MoleditPy 2.2.0a2__py3-none-any.whl → 2.2.1__py3-none-any.whl

moleditpy/plugins/Optimization/conf_search.py

@@ -1,224 +0,0 @@
-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

moleditpy/plugins/Utility/atom_colorizer.py

@@ -1,262 +0,0 @@
-import numpy as np
-import pyvista as pv
-from PyQt6.QtWidgets import (QWidget, QVBoxLayout, QHBoxLayout, QPushButton, 
-                             QLabel, QColorDialog, QDockWidget, QMessageBox, 
-                             QLineEdit, QListWidget, QAbstractItemView, QGroupBox, QDialog)
-from PyQt6.QtGui import QColor, QCloseEvent
-from PyQt6.QtCore import Qt
-import traceback
-import sys
-import os
-import json
-
-# Try importing from the installed package first (pip package structure)
-try:
-    from moleditpy.modules.constants import CPK_COLORS_PV
-except ImportError:
-    # Fallback to local 'modules' if running from source or sys.path is set that way
-    try:
-        from modules.constants import CPK_COLORS_PV
-    except ImportError:
-        # Final fallback map
-        CPK_COLORS_PV = {}
-
-__version__="2025.12.25"
-__author__="HiroYokoyama"
-
-PLUGIN_NAME = "Atom Colorizer"
-
-class AtomColorizerWindow(QDialog):
-    def __init__(self, main_window):
-        super().__init__(parent=main_window)
-        self.mw = main_window
-        self.plotter = self.mw.plotter
-        
-        # Set window properties for modeless behavior
-        self.setModal(False)
-        self.setWindowTitle(PLUGIN_NAME)
-        self.setWindowFlags(Qt.WindowType.Window) # Ensures it has min/max/close buttons
-        
-        # Initialize current_color as QColor object
-        self.current_color = QColor(255, 0, 0) # Default red
-        
-        self.init_ui()
-        
-        # Auto-enable 3D Selection (Measurement Mode) if not already active
-        try:
-            if hasattr(self.mw, 'measurement_mode') and not self.mw.measurement_mode:
-                if hasattr(self.mw, 'toggle_measurement_mode'):
-                    self.mw.toggle_measurement_mode(True)
-                    # Sync UI button state if possible
-                    if hasattr(self.mw, 'measurement_action'):
-                        self.mw.measurement_action.setChecked(True)
-        except Exception as e:
-            print(f"Failed to auto-enable 3D selection: {e}")
-
-    def init_ui(self):
-        layout = QVBoxLayout()
-        
-        # Information Label
-        info_label = QLabel("Select atoms in the 3D viewer and apply color.")
-        info_label.setWordWrap(True)
-        layout.addWidget(info_label)
-
-        # Selection Group
-        sel_group = QGroupBox("Selection")
-        sel_layout = QVBoxLayout()
-        
-        self.le_indices = QLineEdit()
-        self.le_indices.setPlaceholderText("e.g. 0, 1, 5")
-        sel_layout.addWidget(self.le_indices)
-        
-        # Auto-update timer
-        from PyQt6.QtCore import QTimer
-        self.sel_timer = QTimer(self)
-        self.sel_timer.timeout.connect(self._auto_update_selection)
-        self.sel_timer.start(200) # Check every 200ms
-        
-        sel_group.setLayout(sel_layout)
-        layout.addWidget(sel_group)
-
-        # Color Group
-        col_group = QGroupBox("Color")
-        col_layout = QVBoxLayout()
-        
-        self.btn_color = QPushButton("Choose Color")
-        # Initial style based on self.current_color (QColor object)
-        self.btn_color.setStyleSheet(f"background-color: {self.current_color.name()}; color: {'black' if self.current_color.lightness() > 128 else 'white'};")
-        self.btn_color.clicked.connect(self.choose_color)
-        col_layout.addWidget(self.btn_color)
-        
-        btn_apply = QPushButton("Apply Color")
-        btn_apply.clicked.connect(self.apply_color)
-        col_layout.addWidget(btn_apply)
-        
-        col_group.setLayout(col_layout)
-        layout.addWidget(col_group)
-
-        # Reset Group
-        reset_group = QGroupBox("Reset")
-        reset_layout = QVBoxLayout()
-        
-        btn_reset = QPushButton("Reset to Element Colors")
-        btn_reset.clicked.connect(self.reset_colors)
-        reset_layout.addWidget(btn_reset)
-        
-        reset_group.setLayout(reset_layout)
-        layout.addWidget(reset_group)
-        
-        layout.addStretch()
-        
-        # Close Button
-        close_btn = QPushButton("Close")
-        close_btn.clicked.connect(self.close)
-        layout.addWidget(close_btn)
-
-        self.setLayout(layout)
-        
-        # Resize window to a reasonable default
-        self.resize(300, 400)
-
-    def get_selection_from_viewer(self):
-        """
-        Get selected atom indices from the main window.
