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

moleditpy/plugins/Utility/console.py

@@ -0,0 +1,163 @@
+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

moleditpy/plugins/Utility/pubchem_ressolver.py

@@ -0,0 +1,244 @@
+import sys
+import requests # API通信に必要 (pip install requests)
+from PyQt6.QtWidgets import (
+    QDialog, QVBoxLayout, QHBoxLayout, QTableWidget, 
+    QTableWidgetItem, QPushButton, QMessageBox, QLabel, QHeaderView, 
+    QAbstractItemView, QApplication, QLineEdit, QComboBox
+)
+from PyQt6.QtCore import Qt, QPointF
+from rdkit import Chem
+from rdkit.Chem import AllChem
+
+__version__="2025.12.25"
+__author__="HiroYokoyama"
+PLUGIN_NAME = "PubChem Name Resolver"
+
+class MoleculeResolverDialog(QDialog):
+    def __init__(self, main_window, parent=None):
+        super().__init__(parent)
+        self.main_window = main_window
+        self.setWindowTitle("PubChem Name Resolver")
+        self.resize(500, 600)
+        
+        # 取得した候補データのリスト
+        # 各要素は辞書: {'name': str, 'smiles': str, 'formula': str}
+        self.candidates_data = []
+        
+        # 生成されたRDKit分子オブジェクト（一時保存）
+        self.generated_mol = None
+
+        self.init_ui()
+
+    def init_ui(self):
+        layout = QVBoxLayout(self)
+
+        # --- 入力エリア ---
+        input_layout = QHBoxLayout()
+        
+        self.combo_type = QComboBox()
+        self.combo_type.addItems(["Auto (Name/CAS)", "SMILES"])
+        input_layout.addWidget(self.combo_type)
+
+        self.line_input = QLineEdit()
+        self.line_input.setPlaceholderText("Enter Name or SMILES...")
+        self.line_input.returnPressed.connect(self.run_search) # Enterキーで検索
+        input_layout.addWidget(self.line_input)
+        
+        self.btn_search = QPushButton("Search Online")
+        self.btn_search.clicked.connect(self.run_search)
+        input_layout.addWidget(self.btn_search)
+        
+        layout.addLayout(input_layout)
+
+        # --- 説明ラベル ---
+        self.lbl_info = QLabel("Enter a chemical identifier and click Search.")
+        layout.addWidget(self.lbl_info)
+
+        # --- 結果表示用テーブル ---
+        self.table = QTableWidget()
+        self.table.setColumnCount(3)
+        self.table.setHorizontalHeaderLabels(["Name/Synonym", "Formula", "SMILES"])
+        # ヘッダー調整
+        header = self.table.horizontalHeader()
+        header.setSectionResizeMode(0, QHeaderView.ResizeMode.Stretch)
+        header.setSectionResizeMode(1, QHeaderView.ResizeMode.ResizeToContents)
+        header.setSectionResizeMode(2, QHeaderView.ResizeMode.Stretch)
+        
+        self.table.setSelectionBehavior(QAbstractItemView.SelectionBehavior.SelectRows)
+        self.table.setSelectionMode(QAbstractItemView.SelectionMode.SingleSelection)
+        # 選択変更時にロードボタンを有効化するなどの処理を入れるならここ
+        layout.addWidget(self.table)
+
+        # --- ボタンエリア ---
+        btn_layout = QHBoxLayout()
+        
+        self.btn_load = QPushButton("Load to 2D Editor")
+        self.btn_load.clicked.connect(self.load_molecule)
+        
+        self.btn_close = QPushButton("Close")
+        self.btn_close.clicked.connect(self.close)
+
+        btn_layout.addWidget(self.btn_load)
+        btn_layout.addWidget(self.btn_close)
+        layout.addLayout(btn_layout)
+
+    def run_search(self):
+        query = self.line_input.text().strip()
+        if not query:
+            return
+
+        self.lbl_info.setText("Searching PubChem... please wait.")
+        self.btn_search.setEnabled(False)
+        self.table.setRowCount(0)
+        QApplication.setOverrideCursor(Qt.CursorShape.WaitCursor)
+        QApplication.processEvents()
+
+        results = []
+        error_msg = None
+        network_error = False
+
+        try:
+            search_type = self.combo_type.currentText()
+
+            if search_type == "SMILES":
+                # SMILESの場合は直接リストに追加（検証含む）
+                mol = Chem.MolFromSmiles(query)
+                if mol:
+                    results.append({
+                        'name': 'User Input SMILES',
+                        'smiles': query,
+                        'formula': Chem.rdMolDescriptors.CalcMolFormula(mol)
+                    })
+                else:
+                    raise ValueError("Invalid SMILES string.")
+            
+            else: # Auto (PubChem API)
+                # PUG REST APIを使用して検索
+                # プロパティとしてSMILESと分子式を取得
+                # CanonicalSMILESも取得してフォールバックに使用
+                url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{query}/property/IsomericSMILES,CanonicalSMILES,MolecularFormula,Title/JSON"
+                
+                response = requests.get(url, timeout=10)
+                
+                if response.status_code == 200:
+                    data = response.json()
