MoleditPy 2.2.0a2__py3-none-any.whl → 2.2.0a3__py3-none-any.whl

moleditpy/plugins/Input Generator/gaussian_input_generator_neo.py

@@ -1,930 +0,0 @@
-# -*- coding: utf-8 -*-
-import os
-from PyQt6.QtWidgets import (QMessageBox, QDialog, QVBoxLayout, QLabel, 
-                             QLineEdit, QSpinBox, QPushButton, QFileDialog, 
-                             QFormLayout, QGroupBox, QHBoxLayout, QComboBox, QTextEdit, 
-                             QInputDialog, QTabWidget, QCheckBox, QRadioButton, QButtonGroup,
-                             QWidget, QScrollArea)
-from PyQt6.QtGui import QPalette, QColor, QFont
-from PyQt6.QtCore import Qt
-from rdkit import Chem
-import json
-
-__version__="2025.12.16"
-__author__="HiroYokoyama"
-
-PLUGIN_NAME = "Gaussian Input Generator Neo"
-SETTINGS_FILE = os.path.join(os.path.dirname(__file__), "gaussian_input_generator_neo.json")
-
-class RouteBuilderDialog(QDialog):
-    """
-    Dialog to construct the Gaussian Job Route line.
-    """
-    def __init__(self, parent=None, current_route=""):
-        super().__init__(parent)
-        self.setWindowTitle("Route Builder")
-        self.resize(600, 500)
-        self.ui_ready = False  # Flag to prevent premature updates
-        self.current_route = current_route
-        self.setup_ui()
-        self.parse_route(current_route)
-
-    def setup_ui(self):
-        layout = QVBoxLayout()
-        
-        self.tabs = QTabWidget()
-        
-        # --- Tab 1: Method & Basis ---
-        self.tab_method = QWidget()
-        self.setup_method_tab()
-        self.tabs.addTab(self.tab_method, "Method/Basis")
-        
-        # --- Tab 2: Job Type ---
-        self.tab_job = QWidget()
-        self.setup_job_tab()
-        self.tabs.addTab(self.tab_job, "Job Type")
-        
-        # --- Tab 3: Solvation & Disp ---
-        self.tab_solvation = QWidget()
-        self.setup_solvation_tab()
-        self.tabs.addTab(self.tab_solvation, "Solvation/Dispersion")
-        
-        # --- Tab 4: Properties ---
-        self.tab_props = QWidget()
-        self.setup_props_tab()
-        self.tabs.addTab(self.tab_props, "Properties")
-
-        layout.addWidget(self.tabs)
-
-        # --- Preview ---
-        preview_group = QGroupBox("Route Preview")
-        preview_layout = QVBoxLayout()
-        self.preview_label = QLabel()
-        self.preview_label.setWordWrap(True)
-        self.preview_label.setStyleSheet("font-weight: bold; color: blue; font-size: 14px;")
-        preview_layout.addWidget(self.preview_label)
-        preview_group.setLayout(preview_layout)
-        layout.addWidget(preview_group)
-
-        # --- Buttons ---
-        btn_layout = QHBoxLayout()
-        self.btn_ok = QPushButton("Apply to Job")
-        self.btn_ok.clicked.connect(self.accept)
-        self.btn_cancel = QPushButton("Cancel")
-        self.btn_cancel.clicked.connect(self.reject)
-        btn_layout.addStretch()
-        btn_layout.addWidget(self.btn_ok)
-        btn_layout.addWidget(self.btn_cancel)
-        layout.addLayout(btn_layout)
-
-        self.setLayout(layout)
-        
-        # Connect signals to update preview
-        self.connect_signals()
-        
-        self.ui_ready = True  # Enable updates
-        self.update_preview()
-
-    def setup_method_tab(self):
-        layout = QFormLayout()
-
-        # Output Level
-        self.output_level = QComboBox()
-        self.output_level.addItems(["Additional Output (#P)", "Standard Output (#)", "Terse Output (#T)"])
-        # Default to # (Standard)
-        self.output_level.setCurrentIndex(1) 
-        self.output_level.currentIndexChanged.connect(self.update_preview)
-        layout.addRow("Print Level:", self.output_level)
-        
-        # Method Type
-        self.method_type = QComboBox()
-        self.method_type.addItems(["DFT", "Double Hybrid", "MP2", "Hartree-Fock", "Semi-Empirical", "Other"])
-        self.method_type.currentIndexChanged.connect(self.update_method_list)
