MoleditPy-linux 4.1.0__tar.gz → 4.1.2__tar.gz

{moleditpy_linux-4.1.0 → moleditpy_linux-4.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.1.0
+Version: 4.1.2
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -837,9 +837,9 @@ moleditpy
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
   * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
-## License
+## License & Disclaimer
 
-This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**. See the `LICENSE` file for details.
+This project is licensed under the GNU General Public License v3.0 (GPLv3) - see the [LICENSE](LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
 
 ## Citation
 
@@ -971,9 +971,9 @@ moleditpy
   * **化学計算 (RDKit / Open Babel):** 2DデータからRDKit分子オブジェクトを生成し、3D座標生成や分子特性計算を実行します。RDKitでの3D座標生成が失敗した際は、Open Babelにフォールバックします。重い計算処理は別スレッド (`QThread`) で実行し、GUIの応答性を維持しています。
   * **3D可視化 (PyVista / pyvistaqt):** RDKitのコンフォーマ座標からPyVistaのメッシュ（球や円柱）を生成して描画します。カスタムの`vtkInteractorStyle`を実装し、3Dビュー内での原子の直接的なドラッグ＆ドロップ編集を可能にしています。
 
-## ライセンス
+## ライセンス & 免責事項
 
-このプロジェクトは **GNU General Public License v3.0 (GPL-v3)** のもとで公開されています。詳細は `LICENSE` ファイルを参照してください。
+このプロジェクトは GNU General Public License v3.0 (GPLv3) のもとでライセンスされています。詳細は [LICENSE](LICENSE) ファイルを参照してください。オープンソースソフトウェアとして、本ソフトウェアは「現状のまま」提供され、いかなる明示または黙示の保証も行いません。また、本ソフトウェアを使用した結果について、作者は一切の責任や義務を負いません。出力結果は慎重に検証されていますが、学術論文の作成など重要な用途においては、ユーザーご自身で結果を独立して確認および検証することを強くお勧めします。バグに遭遇した場合は、Issueを作成してください。
 
 ## 引用
 

{moleditpy_linux-4.1.0 → moleditpy_linux-4.1.2}/README.md

@@ -134,9 +134,9 @@ moleditpy
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
   * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
-## License
+## License & Disclaimer
 
-This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**. See the `LICENSE` file for details.
+This project is licensed under the GNU General Public License v3.0 (GPLv3) - see the [LICENSE](LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
 
 ## Citation
 
@@ -268,9 +268,9 @@ moleditpy
   * **化学計算 (RDKit / Open Babel):** 2DデータからRDKit分子オブジェクトを生成し、3D座標生成や分子特性計算を実行します。RDKitでの3D座標生成が失敗した際は、Open Babelにフォールバックします。重い計算処理は別スレッド (`QThread`) で実行し、GUIの応答性を維持しています。
   * **3D可視化 (PyVista / pyvistaqt):** RDKitのコンフォーマ座標からPyVistaのメッシュ（球や円柱）を生成して描画します。カスタムの`vtkInteractorStyle`を実装し、3Dビュー内での原子の直接的なドラッグ＆ドロップ編集を可能にしています。
 
-## ライセンス
+## ライセンス & 免責事項
 
-このプロジェクトは **GNU General Public License v3.0 (GPL-v3)** のもとで公開されています。詳細は `LICENSE` ファイルを参照してください。
+このプロジェクトは GNU General Public License v3.0 (GPLv3) のもとでライセンスされています。詳細は [LICENSE](LICENSE) ファイルを参照してください。オープンソースソフトウェアとして、本ソフトウェアは「現状のまま」提供され、いかなる明示または黙示の保証も行いません。また、本ソフトウェアを使用した結果について、作者は一切の責任や義務を負いません。出力結果は慎重に検証されていますが、学術論文の作成など重要な用途においては、ユーザーご自身で結果を独立して確認および検証することを強くお勧めします。バグに遭遇した場合は、Issueを作成してください。
 
 ## 引用
 

{moleditpy_linux-4.1.0 → moleditpy_linux-4.1.2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "4.1.0"
+version = "4.1.2"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-4.1.0 → moleditpy_linux-4.1.2}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.1.0
+Version: 4.1.2
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -837,9 +837,9 @@ moleditpy
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
   * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
-## License
+## License & Disclaimer
 