-        Only checks 3D selection and Measurement selection. 2D selection is ignored per request.
-        """
-        indices = set()
-        
-        # 1. Check direct 3D selection (e.g. from 3D Drag or specific 3D select tools)
-        if hasattr(self.mw, 'selected_atoms_3d') and self.mw.selected_atoms_3d:
-            indices.update(self.mw.selected_atoms_3d)
-
-        # 2. Check measurement selection (commonly used for picking atoms in 3D)
-        if hasattr(self.mw, 'selected_atoms_for_measurement') and self.mw.selected_atoms_for_measurement:
-             # selected_atoms_for_measurement might be list of int or objects, typically ints in this internal API
-             for item in self.mw.selected_atoms_for_measurement:
-                 if isinstance(item, int):
-                     indices.add(item)
-
-        # Update the line edit
-        sorted_indices = sorted(list(indices))
-        new_text = ",".join(map(str, sorted_indices))
-        if self.le_indices.text() != new_text:
-             self.le_indices.setText(new_text)
-
-    def _auto_update_selection(self):
-        """Timer slot to auto-update selection."""
-        if self.le_indices.hasFocus():
-            return
-        self.get_selection_from_viewer()
-
-    def choose_color(self):
-        c = QColorDialog.getColor(initial=self.current_color, title="Select Color")
-        if c.isValid():
-            self.current_color = c
-            # Update button style
-            self.btn_color.setStyleSheet(f"background-color: {c.name()}; color: {'black' if c.lightness() > 128 else 'white'};")
-
-    def apply_color(self):
-        txt = self.le_indices.text().strip()
-        if not txt:
-            QMessageBox.warning(self, "Warning", "No atoms selected. Please select atoms in the 3D viewer first.")
-            return
-
-        try:
-            str_indices = [x.strip() for x in txt.split(',') if x.strip()]
-            target_indices = [int(x) for x in str_indices]
-        except ValueError:
-            QMessageBox.warning(self, "Error", "Invalid indices format.")
-            return
-
-        if not self.mw.current_mol:
-            QMessageBox.warning(self, "Error", "No molecule loaded.")