-        layout.addRow("Method Type:", self.method_type)
-        
-        # Method Name
-        self.method_name = QComboBox()
-        # Initial population
-        # Note: update_method_list calls update_preview, which calls currentText()
-        # We need to make sure update_preview guards against uninitialized widgets
-        self.update_method_list() 
-        layout.addRow("Method:", self.method_name)
-        
-        # Basis Set
-        self.basis_set = QComboBox()
-        basis_groups = [
-            "6-31G(d)", "6-31+G(d,p)", "6-311G(d,p)", "6-311+G(d,p)", # Pople
-            "cc-pVDZ", "cc-pVTZ", "aug-cc-pVDZ", "aug-cc-pVTZ", # Dunning
-            "def2SVP", "def2TZVP", "def2QZVP", # Karlsruhe
-            "LanL2DZ", "SDD", "Gen", "GenECP" # ECP/Gen
-        ]
-        self.basis_set.addItems(basis_groups)
-        layout.addRow("Basis Set:", self.basis_set)
-        
-        self.tab_method.setLayout(layout)
-
-    def update_method_list(self):
-        mtype = self.method_type.currentText()
-        self.method_name.blockSignals(True)
-        self.method_name.clear()
-        
-        if mtype == "DFT":
-            self.method_name.addItems([
-                "B3LYP", "WB97XD", "M062X", "PBE0", "CAM-B3LYP", "APFD", "B97D3", "TPSSTPSS",
-                "MN15", "MN15L", "BHandHLYP"
-            ])
-        elif mtype == "Double Hybrid":
-            self.method_name.addItems(["B2PLYP"])
-        elif mtype == "MP2":
-            self.method_name.addItems(["MP2", "MP3", "MP4", "CCSD", "CCSD(T)"])
-        elif mtype == "Hartree-Fock":
-            self.method_name.addItems(["HF", "ROHF", "UHF"])
-        elif mtype == "Semi-Empirical":
-            self.method_name.addItems(["AM1", "PM6", "PM7", "ZINDO"])
-        else:
-            self.method_name.addItem("Custom")
-            
-        self.method_name.blockSignals(False)
-        self.update_preview()
-
-    def setup_job_tab(self):
-        layout = QVBoxLayout()
-        
-        self.job_type = QComboBox()
-        self.job_type.addItems([
-            "Optimization + Freq (Opt Freq)", 
-            "Optimization Only (Opt)", 
-            "Frequency Only (Freq)", 
-            "Single Point Energy (SP)",
-            "Scan (ModRedundant)",
-            "IRC",
-            "Stability Analysis (Stable)",
-            "Volume"
-        ])
-        layout.addWidget(QLabel("Job Task:"))
-        layout.addWidget(self.job_type)
-        self.job_type.currentIndexChanged.connect(self.update_job_options_visibility)
-        
-        # Opt Options
-        self.opt_group = QGroupBox("Optimization Options")
-        opt_layout = QHBoxLayout()
-        self.opt_tight = QCheckBox("Tight")
-        self.opt_verytight = QCheckBox("VeryTight")
-        self.opt_calcfc = QCheckBox("CalcFC")
-        self.opt_maxcycles = QCheckBox("MaxCycles=100")
-        opt_layout.addWidget(self.opt_tight)
-        opt_layout.addWidget(self.opt_verytight)
-        opt_layout.addWidget(self.opt_calcfc)
-        opt_layout.addWidget(self.opt_maxcycles)
-        self.opt_group.setLayout(opt_layout)
-        layout.addWidget(self.opt_group)
-        
-        # Freq Options
-        self.freq_group = QGroupBox("Freq Options")
-        freq_layout = QHBoxLayout()
-        self.freq_raman = QCheckBox("Raman")
-        self.freq_anharm = QCheckBox("Anharmonic")
-        freq_layout.addWidget(self.freq_raman)
-        freq_layout.addWidget(self.freq_anharm)
-        self.freq_group.setLayout(freq_layout)
-        layout.addWidget(self.freq_group)
-        
-        layout.addStretch()
-        self.tab_job.setLayout(layout)
-        
-        # Initial visibility update
-        self.update_job_options_visibility()
-
-    def update_job_options_visibility(self):
-        job_idx = self.job_type.currentIndex()
-        txt = self.job_type.currentText()
-        
-        # Opt options: Show for Opt, Opt+Freq, Scan, IRC, Stable, Volume (some imply optimization)
-        # Strictly speaking: Opt tasks. 