-This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**. See the `LICENSE` file for details.
+This project is licensed under the GNU General Public License v3.0 (GPLv3) - see the [LICENSE](LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
 
 ## Citation
 
@@ -971,9 +971,9 @@ moleditpy
   * **化学計算 (RDKit / Open Babel):** 2DデータからRDKit分子オブジェクトを生成し、3D座標生成や分子特性計算を実行します。RDKitでの3D座標生成が失敗した際は、Open Babelにフォールバックします。重い計算処理は別スレッド (`QThread`) で実行し、GUIの応答性を維持しています。
   * **3D可視化 (PyVista / pyvistaqt):** RDKitのコンフォーマ座標からPyVistaのメッシュ（球や円柱）を生成して描画します。カスタムの`vtkInteractorStyle`を実装し、3Dビュー内での原子の直接的なドラッグ＆ドロップ編集を可能にしています。
 
-## ライセンス
+## ライセンス & 免責事項
 
-このプロジェクトは **GNU General Public License v3.0 (GPL-v3)** のもとで公開されています。詳細は `LICENSE` ファイルを参照してください。
+このプロジェクトは GNU General Public License v3.0 (GPLv3) のもとでライセンスされています。詳細は [LICENSE](LICENSE) ファイルを参照してください。オープンソースソフトウェアとして、本ソフトウェアは「現状のまま」提供され、いかなる明示または黙示の保証も行いません。また、本ソフトウェアを使用した結果について、作者は一切の責任や義務を負いません。出力結果は慎重に検証されていますが、学術論文の作成など重要な用途においては、ユーザーご自身で結果を独立して確認および検証することを強くお勧めします。バグに遭遇した場合は、Issueを作成してください。
 
 ## 引用
 

{moleditpy_linux-4.1.0 → moleditpy_linux-4.1.2}/src/moleditpy_linux/plugins/plugin_interface.py

@@ -499,6 +499,17 @@ class PluginContext:
         if mw and hasattr(mw, "string_importer_manager"):
             mw.string_importer_manager.load_from_smiles(smiles)
 
+    def show_xyz_data(
+        self, xyz_text: str, source_name: str = "XYZ data"
+    ) -> Optional[Any]:
+        """Display XYZ text in the 3D viewer and return the loaded RDKit Mol."""
+        mw = self.get_main_window()
+        if mw and hasattr(mw, "io_manager"):
+            show = getattr(mw.io_manager, "show_xyz_data", None)
+            if show is not None:
+                return show(xyz_text, source_name=source_name)
+        return None
+
     def to_xyz_block(self) -> Optional[str]:
         """Return the current 3D structure as an XYZ block (only element x y z lines)."""
         mol = self.current_mol

{moleditpy_linux-4.1.0 → moleditpy_linux-4.1.2}/src/moleditpy_linux/ui/calculation_worker.py

@@ -548,7 +548,22 @@ def _perform_direct_conversion(
             _safe_status,
             options=options if backend == "RDKIT" else None,
         ):
-            raise RuntimeError(f"Optimization with {opt_method} failed.")
+            fallback_success = False
+            if backend == "RDKIT" and "MMFF" in method_key:
+                _safe_status("MMFF optimization failed. Auto-falling back to UFF...")
+                fallback_success = opt_func(
+                    mol, "UFF", _check_halted, _safe_status, options=options
+                )
+                if fallback_success:
+                    with contextlib.suppress(Exception):
+                        mol.SetProp("_pme_optimization_method", "UFF_RDKIT")
+
+            if not fallback_success:
+                _safe_status(
+                    "Warning: Optimization failed. Using unoptimized structure."
+                )
+                with contextlib.suppress(Exception):
+                    mol.ClearProp("_pme_optimization_method")
 
