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

moleditpy/plugins/File/paste_xyz.py

@@ -1,336 +0,0 @@
-
-import traceback
-import io
-import contextlib
-from PyQt6.QtWidgets import (
-    QDialog, QVBoxLayout, QTextEdit, QPushButton, QHBoxLayout, 
-    QMessageBox, QLabel, QLineEdit, QDialogButtonBox, QInputDialog
-)
-from PyQt6.QtCore import Qt
-try:
-    from rdkit import Chem
-    from rdkit.Chem import rdGeometry, AllChem
-except ImportError:
-    Chem = None
-
-PLUGIN_NAME = "Paste XYZ"
-__version__="2025.12.25"
-__author__="HiroYokoyama"
-
-class PasteXYZDialog(QDialog):
-    def __init__(self, parent=None):
-        super().__init__(parent)
-        self.setWindowTitle("Paste XYZ")
-        self.resize(600, 400)
-        self.layout = QVBoxLayout(self)
-
-        info_label = QLabel("Paste XYZ coordinates below (Header/Atom count is IGNORED).")
-        self.layout.addWidget(info_label)
-
-        self.text_edit = QTextEdit()
-        self.text_edit.setPlaceholderText("Paste XYZ data here...\nExample:\nC 0.0 0.0 0.0\nH 1.0 0.0 0.0\n...")
-        self.layout.addWidget(self.text_edit)
-
-        btn_layout = QHBoxLayout()
-        self.load_btn = QPushButton("Load")
-        self.cancel_btn = QPushButton("Cancel")
-        btn_layout.addStretch()
-        btn_layout.addWidget(self.load_btn)
-        btn_layout.addWidget(self.cancel_btn)
-        self.layout.addLayout(btn_layout)
-
-        self.load_btn.clicked.connect(self.accept)
-        self.cancel_btn.clicked.connect(self.reject)
-
-    def get_data(self):
-        return self.text_edit.toPlainText()
-
-def run(mw):
-    if Chem is None:
-        QMessageBox.critical(mw, "Error", "RDKit is not available.")
-        return
-
-    dialog = PasteXYZDialog(mw)
-    if dialog.exec() == QDialog.Accepted:
-        xyz_text = dialog.get_data()
-        if not xyz_text.strip():
-            return
-
-        try:
-            # Robust Parsing Logic: Scan for 'Symbol X Y Z' lines
-            atoms_data = []
-            lines = xyz_text.splitlines()
-            
-            for line in lines:
-                parts = line.split()
-                if len(parts) >= 4:
-                    # Check if last 3 are standard floats (coordinates)
-                    try:
-                        x = float(parts[1])
-                        y = float(parts[2])
-                        z = float(parts[3])
-                        symbol = parts[0]
-                        # Verify symbol is likely an element (alpha)
-                        if not symbol[0].isalpha():
-                                # Maybe it's 'Index Symbol X Y Z' or something else?
-                                # Strict requirement: "Header/Atom count ignored", assume Paste is pure or standard XYZ
-                                # If line starts with a number, it's likely count or index, SKIP.
-                                # Standard XYZ atom lines start with Symbol.
