_axis, -half_rotation)
+                conf.SetAtomPosition(atom_idx, new_pos.tolist())
+                self.main_window.atom_positions_3d[atom_idx] = new_pos
+            
+            # Rotate group4 (atom4 side) by +half_rotation
+            for atom_idx in group4_atoms:
+                current_pos = np.array(conf.GetAtomPosition(atom_idx))
+                new_pos = rotate_point_around_axis(current_pos, pos2, rotation_axis, half_rotation)
+                conf.SetAtomPosition(atom_idx, new_pos.tolist())
+                self.main_window.atom_positions_3d[atom_idx] = new_pos
+                
+        elif self.move_group_radio.isChecked():
+            # Move the connected group containing atom4
+            # Find all atoms connected to atom3 (excluding atom2 side)
+            atoms_to_rotate = self.get_connected_group(self.atom3_idx, exclude=self.atom2_idx)
+            
+            # Rotate all atoms in the group
+            for atom_idx in atoms_to_rotate:
+                current_pos = np.array(conf.GetAtomPosition(atom_idx))
+                new_pos = rotate_point_around_axis(current_pos, pos2, rotation_axis, rotation_angle_rad)
+                conf.SetAtomPosition(atom_idx, new_pos.tolist())
+                self.main_window.atom_positions_3d[atom_idx] = new_pos
+        else:
+            # Move only atom4
+            new_pos4 = rotate_point_around_axis(pos4, pos2, rotation_axis, rotation_angle_rad)
+            conf.SetAtomPosition(self.atom4_idx, new_pos4.tolist())
+            self.main_window.atom_positions_3d[self.atom4_idx] = new_pos4
+        
+        # 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