     if _check_halted():
         raise WorkerHaltError("Halted")
@@ -664,15 +679,30 @@ print(ob_mol.write("mol"))
             _safe_status,
             options=options if backend == "RDKIT" else None,
         ):
-            _safe_status("Warning: Optimization failed. Using unoptimized structure.")
-            # Best-effort property cleanup if optimization was skipped
-            with contextlib.suppress(AttributeError, RuntimeError, TypeError):
-                rd_mol.ClearProp("_pme_optimization_method")
+            fallback_success = False
+            if backend == "RDKIT" and "MMFF" in method_key:
+                _safe_status("MMFF optimization failed. Auto-falling back to UFF...")
+                fallback_success = opt_func(
+                    rd_mol, "UFF", _check_halted, _safe_status, options=options
+                )
+                if fallback_success:
+                    with contextlib.suppress(Exception):
+                        rd_mol.SetProp("_pme_optimization_method", "UFF_RDKIT")
+
+            if not fallback_success:
+                _safe_status(
+                    "Warning: Optimization failed. Using unoptimized structure."
+                )
+                with contextlib.suppress(Exception):
+                    rd_mol.ClearProp("_pme_optimization_method")
 
         if _check_halted():
             raise WorkerHaltError("Halted")
         # Final status message before finishing (to ensure it doesn't overwrite error/halt messages)
-        opt_label = _OPT_METHOD_LABELS.get(opt_method, opt_method)
+        final_opt = "Unoptimized"
+        if rd_mol.HasProp("_pme_optimization_method"):
+            final_opt = rd_mol.GetProp("_pme_optimization_method")
+        opt_label = _OPT_METHOD_LABELS.get(final_opt, final_opt)
         _safe_status(f"Process completed (Open Babel Conversion / {opt_label}).")
         _safe_finished((worker_id, rd_mol))
         return True
@@ -925,9 +955,22 @@ class CalculationWorker(QObject):
             _safe_status,
             options=options if backend == "RDKIT" else None,
         ):
-            _safe_status("Warning: Optimization failed. Using unoptimized structure.")
-            with contextlib.suppress(Exception):
-                mol.ClearProp("_pme_optimization_method")
+            fallback_success = False
+            if backend == "RDKIT" and "MMFF" in method_key:
+                _safe_status("MMFF optimization failed. Auto-falling back to UFF...")
+                fallback_success = opt_func(
+                    mol, "UFF", _check_halted, _safe_status, options=options
+                )
+                if fallback_success:
+                    with contextlib.suppress(Exception):
+                        mol.SetProp("_pme_optimization_method", "UFF_RDKIT")
+
+            if not fallback_success:
+                _safe_status(
+                    "Warning: Optimization failed. Using unoptimized structure."
+                )
+                with contextlib.suppress(Exception):
+                    mol.ClearProp("_pme_optimization_method")
 
         # Final stereo restoration check
         for b_idx, s, satoms in orig_stereo:
@@ -939,7 +982,10 @@ class CalculationWorker(QObject):
         if _check_halted():
             raise WorkerHaltError("Halted")
         # Final status message before finishing (to ensure it doesn't overwrite error/halt messages)
-        opt_label = _OPT_METHOD_LABELS.get(opt_method, opt_method)
+        final_opt = "Unoptimized"
+        if mol.HasProp("_pme_optimization_method"):
+            final_opt = mol.GetProp("_pme_optimization_method")
+        opt_label = _OPT_METHOD_LABELS.get(final_opt, final_opt)
         _safe_status(f"Process completed (RDKit Conversion / {opt_label}).")
         _safe_finished((w_id, mol))
         return True
@@ -972,9 +1018,11 @@ class CalculationWorker(QObject):
         )
         # Final status message before finishing (to ensure it doesn't overwrite error/halt messages)
         _safe_status = helpers["status"]
-        opt_method = (options or {}).get("optimization_method") or "MMFF94s_RDKIT"
         if (options or {}).get("do_optimize", True):
-            opt_label = _OPT_METHOD_LABELS.get(opt_method, opt_method)
+            final_opt = "Unoptimized"
+            if mol.HasProp("_pme_optimization_method"):
+                final_opt = mol.GetProp("_pme_optimization_method")
+            opt_label = _OPT_METHOD_LABELS.get(final_opt, final_opt)
             _safe_status(f"Process completed (Direct 2D->3D Conversion / {opt_label}).")
         else:
             _safe_status("Process completed (Direct 2D->3D Conversion).")