-                                continue
-                        
-                        atoms_data.append((symbol, x, y, z))
-                    except ValueError:
-                        # Not coordinates, skip (likely header or title)
-                        continue
-
-            if not atoms_data:
-                QMessageBox.warning(mw, "Paste XYZ", "No valid coordinate lines found.\nExpected format: Symbol X Y Z")
-                return
-
-            # Clean workspace
-            if hasattr(mw, 'clear_all'):
-                mw.clear_all()
-            elif hasattr(mw, 'plotter'):
-                mw.plotter.clear()
-            
-            # Create RWMol and add atoms/conformers
-            mol = Chem.RWMol()
-            for i, (symbol, x, y, z) in enumerate(atoms_data):
-                atom = Chem.Atom(symbol)
-                atom.SetIntProp("xyz_unique_id", i)
-                mol.AddAtom(atom)
-            
-            conf = Chem.Conformer(len(atoms_data))
-            for i, (symbol, x, y, z) in enumerate(atoms_data):
-                conf.SetAtomPosition(i, rdGeometry.Point3D(x, y, z))
-            mol.AddConformer(conf)
-
-            # --- Chemistry Check Logic (Adapted from main_window_molecular_parsers.py) ---
-            
-            # Helper: prompt for charge
-            def prompt_for_charge():
-                try:
-                    dialog = QDialog(mw)
-                    dialog.setWindowTitle("Import XYZ Charge")
-                    layout = QVBoxLayout(dialog)
-                    label = QLabel("Enter total molecular charge:")
-                    line_edit = QLineEdit(dialog)
-                    line_edit.setText("")
-                    btn_box = QDialogButtonBox(QDialogButtonBox.Ok | QDialogButtonBox.Cancel, parent=dialog)
-                    skip_btn = QPushButton("Skip chemistry", dialog)
-                    hl = QHBoxLayout()
-                    hl.addWidget(btn_box)
-                    hl.addWidget(skip_btn)
-                    layout.addWidget(label)
-                    layout.addWidget(line_edit)
-                    layout.addLayout(hl)
-                    
-                    result = {"accepted": False, "skip": False}
-                    def on_ok():
-                        result["accepted"] = True
-                        dialog.accept()
-                    def on_cancel():
-                        dialog.reject()
-                    def on_skip():
-                        result["skip"] = True
-                        dialog.accept()
-
-                    try:
-                        btn_box.button(QDialogButtonBox.Ok).clicked.connect(on_ok)
-                        btn_box.button(QDialogButtonBox.Cancel).clicked.connect(on_cancel)
-                    except Exception:
-                        btn_box.accepted.connect(on_ok)
-                        btn_box.rejected.connect(on_cancel)
-                    skip_btn.clicked.connect(on_skip)
-
-                    if dialog.exec() != QDialog.Accepted:
-                        return None, False, False
-                    if result["skip"]:
-                        return 0, True, True
-                    if not result["accepted"]:
-                        return None, False, False
-                    
-                    charge_text = line_edit.text()
-                except Exception:
-                    # Fallback to simple input
-                    try:
-                        charge_text, ok = QInputDialog.getText(mw, "Import XYZ Charge", "Enter total molecular charge:", text="0")
-                        if not ok: return None, False, False
-                    except Exception:
-                        return 0, True, False
-
-                try:
-                    return int(str(charge_text).strip()), True, False
-                except Exception:
-                    try:
-                        return int(float(str(charge_text).strip())), True, False
-                    except Exception:
-                        return 0, True, False
-
-            # Inner helper: process with charge
-            def _process_with_charge(charge_val):
-                buf = io.StringIO()
-                used_rd_determine = False
-                mol_to_finalize = None
-                with contextlib.redirect_stderr(buf):
-                    try:
-                        from rdkit.Chem import rdDetermineBonds
-                        try:
-                            # Try to copy mol
-                            try:
-                                mol_candidate = Chem.RWMol(Chem.Mol(mol))
-                            except Exception:
-                                mol_candidate = Chem.RWMol(mol)
-                            
-                            rdDetermineBonds.DetermineBonds(mol_candidate, charge=charge_val)
-                            mol_to_finalize = mol_candidate
-                            used_rd_determine = True
-                        except Exception:
-                            # DetermineBonds failed
-                            raise RuntimeError("DetermineBondsFailed")
-                    except RuntimeError:
-                        raise
-                    except Exception:
-                        used_rd_determine = False
-                        mol_to_finalize = mol
-                    
-                    if not used_rd_determine:
-                        # Fallback to distance based
-                        if hasattr(mw, 'estimate_bonds_from_distances'):
-                                mw.estimate_bonds_from_distances(mol_to_finalize)
-
-                    try:
-                            candidate_mol = mol_to_finalize.GetMol()
-                    except Exception:
-                            candidate_mol = None
-
-                    if candidate_mol is None:
-                            # Salvage
-                            try:
-                                candidate_mol = mol.GetMol()
-                            except Exception:
-                                candidate_mol = None
-                    