-        # 0: Opt+Freq, 1: Opt, 4: Scan (ModRedundant), 5: IRC
-        is_opt = job_idx in [0, 1, 4, 5] 
-        self.opt_group.setVisible(is_opt)
-        
-        # Freq options: Show for Opt+Freq, Freq
-        # 0: Opt+Freq, 2: Freq
-        is_freq = job_idx in [0, 2]
-        self.freq_group.setVisible(is_freq)
-
-    def setup_solvation_tab(self):
-        layout = QFormLayout()
-        
-        self.solv_model = QComboBox()
-        self.solv_model.addItems(["None", "PCM", "CPCM", "SMD", "IEFPCM"])
-        layout.addRow("Solvation Model:", self.solv_model)
-        
-        self.solvent = QComboBox()
-        solvents = [
-            "Water", "Acetonitrile", "Methanol", "Ethanol", 
-            "Chloroform", "Dichloromethane", "Toluene", 
-            "Tetrahydrofuran", "DimethylSulfoxide", "Cyclohexane", 
-            "Benzene", "Acetone"
-        ]
-        self.solvent.addItems(solvents)
-        layout.addRow("Solvent:", self.solvent)
-        
-        layout.addRow(QLabel(" ")) # Spacer
-        
-        self.dispersion = QCheckBox("EmpiricalDispersion=GD3BJ")
-        layout.addRow("Dispersion:", self.dispersion)
-        
-        self.tab_solvation.setLayout(layout)
-
-    def setup_props_tab(self):
-        layout = QFormLayout()
-        
-        self.pop_analysis = QComboBox()
-        self.pop_analysis.addItems(["None", "NBO (Pop=NBO)", "Hirshfeld", "MK (Merz-Kollman)", "Regular (Pop=Reg)"])
-        layout.addRow("Population Analysis:", self.pop_analysis)
-        
-        self.density_chk = QCheckBox("Density=Current")
-        layout.addRow(QLabel("Density:"), self.density_chk)
-        
-        self.symmetry_combo = QComboBox()
-        self.symmetry_combo.addItems(["Default", "Loose", "None (NoSymm)"])
-        layout.addRow("Symmetry:", self.symmetry_combo)
-        
-        self.grid_combo = QComboBox()
-        self.grid_combo.addItems(["Default", "FineGrid", "UltraFine", "SuperFine"])
-        layout.addRow("Integration Grid:", self.grid_combo)
-
-        # TD-DFT Section
-        td_group = QGroupBox("Excited States (TD-DFT)")
-        td_layout = QHBoxLayout()
-        self.td_chk = QCheckBox("Enable TD")
-        self.td_nstates = QSpinBox()
-        self.td_nstates.setValue(6)
-        self.td_nstates.setPrefix("NStates=")
-        td_layout.addWidget(self.td_chk)
-        td_layout.addWidget(self.td_nstates)
-        td_group.setLayout(td_layout)
-        layout.addRow(td_group)
-
-        self.tab_props.setLayout(layout)
-
-    def connect_signals(self):
-        # Connect all widgets to update_preview
-        widgets = [
-            self.method_type, self.method_name, self.basis_set,
-            self.job_type, self.opt_tight, self.opt_verytight, self.opt_calcfc, self.opt_maxcycles,
-            self.freq_raman, self.freq_anharm,
-            self.solv_model, self.solvent, self.dispersion,
-            self.pop_analysis, self.density_chk, self.symmetry_combo, self.grid_combo,
-            self.td_chk, self.td_nstates
-        ]
-        for w in widgets:
-            if isinstance(w, QComboBox):
-                w.currentIndexChanged.connect(self.update_preview)
-            elif isinstance(w, QCheckBox):
-                w.toggled.connect(self.update_preview)
-            elif isinstance(w, QSpinBox):
-                w.valueChanged.connect(self.update_preview)
-
-    def update_preview(self):
-        if not getattr(self, 'ui_ready', False):
-            return
-
-        # Output Level
-        lvl_map = {0: "#P", 1: "#", 2: "#T"}
-        prefix = lvl_map.get(self.output_level.currentIndex(), "#P")
-        route_parts = [prefix]
-        
-        # Method / Basis
-        method = self.method_name.currentText()
-        basis = self.basis_set.currentText()
-        route_parts.append(f"{method}/{basis}")
-        
-        # Job Type
-        job_idx = self.job_type.currentIndex()
-        if job_idx == 0: route_parts.extend(["Opt", "Freq"])
-        elif job_idx == 1: route_parts.append("Opt")
-        elif job_idx == 2: route_parts.append("Freq")
-        elif job_idx == 3: route_parts.append("SP")
-        elif job_idx == 4: route_parts.append("Scan") # ModRedundant usually implies Opt=ModRedundant but simple Scan is obsolete
-        elif job_idx == 5: route_parts.append("IRC")
-        elif job_idx == 6: route_parts.append("Stable")
-        elif job_idx == 7: route_parts.append("Volume")
-        
-        # Opt Options
-        opt_opts = []
-        if self.opt_tight.isChecked(): opt_opts.append("Tight")
-        if self.opt_verytight.isChecked(): opt_opts.append("VeryTight")
-        if self.opt_calcfc.isChecked(): opt_opts.append("CalcFC")
-        if self.opt_maxcycles.isChecked(): opt_opts.append("MaxCycles=100")
-        
-        # If Opt is in route and we have options, combine them
-        # Note: In Gaussian, it's usually Opt=(Tight, CalcFC)
-        # But if we just appended "Opt", we need to replace it or append.
-        # Simplified approach: If Opt is present, modify the Opt string.