{moleditpy_linux-4.1.0 → moleditpy_linux-4.1.2}/src/moleditpy_linux/ui/compute_logic.py

@@ -484,13 +484,13 @@ class ComputeManager:
             method_key = None
             if mol and mol.HasProp("_pme_optimization_method"):
                 method_key = mol.GetProp("_pme_optimization_method")
-            if not method_key:
-                method_key = self.host.init_manager.optimization_method
             if method_key:
                 labels = self.host.init_manager.opt3d_method_labels or {}
                 self.last_successful_optimization_method = labels.get(
                     method_key, method_key
                 )
+            else:
+                self.last_successful_optimization_method = "Unoptimized"
         except (AttributeError, TypeError):
             # Safe defensive fallback catching AttributeError, TypeError
             pass
@@ -539,7 +539,7 @@ class ComputeManager:
                     "Retry with UFF?",
                     f"{msg}\n\nWould you like to retry using UFF (RDKit) instead?",
                     QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No,
-                    QMessageBox.StandardButton.No,
+                    QMessageBox.StandardButton.Yes,
                 )
                 if reply == QMessageBox.StandardButton.Yes:
                     self.optimize_3d_structure("UFF_RDKIT")

{moleditpy_linux-4.1.0 → moleditpy_linux-4.1.2}/src/moleditpy_linux/ui/io_logic.py

@@ -34,7 +34,7 @@ from PyQt6.QtWidgets import (
 from rdkit import Chem
 from rdkit.Chem import AllChem, rdGeometry, rdMolTransforms, Descriptors
 
-from ..utils.constants import COVALENT_RADII, VERSION
+from ..utils.constants import COVALENT_RADII, DUMMY_XYZ_SYMBOLS, VERSION
 
 
 class IOManager:
@@ -84,139 +84,210 @@ class IOManager:
         lines[3] = self.fix_mol_counts_line(lines[3])
         return "\n".join(lines)
 
-    def load_xyz_file(self, file_path: str) -> Optional[Any]:
-        """Load XYZ file and create RDKit Mol with charge prompt and bond determination."""
-        if not self.host.state_manager.check_unsaved_changes():
-            return None
-
+    def _normalize_xyz_symbol(self, raw_symbol: str) -> Tuple[str, bool]:
+        """Return the RDKit symbol for an XYZ atom and whether it is a dummy."""
+        stripped = raw_symbol.strip()
+        if ":" in stripped:
+            return "*", True
+        if stripped.upper() in DUMMY_XYZ_SYMBOLS:
+            return "*", True
+        symbol = stripped.capitalize()
+        try:
+            atomic_num = Chem.GetPeriodicTable().GetAtomicNumber(symbol)
+        except (RuntimeError, ValueError, TypeError):
+            return "*", True
+        if atomic_num <= 0:
+            return "*", True
+        return symbol, False
+
+    def _mol_from_xyz_lines(self, raw_lines: list[str]) -> Any:
+        """Create an RDKit molecule from XYZ text lines."""
+        lines = [ln.strip() for ln in raw_lines if not ln.strip().startswith("#")]
+        while lines and not lines[0]:
+            lines.pop(0)
+
+        if not lines:
+            raise ValueError("XYZ file format error: too few lines")
+
+        atom_start = 2
         try:
-            with open(file_path, "r", encoding="utf-8") as f:
-                raw_lines = f.readlines()
-
-            lines = [ln.strip() for ln in raw_lines if not ln.strip().startswith("#")]
-            while lines and not lines[0]:
-                lines.pop(0)
-
             if len(lines) < 2:
                 raise ValueError("XYZ file format error: too few lines")
-
             num_atoms = int(lines[0])
             if num_atoms == 0:
                 raise ValueError("XYZ file has zero atoms")
+        except ValueError as exc:
+            # Not a standard headed XYZ — treat all lines as atom rows
+            if "zero atoms" in str(exc) or "too few" in str(exc):
+                raise
+            num_atoms = len(lines)
+            atom_start = 0
+
+        atoms_data = []
+        has_dummy_atoms = False
+        atom_lines = lines[atom_start : atom_start + num_atoms]
+        if len(atom_lines) < num_atoms:
+            raise ValueError("XYZ file format error: fewer atom rows than expected")
+
+        for i, line in enumerate(atom_lines):
+            parts = line.split()
+            if len(parts) < 4:
+                raise ValueError(f"Invalid atom data at line {atom_start + i + 1}")
+            raw_symbol = parts[0]
+            symbol, is_dummy = self._normalize_xyz_symbol(raw_symbol)
+            has_dummy_atoms = has_dummy_atoms or is_dummy
+            atoms_data.append(
+                (symbol, float(parts[1]), float(parts[2]), float(parts[3]))
+            )
 