-                    if candidate_mol is None:
-                        raise ValueError("Failed to create valid molecule object")
-
-                    # Attach charge prop
-                    try:
-                        candidate_mol.SetIntProp("_xyz_charge", int(charge_val))
-                    except Exception:
-                            pass
-                    
-                    # Apply chem check flags (if available in main_window)
-                    if hasattr(mw, '_apply_chem_check_and_set_flags'):
-                        mw._apply_chem_check_and_set_flags(candidate_mol, source_desc='PasteXYZ')
-
-                    return candidate_mol
-
-            # Main Logic Loop
-            final_mol = None
-            
-            # Check settings if available (defaulting to safe behavior)
-            settings = getattr(mw, 'settings', {})
-            always_ask = bool(settings.get('always_ask_charge', False))
-            skip_checks_global = bool(settings.get('skip_chemistry_checks', False))
-
-            if skip_checks_global:
-                    # Skip path
-                    if hasattr(mw, 'estimate_bonds_from_distances'):
-                        try: mw.estimate_bonds_from_distances(mol)
-                        except: pass
-                    try:
-                        final_mol = mol.GetMol()
-                        final_mol.SetIntProp("_xyz_skip_checks", 1)
-                        # Disable optimization for this mol
-                        mw.current_mol = final_mol
-                        mw.is_xyz_derived = True
-                    except: pass
-            else:
-                # Normal path
-                try:
-                    if not always_ask:
-                        try:
-                            final_mol = _process_with_charge(0)
-                        except RuntimeError:
-                            # DetermineBonds failed for 0, loop prompt
-                            while True:
-                                charge_val, ok, skip_flag = prompt_for_charge()
-                                if not ok: return # User cancel
-                                if skip_flag:
-                                    # User skipped
-                                    if hasattr(mw, 'estimate_bonds_from_distances'):
-                                        try: mw.estimate_bonds_from_distances(mol)
-                                        except: pass
-                                    try:
-                                        final_mol = mol.GetMol()
-                                        final_mol.SetIntProp("_xyz_skip_checks", 1)
-                                    except: pass
-                                    break
-                                
-                                try:
-                                    final_mol = _process_with_charge(charge_val)
-                                    break
-                                except RuntimeError:
-                                    mw.statusBar().showMessage("DetermineBonds failed for that charge...")
-                                    continue
-                                except Exception:
-                                    # Other error, try salvage if skip checks allowed? No, here we just continue or break
-                                    continue
-                    else:
-                        # Always ask
-                        while True:
-                            charge_val, ok, skip_flag = prompt_for_charge()
-                            if not ok: return
-                            if skip_flag:
-                                if hasattr(mw, 'estimate_bonds_from_distances'):
-                                    try: mw.estimate_bonds_from_distances(mol)
-                                    except: pass
-                                try:
-                                    final_mol = mol.GetMol()
-                                    final_mol.SetIntProp("_xyz_skip_checks", 1)
-                                except: pass
-                                break
-                            try:
-                                final_mol = _process_with_charge(charge_val)
-                                break
-                            except RuntimeError:
-                                mw.statusBar().showMessage("DetermineBonds failed...")
-                                continue
-                            except Exception:
-                                continue
-                except Exception:
-                        # Any other unhandled fallback
-                        pass
-
-            # If failed to get final_mol, fallback to raw
-            if final_mol is None:
-                if hasattr(mw, 'estimate_bonds_from_distances'):
-                    try: mw.estimate_bonds_from_distances(mol)
-                    except: pass
-                try: final_mol = mol.GetMol()
-                except: pass
-
-            if final_mol:
-                # We need RWMol for editing
-                rw_mol = Chem.RWMol(final_mol)
-                mw.current_mol = rw_mol
-                mw.current_file_path = None
-                mw.has_unsaved_changes = True
-
-                if hasattr(mw, 'update_window_title'): mw.update_window_title()
-                if hasattr(mw, 'reset_undo_stack'): mw.reset_undo_stack()
-                if hasattr(mw, 'draw_molecule_3d'): mw.draw_molecule_3d(rw_mol)
-                if hasattr(mw, 'fit_to_view'): mw.fit_to_view()
-                if hasattr(mw, 'statusBar'): mw.statusBar().showMessage(f"Loaded {len(atoms_data)} atoms from clipboard data.")
-                
-                # Enter 3D only mode as requested
-                if hasattr(mw, '_enter_3d_viewer_ui_mode'):
-                    try:
-                        mw._enter_3d_viewer_ui_mode()
-                    except Exception as e:
-                        print(f"Could not switch to 3D mode: {e}")
-
-        except Exception as e:
-            traceback.print_exc()
-            QMessageBox.critical(mw, "Error", f"Failed to parse or load data:\n{e}")