+                    props = data.get('PropertyTable', {}).get('Properties', [])
+                    for p in props:
+                        # SMILESの取得（Isomericを優先、なければCanonical、それでもなければキー検索）
+                        smiles = p.get('IsomericSMILES')
+                        if not smiles:
+                            smiles = p.get('CanonicalSMILES')
+                        
+                        # まだ取得できていない場合、キー名に'SMILES'が含まれるものを探す
+                        if not smiles:
+                            for k in p.keys():
+                                if 'SMILES' in k:
+                                    smiles = p[k]
+                                    if smiles:
+                                        break
+                        
+                        if not smiles:
+                            smiles = "" # 見つからない場合
+
+                        results.append({
+                            'name': p.get('Title', query),
+                            'smiles': smiles,
+                            'formula': p.get('MolecularFormula', '')
+                        })
+                else:
+                    # found nothing or error status
+                    pass
+
+        except requests.exceptions.RequestException:
+            network_error = True
+        except Exception as e:
+            error_msg = str(e)
+        finally:
+            QApplication.restoreOverrideCursor()
+            self.btn_search.setEnabled(True)
+
+        # UI updates after cursor restore
+        if network_error:
+            QMessageBox.critical(self, PLUGIN_NAME, "Network error. Please check your internet connection.")
+            self.lbl_info.setText("Network error.")
+        elif error_msg:
+            QMessageBox.critical(self, PLUGIN_NAME, f"Error: {error_msg}")
+            self.lbl_info.setText("Error occurred.")
+        elif not results and 'response' in locals() and response.status_code != 200:
+            self.lbl_info.setText("Not found in PubChem search.")
+        else:
+            # データを保持
+            self.candidates_data = results
+            self.update_table()
+            
+            if results:
+                self.lbl_info.setText(f"Found {len(results)} candidates. Select one and click Load to 2D Editor.")
+            else:
+                self.lbl_info.setText("No results found.")
+
+    def update_table(self):
+        self.table.setRowCount(0)
+        
+        for i, data in enumerate(self.candidates_data):
+            row_idx = self.table.rowCount()
+            self.table.insertRow(row_idx)
+            
+            self.table.setItem(row_idx, 0, QTableWidgetItem(str(data['name'])))
+            self.table.setItem(row_idx, 1, QTableWidgetItem(str(data['formula'])))
+            self.table.setItem(row_idx, 2, QTableWidgetItem(str(data['smiles'])))
+
+    def load_molecule(self):
+        """選択された行のSMILESから2D構造を生成し、メインウィンドウのエディタに入れる"""
+        selected_items = self.table.selectedItems()
+        if not selected_items:
+            QMessageBox.warning(self, PLUGIN_NAME, "Please select a molecule from the list.")
+            return
+            
+        row = selected_items[0].row()
+        smiles = self.candidates_data[row]['smiles']
+        name = self.candidates_data[row]['name']
+        
+        if not smiles:
+             QMessageBox.warning(self, PLUGIN_NAME, "No SMILES data available for this entry.")
+             return
+
+        self.lbl_info.setText("Loading into 2D Editor...")
+        QApplication.setOverrideCursor(Qt.CursorShape.WaitCursor)
+        QApplication.processEvents()
+
+        success = False
+        error_msg = None
+
+        try:
+            # メインウィンドウのSMILES読み込み機能を使用
+            if hasattr(self.main_window, "load_from_smiles"):
+                self.main_window.load_from_smiles(smiles)
+                success = True
+            else:
+                error_msg = "Main window does not support 'load_from_smiles'."
+
+        except Exception as e:
+            error_msg = str(e)
+            
+        finally:
+            QApplication.restoreOverrideCursor()
+
+        if success:
+             self.lbl_info.setText(f"Loaded: {name}")
+             QMessageBox.information(self, PLUGIN_NAME, f"Successfully loaded: {name}")
+             self.accept() # ダイアログを閉じる
+        elif error_msg:
+             QMessageBox.critical(self, PLUGIN_NAME, f"Error: {error_msg}")
+             self.lbl_info.setText("Load failed.")
+
+def run(mw):
+    if hasattr(mw, "_molecule_resolver_dialog") and mw._molecule_resolver_dialog.isVisible():
+        mw._molecule_resolver_dialog.raise_()
+        mw._molecule_resolver_dialog.activateWindow()
+        return
+
+    dialog = MoleculeResolverDialog(mw, parent=mw)
+    mw._molecule_resolver_dialog = dialog
+    dialog.show()
+
+# initialize removed as it only registered the menu action