MoleditPy 2.2.0a1__py3-none-any.whl → 2.2.0a3__py3-none-any.whl

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

moleditpy/plugins/Utility/pubchem_ressolver.py

@@ -1,244 +0,0 @@
-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