-        if "Opt" in route_parts and opt_opts:
-             # Find index of "Opt"
-             idx = route_parts.index("Opt")
-             route_parts[idx] = f"Opt=({', '.join(opt_opts)})"
-        
-        # Freq Options
-        freq_opts = []
-        if self.freq_raman.isChecked(): freq_opts.append("Raman")
-        if self.freq_anharm.isChecked(): freq_opts.append("Anharmonic")
-        
-        if "Freq" in route_parts and freq_opts:
-             idx = route_parts.index("Freq")
-             route_parts[idx] = f"Freq=({', '.join(freq_opts)})"
-
-        # Solvation
-        solv = self.solv_model.currentText()
-        if solv != "None":
-            solvent = self.solvent.currentText()
-            scrf_opts = [f"{solv}", f"Solvent={solvent}"]
-            route_parts.append(f"SCRF=({', '.join(scrf_opts)})")
-            
-        # Dispersion
-        if self.dispersion.isChecked():
-            route_parts.append("EmpiricalDispersion=GD3BJ")
-            
-        # Properties
-        pop = self.pop_analysis.currentText()
-        if "NBO" in pop: route_parts.append("Pop=NBO")
-        elif "Hirshfeld" in pop: route_parts.append("Pop=Hirshfeld")
-        elif "MK" in pop: route_parts.append("Pop=MK")
-        elif "Reg" in pop: route_parts.append("Pop=Reg")
-        
-        if self.density_chk.isChecked():
-            route_parts.append("Density=Current")
-            
-        sym = self.symmetry_combo.currentText()
-        if "Loose" in sym: route_parts.append("Symmetry=Loose")
-        elif "None" in sym: route_parts.append("NoSymm")
-        
-        grid = self.grid_combo.currentText()
-        if grid != "Default":
-             route_parts.append(f"Integral({grid})")
-             
-        # TD-DFT
-        if self.td_chk.isChecked():
-            route_parts.append(f"TD=(NStates={self.td_nstates.value()})")
-            
-        self.preview_str = " ".join(route_parts)
-        self.preview_label.setText(self.preview_str)
-
-    def get_route(self):
-        return self.preview_str
-
-    def parse_route(self, route):
-        # Very basic parsing to try and populate fields from an existing string
-        # This is hard to do perfectly, so we might just best-effort match.
-        # For now, we will leave everything as default if loading, 
-        # or maybe we can try to at least Find B3LYP or Opt.
-        # Since this is "Advanced", users might type weird things.
-        # Let's just try to match Method/Basis/Job.
-        
-        route = route.upper()
-        
-        # Check Job Type
-        if "OPT" in route and "FREQ" in route: self.job_type.setCurrentIndex(0)
-        elif "OPT" in route: self.job_type.setCurrentIndex(1)
-        elif "FREQ" in route: self.job_type.setCurrentIndex(2)
-        elif "SP" in route: self.job_type.setCurrentIndex(3)
-        elif "SCAN" in route: self.job_type.setCurrentIndex(4)
-        elif "IRC" in route: self.job_type.setCurrentIndex(5)
-        elif "STABLE" in route: self.job_type.setCurrentIndex(6)
-        elif "VOLUME" in route: self.job_type.setCurrentIndex(7)
-        
-        # Check Method (Just a few examples)
-        if "WB97XD" in route: 
-            self.method_type.setCurrentText("DFT")
-            self.method_name.setCurrentText("WB97XD")
-        elif "B3LYP" in route:
-            self.method_type.setCurrentText("DFT")
-            self.method_name.setCurrentText("B3LYP")
-        elif "M062X" in route:
-            self.method_type.setCurrentText("DFT")
-            self.method_name.setCurrentText("M062X")
-        elif "HF" in route:
-            self.method_type.setCurrentText("Hartree-Fock")
-            self.method_name.setCurrentText("HF")
-            
-        # Check Basis
-        if "6-31G(D)" in route: self.basis_set.setCurrentText("6-31G(d)")
-        elif "CC-PVTZ" in route: self.basis_set.setCurrentText("cc-pVTZ")
-        elif "DEF2TZVP" in route: self.basis_set.setCurrentText("def2TZVP")
-        elif "GEN" in route: self.basis_set.setCurrentText("Gen")
-        
-        # Solvation
-        if "SCRF" in route:
-            if "SMD" in route: self.solv_model.setCurrentText("SMD")
-            elif "CPCM" in route: self.solv_model.setCurrentText("CPCM")
-            else: self.solv_model.setCurrentText("PCM")
-
-class GaussianSetupDialog(QDialog):
-    """
-    Gaussianインプット作成のための高機能設定ダイアログ
-    Link 0, Route, Title, Charge/Mult, および追記データに対応
-    """
-    def __init__(self, parent=None, mol=None):
-        super().__init__(parent)
-        self.setWindowTitle("Gaussian Input Setup")
-        self.resize(500, 600) # 少し大きめに設定
-        self.mol = mol
-        self.setup_ui()
-
-    def setup_ui(self):
-        main_layout = QVBoxLayout()
-
-        # --- 0. Preset Management ---
-        preset_group = QGroupBox("Preset Management")
-        preset_layout = QHBoxLayout()
-        
-        self.preset_combo = QComboBox()
-        self.preset_combo.currentIndexChanged.connect(self.apply_selected_preset)
-        preset_layout.addWidget(QLabel("Preset:"))
-        preset_layout.addWidget(self.preset_combo, 1)
-
-        self.btn_save_preset = QPushButton("Save New...")