-            return
-
-        try:
-            # Use the API to set atom colors
-            hex_color = self.current_color.name()
-            
-            for idx in target_indices:
-                if 0 <= idx < self.mw.current_mol.GetNumAtoms():
-                    # Access via main_window_view_3d proxy
-                    if hasattr(self.mw, 'main_window_view_3d'):
-                        self.mw.main_window_view_3d.update_atom_color_override(idx, hex_color)
-                    else:
-                         # Fallback if unproxied (unlikely in this architecture)
-                         pass
-                    
-        except Exception as e:
-            QMessageBox.critical(self, "Error", f"Failed to apply color: {e}")
-            traceback.print_exc()
-
-    def reset_colors(self):
-        if not self.mw.current_mol:
-            return
-
-        try:
-            # Clear all color overrides using the API
-            for i in range(self.mw.current_mol.GetNumAtoms()):
-                if hasattr(self.mw, 'main_window_view_3d'):
-                    self.mw.main_window_view_3d.update_atom_color_override(i, None)
-                
-        except Exception as e:
-            QMessageBox.critical(self, "Error", f"Failed to reset colors: {e}")
-
-
-# Global reference to keep window alive
-_atom_colorizer_window = None
-
-def run(mw):
-    global _atom_colorizer_window
-    
-    # Check if window already exists
-    if _atom_colorizer_window is None:
-        _atom_colorizer_window = AtomColorizerWindow(mw)
-        # Handle cleanup when window is closed
-        _atom_colorizer_window.finished.connect(lambda: _cleanup_window())
-    
-    _atom_colorizer_window.show()
-    _atom_colorizer_window.raise_()
-    _atom_colorizer_window.activateWindow()
-
-def _cleanup_window():
-    global _atom_colorizer_window
-    _atom_colorizer_window = None
-
-
-def initialize(context):
-    """
-    Register plugin save/load handlers for persistence.
-    """
-    mw = context.get_main_window()
-    
-    def save_handler():
-        """Save color overrides to project file."""
-        # _plugin_color_overrides is stored on the MainWindow instance by the API
-        if not hasattr(mw, '_plugin_color_overrides'):
-            return {}
-        
-        # Convert color overrides to JSON-serializable format
-        return {
-            "atom_colors": {str(k): v for k, v in mw._plugin_color_overrides.items()}
-        }
-    
-    def load_handler(data):
-        """Load color overrides from project file."""
-        if not data:
-            return
-        
-        atom_colors = data.get("atom_colors", {})
-        
-        # Restore color overrides using the API
-        if hasattr(mw, 'main_window_view_3d'):
-            for atom_idx_str, hex_color in atom_colors.items():
-                try:
-                    atom_idx = int(atom_idx_str)
-                    mw.main_window_view_3d.update_atom_color_override(atom_idx, hex_color)
-                except Exception as e:
-                    print(f"Failed to restore color for atom {atom_idx_str}: {e}")
-    
-    # Register handlers
-    context.register_save_handler(save_handler)
-    context.register_load_handler(load_handler)

moleditpy/plugins/Utility/console.py

@@ -1,163 +0,0 @@
-import sys
-import io
-import code
-import traceback
-from contextlib import redirect_stdout, redirect_stderr
-from PyQt6.QtWidgets import (
-    QDialog, QVBoxLayout, QTextEdit, QLineEdit, 
-    QPushButton, QLabel, QWidget
-)
-from PyQt6.QtGui import QFont, QColor
-from PyQt6.QtCore import Qt
-import rdkit.Chem as Chem
-
-__version__="2025.12.25"
-__author__="HiroYokoyama"
-PLUGIN_NAME = "Python Console"
-
-class HistoryLineEdit(QLineEdit):
-    def __init__(self, parent=None):
-        super().__init__(parent)
-        self.history = []
-        self.history_index = 0
-    
-    def append_history(self, text):
-        if text and (not self.history or self.history[-1] != text):
-            self.history.append(text)
-        self.history_index = len(self.history)
-    
-    def keyPressEvent(self, event):
-        if event.key() == Qt.Key.Key_Up:
-            if self.history_index > 0:
-                self.history_index -= 1
-                self.setText(self.history[self.history_index])
-        elif event.key() == Qt.Key.Key_Down:
-            if self.history_index < len(self.history) - 1:
-                self.history_index += 1
-                self.setText(self.history[self.history_index])
-            else:
-                self.history_index = len(self.history)
-                self.clear()
-        else:
-            super().keyPressEvent(event)
-
-class PythonConsoleDialog(QDialog):
-    def __init__(self, main_window):
-        super().__init__(main_window)
-        self.main_window = main_window
-        self.setWindowTitle("MoleditPy Python Console")
-        self.resize(600, 400)
-        
-        # UI Setup
-        layout = QVBoxLayout()
-        
-        # Output Area (Log)
-        self.output_area = QTextEdit()
-        self.output_area.setReadOnly(True)
-        self.output_area.setStyleSheet("background-color: #1e1e1e; color: #dcdcdc;")
-        self.output_area.setFont(QFont("Consolas", 10))
-        layout.addWidget(self.output_area)
-        
-        # Input Area with History
-        self.input_line = HistoryLineEdit()
-        self.input_line.setPlaceholderText("Enter Python code...")