-            atoms_data = []
-            for i, line in enumerate(lines[2 : 2 + num_atoms]):
-                parts = line.split()
-                if len(parts) < 4:
-                    raise ValueError(f"Invalid atom data at line {i + 3}")
-                symbol = parts[0].capitalize()
-                try:
-                    Chem.Atom(symbol)
-                except (RuntimeError, ValueError):
-                    settings = self.host.init_manager.settings
-                    if settings.get("skip_chemistry_checks", False):
-                        symbol = "C"
-                    else:
-                        raise ValueError(f"Unrecognized element symbol: {parts[0]}")
-                atoms_data.append(
-                    (symbol, float(parts[1]), float(parts[2]), float(parts[3]))
-                )
-
-            if not atoms_data:
-                raise ValueError("No valid atoms found in XYZ file")
+        if not atoms_data:
+            raise ValueError("No valid atoms found in XYZ file")
 
-            mol = Chem.RWMol()
-            conf = Chem.Conformer(len(atoms_data))
-            for i, (symbol, x, y, z) in enumerate(atoms_data):
-                atom = Chem.Atom(symbol)
-                atom.SetIntProp("xyz_unique_id", i)
-                mol.AddAtom(atom)
-                conf.SetAtomPosition(i, rdGeometry.Point3D(x, y, z))
-            mol.AddConformer(conf)
+        mol = Chem.RWMol()
+        conf = Chem.Conformer(len(atoms_data))
+        for i, (symbol, x, y, z) in enumerate(atoms_data):
+            atom = Chem.Atom(symbol)
+            atom.SetIntProp("xyz_unique_id", i)
+            if atom.GetAtomicNum() == 0:
+                atom.SetProp("xyz_original_symbol", atom_lines[i].split()[0])
+            mol.AddAtom(atom)
+            conf.SetAtomPosition(i, rdGeometry.Point3D(x, y, z))
+        mol.AddConformer(conf)
 
-            settings = self.host.init_manager.settings
-            skip_checks = bool(settings.get("skip_chemistry_checks", False))
+        settings = self.host.init_manager.settings
+        skip_checks = bool(settings.get("skip_chemistry_checks", False))
 
-            def _set_prop(m: Chem.Mol, key: str, val: Any) -> None:
+        def _set_prop(m: Chem.Mol, key: str, val: Any) -> None:
+            try:
+                if isinstance(val, int):
+                    m.SetIntProp(key, val)
+                elif isinstance(val, float):
+                    m.SetDoubleProp(key, val)
+            except (RuntimeError, TypeError, ValueError):
+                # Safe defensive fallback catching RuntimeError, TypeError, ValueError
+                pass
+
+        def _process(charge_val: int, use_rd_determine: bool = True) -> Any:
+            if use_rd_determine:
                 try:
-                    if isinstance(val, int):
-                        m.SetIntProp(key, val)
-                    elif isinstance(val, float):
-                        m.SetDoubleProp(key, val)
-                except (RuntimeError, TypeError, ValueError):
-                    # Safe defensive fallback catching RuntimeError, TypeError, ValueError
-                    pass
-
-            def _process(charge_val: int, use_rd_determine: bool = True) -> Any:
-                if use_rd_determine:
-                    try:
-                        from rdkit.Chem import rdDetermineBonds
+                    from rdkit.Chem import rdDetermineBonds
 