-        self.btn_save_preset.clicked.connect(self.save_preset_dialog)
-        preset_layout.addWidget(self.btn_save_preset)
-
-        self.btn_del_preset = QPushButton("Delete")
-        self.btn_del_preset.clicked.connect(self.delete_preset)
-        preset_layout.addWidget(self.btn_del_preset)
-
-        preset_group.setLayout(preset_layout)
-        main_layout.addWidget(preset_group)
-
-        # --- 1. Link 0 Section (System Resources) ---
-        link0_group = QGroupBox("Link 0 Commands (System Resources)")
-        link0_layout = QFormLayout()
-
-        # Memory
-        mem_layout = QHBoxLayout()
-        self.mem_spin = QSpinBox()
-        self.mem_spin.setRange(1, 999999)
-        self.mem_spin.setValue(4) # Default
-        self.mem_unit = QComboBox()
-        self.mem_unit.addItems(["GB", "MB", "MW"])
-        mem_layout.addWidget(self.mem_spin)
-        mem_layout.addWidget(self.mem_unit)
-        link0_layout.addRow("Memory (%mem):", mem_layout)
-
-        # Processors
-        self.nproc_spin = QSpinBox()
-        self.nproc_spin.setRange(1, 128)
-        self.nproc_spin.setValue(4) # Default
-        link0_layout.addRow("Processors (%nprocshared):", self.nproc_spin)
-        
-        # Checkpoint (Optional override)
-        self.chk_edit = QLineEdit()
-        self.chk_edit.setPlaceholderText("Auto-generated from filename if empty")
-        link0_layout.addRow("Checkpoint (%chk):", self.chk_edit)
-
-        link0_group.setLayout(link0_layout)
-        main_layout.addWidget(link0_group)
-
-        # --- 2. Job Specification (Route & Title) ---
-        job_group = QGroupBox("Job Specification")
-        job_layout = QFormLayout()
-
-        # Route section
-        # Route section
-        route_layout = QHBoxLayout()
-        self.keywords_edit = QLineEdit("#P B3LYP/6-31G(d) Opt Freq")
-        self.btn_route_builder = QPushButton("Route Builder...")
-        self.btn_route_builder.clicked.connect(self.open_route_builder)
-        route_layout.addWidget(self.keywords_edit)
-        route_layout.addWidget(self.btn_route_builder)
-        job_layout.addRow("Route Section (#):", route_layout)
-
-        # Title
-        self.title_edit = QLineEdit("Generated by MoleditPy Plugin")
-        job_layout.addRow("Title:", self.title_edit)
-
-        job_group.setLayout(job_layout)
-        main_layout.addWidget(job_group)
-
-        # --- 3. Molecular State ---
-        mol_group = QGroupBox("Molecular Specification")
-        mol_layout = QHBoxLayout()
-        
-        self.charge_spin = QSpinBox()
-        self.charge_spin.setRange(-10, 10)
-        self.charge_spin.valueChanged.connect(self.validate_charge_mult)
-        
-        # Save default palette for restoration
-        self.default_palette = self.charge_spin.palette()
-
-        # Multiplicity
-        self.mult_spin = QSpinBox()
-        self.mult_spin.setRange(1, 10)
-        self.mult_spin.valueChanged.connect(self.validate_charge_mult)
-
-        mol_layout.addWidget(QLabel("Charge:"))
-        mol_layout.addWidget(self.charge_spin)
-        mol_layout.addWidget(QLabel("Multiplicity:"))
-        mol_layout.addWidget(self.mult_spin)
-
-        mol_group.setLayout(mol_layout)
-        main_layout.addWidget(mol_group)
-        
-        # Calculate initial values
-        self.calc_initial_charge_mult()
-
-        # --- 4. Additional Input (The "Everything" section) ---
-        tail_group = QGroupBox("Additional Input (Post-Coordinates)")
-        tail_layout = QVBoxLayout()
-        
-        help_label = QLabel("For ModRedundant, Basis Sets (Gen), or Link1.\nAppended after the molecule specification.")
-        help_label.setStyleSheet("color: gray; font-size: 10px;")
-        tail_layout.addWidget(help_label)
-
-        self.tail_edit = QTextEdit()
-        self.tail_edit.setPlaceholderText("Example:\nD 1 2 3 4 S 10 10.0\n\nOr basis set data for Gen/GenECP...")