-        self.input_line.setStyleSheet("background-color: #2d2d2d; color: #ffffff; border: 1px solid #3e3e3e;")
-        self.input_line.setFont(QFont("Consolas", 10))
-        self.input_line.returnPressed.connect(self.run_code)
-        layout.addWidget(self.input_line)
-        
-        # Help Label
-        help_text = QLabel("Available vars: 'mw' (MainWindow), 'mol' (current_mol), 'Chem' (rdkit.Chem)")
-        help_text.setStyleSheet("color: gray; font-size: 10px;")
-        layout.addWidget(help_text)
-
-        self.setLayout(layout)
-        
-        # Initialize execution environment (namespace)
-        self.local_scope = {
-            'mw': self.main_window,
-            'Chem': Chem,
-            'mol': self._get_best_mol(),
-        }
-
-        # Initialize Interpreter
-        self.interpreter = code.InteractiveInterpreter(self.local_scope)
-
-        self.append_output("MoleditPy Console Ready.")
-        self.append_output(">>> Type commands and press Enter.")
-
-    def _get_best_mol(self):
-        """Helper to get the most relevant RDKit molecule object.
-        """
-        mol = getattr(self.main_window, 'current_mol', None)
-
-        return mol
-
-    def append_output(self, text, color=None):
-        if color:
-            self.output_area.append(f"<span style='color: {color};'>{text}</span>")
-        else:
-            self.output_area.append(text)
-
-    def run_code(self):
-        command = self.input_line.text()
-        if not command:
-            return
-
-        # Handle History
-        self.input_line.append_history(command)
-        self.input_line.clear()
-
-        # Display Input
-        self.append_output(f">>> {command}", color="#4CAF50")
-        
-        # Sync variables
-        self.local_scope['mol'] = self._get_best_mol()
-        
-        if self.local_scope['mol'] is None:
-             # Optional: warn user if they try to use 'mol' and it's still None
-             # but only if 'mol' appears in command to avoid spam
-             if 'mol' in command:
-                 print("Warning: 'mol' is None (no valid 2D or 3D structure found).")
-
-        # Capture Output
-        stdout_capture = io.StringIO()
-        stderr_capture = io.StringIO()
-
-        try:
-            with redirect_stdout(stdout_capture), redirect_stderr(stderr_capture):
-                # runsource handles compilation and syntax errors.
-                # It returns True if more input is needed (incomplete code), which we can handle or just report.
-                more = self.interpreter.runsource(command, "<console>", "single")
-                
-                if more:
-                    print("(Incomplete input - multiline not fully supported yet)")
-        except Exception:
-            # This catches errors OUTSIDE runsource's internal handling if any
-            traceback.print_exc(file=stderr_capture)
-
-        # Process Captured Output
-        out_str = stdout_capture.getvalue()
-        err_str = stderr_capture.getvalue()
-
-        if out_str:
-            self.output_area.append(out_str.strip())
-        if err_str:
-            self.append_output(err_str.strip(), color="#FF5252")
-
-        # Refresh UI if needed
-        # If the user modified 'mol', we might want to push it back?
-        # For now, read-only assumption for simpler integration, 
-        # but if they modify 'mw.data' directly, we might need a refresh.
-        pass
-
-# Plugin Entry Point
-def run(mw):
-    if not hasattr(mw, 'python_console_dialog'):
-        mw.python_console_dialog = PythonConsoleDialog(mw)
-    
-    mw.python_console_dialog.show()
-    mw.python_console_dialog.raise_()
-    mw.python_console_dialog.activateWindow()
-
-# initialize removed as it only registered the menu action