-                        mol_copy = Chem.RWMol(mol)
-                        rdDetermineBonds.DetermineBonds(mol_copy, charge=charge_val)
-                        candidate = mol_copy.GetMol()
-                        _set_prop(candidate, "_xyz_charge", charge_val)
-                        return candidate
-                    except (RuntimeError, ValueError, TypeError) as e:
-                        raise e
-                else:
-                    self.estimate_bonds_from_distances(mol)
-                    candidate = mol.GetMol()
+                    mol_copy = Chem.RWMol(mol)
+                    rdDetermineBonds.DetermineBonds(mol_copy, charge=charge_val)
+                    candidate = mol_copy.GetMol()
                     _set_prop(candidate, "_xyz_charge", charge_val)
                     return candidate
-
-            if skip_checks:
-                final_mol = _process(0, use_rd_determine=False)
-                _set_prop(final_mol, "_xyz_skip_checks", 1)
+                except (RuntimeError, ValueError, TypeError):
+                    raise
             else:
-                final_mol = None
-                settings = self.host.init_manager.settings
-                # First try with charge 0 (per user's 'first try with 0 then ask' requirement)
-                # but only if "Always ask" is not explicitly enabled in settings.
-                if not settings.get("always_ask_charge", False):
-                    try:
-                        final_mol = _process(0, use_rd_determine=True)
-                    except (RuntimeError, ValueError, TypeError):
-                        final_mol = None
-
-                # If still no final_mol (because always_ask is True, or charge 0 failed)
-                if final_mol is None:
-                    while True:
-                        prompt_fn = getattr(self, "prompt_for_charge", None)
-                        if callable(prompt_fn):
-                            result = prompt_fn()
-                            if isinstance(result, tuple) and len(result) == 3:
-                                charge_val, ok, skip_flag = result
-                            else:
-                                charge_val, ok, skip_flag = 0, True, False
+                self.estimate_bonds_from_distances(mol)
+                candidate = mol.GetMol()
+                _set_prop(candidate, "_xyz_charge", charge_val)
+                return candidate
+
+        if skip_checks or has_dummy_atoms:
+            final_mol = _process(0, use_rd_determine=False)
+            _set_prop(final_mol, "_xyz_skip_checks", 1)
+        else:
+            final_mol = None
+            # First try with charge 0 (per user's 'first try with 0 then ask' requirement)
+            # but only if "Always ask" is not explicitly enabled in settings.
+            if not settings.get("always_ask_charge", False):
+                try:
+                    final_mol = _process(0, use_rd_determine=True)
+                except (RuntimeError, ValueError, TypeError):
+                    final_mol = None
+
+            # If still no final_mol (because always_ask is True, or charge 0 failed)
+            if final_mol is None:
+                while True:
+                    prompt_fn = getattr(self, "prompt_for_charge", None)
+                    if callable(prompt_fn):
+                        result = prompt_fn()
+                        if isinstance(result, tuple) and len(result) == 3:
+                            charge_val, ok, skip_flag = result
                         else:
                             charge_val, ok, skip_flag = 0, True, False
+                    else:
+                        charge_val, ok, skip_flag = 0, True, False
+
+                    if not ok:
+                        return None
+                    if skip_flag:
+                        final_mol = _process(0, use_rd_determine=False)
+                        _set_prop(final_mol, "_xyz_skip_checks", 1)
+                        break
+                    try:
+                        final_mol = _process(charge_val, use_rd_determine=True)
+                        break
+                    except (RuntimeError, ValueError, TypeError) as e:
+                        if self.host.statusBar():
+                            self.host.statusBar().showMessage(
+                                f"Chemistry failed for charge {charge_val}: {e}. Try a different charge or skip."
+                            )
+                        if not callable(prompt_fn):
+                            raise e
 
-                        if not ok:
-                            return None
-                        if skip_flag:
-                            final_mol = _process(0, use_rd_determine=False)
-                            _set_prop(final_mol, "_xyz_skip_checks", 1)
-                            break
-                        try:
-                            final_mol = _process(charge_val, use_rd_determine=True)
-                            break
-                        except (RuntimeError, ValueError, TypeError) as e:
-                            if self.host.statusBar():
-                                self.host.statusBar().showMessage(
-                                    f"Chemistry failed for charge {charge_val}: {e}. Try a different charge or skip."
-                                )
-                            if not callable(prompt_fn):
-                                raise e
-
-                if final_mol:
-                    final_mol.xyz_atom_data = atoms_data
-            return final_mol
+        if final_mol:
+            final_mol.xyz_atom_data = atoms_data
+        return final_mol
+
+    def load_xyz_file(self, file_path: str) -> Optional[Any]:
+        """Load XYZ file and create RDKit Mol with charge prompt and bond determination."""
+        if not self.host.state_manager.check_unsaved_changes():
+            return None
 