-        tail_layout.addWidget(self.tail_edit)
-
-        tail_group.setLayout(tail_layout)
-        main_layout.addWidget(tail_group)
-
-        # --- Save Button ---
-        # --- Save/Preview Buttons ---
-        btn_box = QHBoxLayout()
-        
-        self.btn_preview = QPushButton("Preview Input")
-        self.btn_preview.clicked.connect(self.preview_file)
-        btn_box.addWidget(self.btn_preview)
-
-        self.save_btn = QPushButton("Save Input File...")
-        self.save_btn.clicked.connect(self.save_file)
-        self.save_btn.setStyleSheet("font-weight: bold; padding: 5px;")
-        btn_box.addWidget(self.save_btn)
-        
-        main_layout.addLayout(btn_box)
-
-        self.setLayout(main_layout)
-
-    def get_coords_string(self):
-        """
-        分子オブジェクトから原子座標文字列を生成する
-        """
-        if not self.mol:
-            return ""
-        
-        lines = []
-        try:
-            # RDKitの場合の座標取得
-            conf = self.mol.GetConformer()
-            for i in range(self.mol.GetNumAtoms()):
-                pos = conf.GetAtomPosition(i)
-                atom = self.mol.GetAtomWithIdx(i)
-                symbol = atom.GetSymbol()
-                # Symbol X Y Z formatted
-                lines.append(f"{symbol: <4} {pos.x: >12.6f} {pos.y: >12.6f} {pos.z: >12.6f}")
-        except Exception as e:
-            return f"Error extracting coordinates: {str(e)}"
-            
-        return "\n".join(lines)
-
-    def generate_input_content(self):
-        """Generates the full content of the input file as a string."""
-        lines = []
-        
-        # --- Link 0 Section ---
-        lines.append(f"%nprocshared={self.nproc_spin.value()}")
-        lines.append(f"%mem={self.mem_spin.value()}{self.mem_unit.currentText()}")
-        
-        chk_name = self.chk_edit.text().strip()
-        if chk_name and not chk_name.endswith(".chk"): chk_name += ".chk"
-        if chk_name: lines.append(f"%chk={chk_name}")
-
-        # --- Route Section ---
-        route_line = self.keywords_edit.text().strip()
-        if not route_line.startswith("#"):
-            route_line = "# " + route_line
-        lines.append(f"{route_line}")
-        lines.append("") # Blank line required
-        
-        # --- Title Section ---
-        title_line = self.title_edit.text().strip()
-        if not title_line:
-            title_line = "Gaussian Job"
-        lines.append(f"{title_line}")
-        lines.append("") # Blank line required
-        
-        # --- Charge & Multiplicity ---
-        lines.append(f"{self.charge_spin.value()} {self.mult_spin.value()}")
-        
-        # --- Molecule Specification ---
-        coords_block = self.get_coords_string()
-        if "Error" in coords_block:
-            return f"# Error generating coordinates: {coords_block}"
-        lines.append(coords_block)
-        lines.append("") # Must end coord block with newline
-        
-        # --- Additional Input (Tail) ---
-        tail_content = self.tail_edit.toPlainText()
-        if tail_content.strip():
-            # Ensure blank line before tail if needed (already added above)
-            # Actually, standard Gaussian input format:
-            # Route
-            # <blank>
-            # Title
-            # <blank>
-            # Charge Mult
-            # Coords
-            # <blank>
-            # Tail
-            # <blank>
-            lines.append(tail_content)
-            # Ensure tail ends with newline (managed by join)
-        
-        # Final blank line
-        lines.append("")
-        
-        return "\n".join(lines)
-
-    def preview_file(self):
-        content = self.generate_input_content()
-        
-        d = QDialog(self)
-        d.setWindowTitle("Preview Input - Gaussian Neo")
-        d.resize(600, 500)
-        l = QVBoxLayout()
-        t = QTextEdit()
-        t.setPlainText(content)
-        t.setReadOnly(True)
-        t.setFont(QFont("Courier New", 10))
-        l.addWidget(t)
-        
-        btn = QPushButton("Close")
-        btn.clicked.connect(d.accept)
-        l.addWidget(btn)
-        d.setLayout(l)
-        d.exec()
-
-    def save_file(self):
-        # 座標データの取得 (Check for error first)
-        coords_block = self.get_coords_string()
-        if "Error" in coords_block:
-            QMessageBox.critical(self, "Error", coords_block)
-            return
-
-        # ファイル保存ダイアログ
-        file_path, _ = QFileDialog.getSaveFileName(
-            self, "Save Gaussian Input", "", "Gaussian Input (*.gjf *.com );;All Files (*)"
-        )
-
-        if file_path:
-            try:
-                # ファイル名に基づいてchk名を決定（ユーザー入力がない場合）
-                filename_base = os.path.splitext(os.path.basename(file_path))[0]
-                chk_name = self.chk_edit.text().strip()
-                if not chk_name:
-                    # Set temporary chk name for generation, but we need to update the content?
-                    # The generate_input_content uses self.chk_edit.
-                    # If empty, it doesn't add %chk line (or we should add logic there).
-                    # Wait, old code logic: if empty, used filename_base.chk.
-                    # I should replicate that logic to be safe, or just auto-fill chk_edit on save?
-                    # Let's auto-fill the field if empty? Or just pass it.
-                    # To be consistent with preview, maybe we should update the UI field?
-                    # Or just construct content with the filename.
-                    pass
-                
-                # Special handling for %chk auto-generation if field is empty
-                # We want the content to have the chk name based on the file unless specified.
-                # Let's temporarily set the chk text if empty, then restore?
-                # Or pass an argument to generate_input_content.
-                # Simpler: just use generate_input_content as is.
-                # BUT, original code did: `if not chk_name: chk_name = f"{filename_base}.chk"`
-                # So if I use `generate_input_content`, I miss this feature if I don't handle it.
-                
-                # Let's modify generate_input_content to handle "auto" chk?
-                # No, let's just do it here properly.
-                
-                # Update CHK field if empty?
-                original_chk = self.chk_edit.text()
-                if not original_chk.strip():
-                     self.chk_edit.setText(f"{filename_base}.chk")
-                
-                content = self.generate_input_content()
-                
-                # Restore if we want? Maybe keep it.
-                # If we keep it, the user sees what was used. Good.
-
-                with open(file_path, 'w', encoding='utf-8') as f:
-                    f.write(content)
-
-                QMessageBox.information(self, "Success", f"File saved:\n{file_path}")
-                self.accept()
-            except Exception as e:
-                QMessageBox.critical(self, "Error", f"Failed to save file:\n{str(e)}")
-
-    def open_route_builder(self):
-        """Open the Route Builder dialog."""
-        dialog = RouteBuilderDialog(self, self.keywords_edit.text())
-        if dialog.exec() == QDialog.DialogCode.Accepted:
-            self.keywords_edit.setText(dialog.get_route())
-
-    def calc_initial_charge_mult(self):
-        """
-        Calculate default charge and multiplicity from the molecule.
-        """
-        if not self.mol:
-            return
-
-        try:
-            # Logic taken from ORCA xyz2inp GUI
-            
-            # Charge
-            # Use Chem.GetFormalCharge for consistency
-            try:
-                charge = Chem.GetFormalCharge(self.mol)
-            except:
-                # Fallback if Chem.GetFormalCharge fails
-                charge = 0
-                if hasattr(self.mol, "GetFormalCharge"):
-                   charge = self.mol.GetFormalCharge()
-
-            # Multiplicity
-            # RDKit keeps track of radical electrons on atoms
-            num_radical_electrons = sum(atom.GetNumRadicalElectrons() for atom in self.mol.GetAtoms())
-            mult = num_radical_electrons + 1
-            
-            # Note: The ORCA plugin logic is simple (radicals + 1).
-            # It does not force even-electron systems to be doublets explicitly if no radicals are set.
-            # But the user said "orca... works well", so we trust this primary logic.
-            
-            # Set values
-            self.charge_spin.setValue(int(charge))
-            self.mult_spin.setValue(int(mult))
-            self.validate_charge_mult()
-            
-        except Exception as e:
-            print(f"Error calculating charge/mult: {e}")
-
-    def validate_charge_mult(self):
-        """
-        Validate if the charge/multiplicity combination is chemically consistent.
-        Turns input red if invalid.
-        """
-        if not self.mol:
-            return
-
-        try:
-            charge = self.charge_spin.value()
-            mult = self.mult_spin.value()
-            
-            total_protons = 0
-            for i in range(self.mol.GetNumAtoms()):
-                atom = self.mol.GetAtomWithIdx(i)
-                total_protons += atom.GetAtomicNum()
-                
-            total_electrons = total_protons - charge
-            
-            # Check consistency
-            # If electrons are even, multiplicity must be odd (1, 3, 5)
-            # If electrons are odd, multiplicity must be even (2, 4, 6)
-            is_valid = False
-            if total_electrons % 2 == 0:
-                if mult % 2 != 0: is_valid = True
-            else:
-                if mult % 2 == 0: is_valid = True
-                
-            if is_valid:
-                self.charge_spin.setPalette(self.default_palette)
-                self.mult_spin.setPalette(self.default_palette)
-            else:
-                p = self.charge_spin.palette()
-                p.setColor(QPalette.ColorRole.Base, QColor("#FFDDDD"))
-                p.setColor(QPalette.ColorRole.Text, Qt.GlobalColor.red)
-                self.charge_spin.setPalette(p)
-                self.mult_spin.setPalette(p)
-            
-        except Exception as e:
-            print(f"Validation error: {e}")
-
-    # --- Preset Management Methods ---
-
-    def load_presets_from_file(self):
-        """Load presets from JSON file and populate combo box."""