+        try:
+            with open(file_path, "r", encoding="utf-8") as f:
+                return self._mol_from_xyz_lines(f.readlines())
         except (RuntimeError, TypeError, ValueError, UnicodeDecodeError) as e:
             self.host.statusBar().showMessage(f"Error parsing XYZ file: {e}")
             return None
 
+    def load_xyz_block(self, xyz_text: str) -> Optional[Any]:
+        """Load XYZ text and create an RDKit Mol without opening a file dialog."""
+        try:
+            return self._mol_from_xyz_lines(xyz_text.splitlines())
+        except (RuntimeError, TypeError, ValueError, UnicodeDecodeError) as e:
+            self.host.statusBar().showMessage(f"Error parsing XYZ data: {e}")
+            return None
+
+    def show_xyz_data(
+        self, xyz_text: str, source_name: str = "XYZ data"
+    ) -> Optional[Any]:
+        """Load XYZ text, set it as the current molecule, and draw it in 3D."""
+        try:
+            mol = self.load_xyz_block(xyz_text)
+            if mol is None:
+                return None
+
+            self.host.edit_actions_manager.clear_all(skip_check=True)
+            self.host.set_current_molecule(mol)
+            self.host.set_atom_id_to_rdkit_idx_map({})
+
+            skip_flag = False
+            if mol.HasProp("_xyz_skip_checks"):
+                skip_flag = bool(mol.GetIntProp("_xyz_skip_checks"))
+            self.host.is_xyz_derived = skip_flag or (mol.GetNumBonds() == 0)
+
+            self.host.view_3d_manager.draw_molecule_3d(mol)
+            self.host.ui_manager.enter_3d_viewer_mode()
+            self.host.ui_manager.enable_3d_features(True)
+            self.host.view_3d_manager.update_atom_id_menu_text()
+            self.host.view_3d_manager.update_atom_id_menu_state()
+
+            if self.host.statusBar():
+                self.host.statusBar().showMessage(
+                    f"3D Viewer Mode: Loaded {source_name}"
+                )
+            self.host.set_has_unsaved_changes(False)
+            self.host.state_manager.update_window_title()
+            return mol
+        except (RuntimeError, TypeError, ValueError, AttributeError) as e:
+            if self.host.statusBar():
+                self.host.statusBar().showMessage(f"XYZ display failed: {e}")
+            return None
+
     def prompt_for_charge(self) -> Tuple[Optional[int], bool, bool]:
         """Show dialog to prompt user for molecular charge when loading XYZ files."""
         dialog = QDialog(self.host)
@@ -261,6 +332,8 @@ class IOManager:
             for j in range(i + 1, num_atoms):
                 atom_i = mol.GetAtomWithIdx(i)
                 atom_j = mol.GetAtomWithIdx(j)
+                if atom_i.GetAtomicNum() == 0 or atom_j.GetAtomicNum() == 0:
+                    continue
                 distance = rdMolTransforms.GetBondLength(conf, i, j)
                 symbol_i = atom_i.GetSymbol()
                 symbol_j = atom_j.GetSymbol()

{moleditpy_linux-4.1.0 → moleditpy_linux-4.1.2}/src/moleditpy_linux/utils/constants.py

@@ -55,6 +55,11 @@ BOND_OFFSET = 3.5
 DEFAULT_BOND_LENGTH = 75  # Standard bond length used in templates
 CLIPBOARD_MIME_TYPE = "application/x-moleditpy-fragment"
 
+# XYZ dummy/pseudo-atom labels that map to RDKit wildcard atom (*)
+DUMMY_XYZ_SYMBOLS: frozenset[str] = frozenset(
+    {"*", "-", "X", "DA", "DU", "DUM", "DUMMY", "Q", "BQ", "LP"}
+)
+
 # Physical bond length (approximate) used to convert scene pixels to angstroms.
 # DEFAULT_BOND_LENGTH is the length in pixels used in the editor UI for a typical bond.
 # Many molecular file formats expect coordinates in angstroms; use ~1.5 Å as a typical single-bond length.