-        self.presets_data = {}
-        if os.path.exists(SETTINGS_FILE):
-            try:
-                with open(SETTINGS_FILE, 'r', encoding='utf-8') as f:
-                    self.presets_data = json.load(f)
-            except Exception as e:
-                print(f"Error loading presets: {e}")
-        
-        # Ensure Default exists if empty
-        if "Default" not in self.presets_data:
-            self.presets_data["Default"] = {
-                "nproc": 4, "mem_val": 4, "mem_unit": "GB", "chk": "",
-                "route": "# B3LYP/6-31G(d) Opt Freq", 
-                "tail": ""
-            }
-        
-        self.update_preset_combo()
-
-    def update_preset_combo(self):
-        """Update the combobox items from self.presets_data."""
-        current = self.preset_combo.currentText()
-        self.preset_combo.blockSignals(True)
-        self.preset_combo.clear()
-        self.preset_combo.addItems(sorted(self.presets_data.keys()))
-        
-        # Restore selection or select Default
-        if current in self.presets_data:
-            self.preset_combo.setCurrentText(current)
-        elif "Default" in self.presets_data:
-            self.preset_combo.setCurrentText("Default")
-        self.preset_combo.blockSignals(False)
-        
-        # Apply the current selection
-        self.apply_selected_preset()
-
-    def apply_selected_preset(self):
-        """Apply the settings from the selected preset to the UI."""
-        name = self.preset_combo.currentText()
-        if name not in self.presets_data:
-            return
-            
-        data = self.presets_data[name]
-        
-        # Apply values
-        self.nproc_spin.setValue(data.get("nproc", 4))
-        self.mem_spin.setValue(data.get("mem_val", 4))
-        self.mem_unit.setCurrentText(data.get("mem_unit", "GB"))
-        self.chk_edit.setText(data.get("chk", ""))
-        self.keywords_edit.setText(data.get("route", ""))
-        # DO NOT set Title, Charge, Mult (Molecule specific)
-        self.tail_edit.setPlainText(data.get("tail", ""))
-
-    def get_current_ui_settings(self):
-        """Return a dict of current UI settings."""
-        return {
-            "nproc": self.nproc_spin.value(),
-            "mem_val": self.mem_spin.value(),
-            "mem_unit": self.mem_unit.currentText(),
-            "chk": self.chk_edit.text(),
-            "route": self.keywords_edit.text(),
-            # DO NOT save Title, Charge, Mult
-            "tail": self.tail_edit.toPlainText()
-        }
-
-    def save_presets_to_file(self):
-        """Save self.presets_data to JSON file."""
-        try:
-            with open(SETTINGS_FILE, 'w', encoding='utf-8') as f:
-                json.dump(self.presets_data, f, indent=4)
-        except Exception as e:
-            QMessageBox.warning(self, "Error", f"Failed to save presets:\n{e}")
-
-    def save_preset_dialog(self):
-        """Show dialog to save current settings as a new preset."""
-        name, ok = QInputDialog.getText(self, "Save Preset", "Preset Name:", text=self.preset_combo.currentText())
-        if ok and name:
-            name = name.strip()
-            if not name:
-                return
-            
-            # Confirm overwrite
-            if name in self.presets_data:
-                ret = QMessageBox.question(self, "Overwrite", f"Preset '{name}' already exists. Overwrite?",
-                                           QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No)
-                if ret != QMessageBox.StandardButton.Yes:
-                    return
-
-            # Save
-            self.presets_data[name] = self.get_current_ui_settings()
-            self.save_presets_to_file()
-            self.update_preset_combo()
-            self.preset_combo.setCurrentText(name) # Select the new one
-
-    def delete_preset(self):
-        """Delete the currently selected preset."""
-        name = self.preset_combo.currentText()
-        if name == "Default":
-            QMessageBox.warning(self, "Warning", "Cannot delete 'Default' preset.")
-            return
-
-        ret = QMessageBox.question(self, "Delete Preset", f"Are you sure you want to delete '{name}'?",
-                                   QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No)
-        if ret == QMessageBox.StandardButton.Yes:
-            if name in self.presets_data:
-                del self.presets_data[name]
-                self.save_presets_to_file()
-                self.update_preset_combo()
-
-def run(mw):
-    mol = getattr(mw, 'current_mol', None)
-    
-    if not mol or mol.GetNumAtoms() == 0:
-        QMessageBox.warning(mw, PLUGIN_NAME, "No molecule loaded or molecule is empty.")
-        return
-
-    dialog = GaussianSetupDialog(parent=mw, mol=mol)
-    dialog.load_presets_from_file() # Load presets after init
-    dialog.exec()
-
-# initialize removed as it only registered the menu action
-