MoleditPy-linux 4.11.2__tar.gz → 4.11.3__tar.gz

{moleditpy_linux-4.11.2 → moleditpy_linux-4.11.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.11.2
+Version: 4.11.3
 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

{moleditpy_linux-4.11.2 → moleditpy_linux-4.11.3}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "4.11.2"
+version = "4.11.3"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-4.11.2 → moleditpy_linux-4.11.3}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.11.2
+Version: 4.11.3
 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

{moleditpy_linux-4.11.2 → moleditpy_linux-4.11.3}/src/moleditpy_linux/core/molecular_data.py

@@ -438,13 +438,16 @@ class MolecularData:
                     bond.SetStereo(Chem.BondStereo.STEREOE)
                 ez_wanted[bond_idx] = "Z" if stereo_type == 3 else "E"
 
-                # Clear BondDir (wedge/dash) of adjacent single bonds assigned via coordinates to avoid label conflicts
-                b1 = final_mol.GetBondBetweenAtoms(begin_atom_idx, neigh1_idx)
-                b2 = final_mol.GetBondBetweenAtoms(end_atom_idx, neigh2_idx)
-                if b1 is not None:
-                    b1.SetBondDir(Chem.BondDir.NONE)
-                if b2 is not None:
-                    b2.SetBondDir(Chem.BondDir.NONE)
+                # Preserve explicit wedge/dash labels, including those applied later.
+                for center_idx, neighbor_idx in (
+                    (begin_atom_idx, neigh1_idx),
+                    (end_atom_idx, neigh2_idx),
+                ):
+                    adjacent = final_mol.GetBondBetweenAtoms(center_idx, neighbor_idx)
+                    if adjacent is not None and bond_stereo_info.get(
+                        adjacent.GetIdx(), {}
+                    ).get("type") not in (1, 2):
+                        adjacent.SetBondDir(Chem.BondDir.NONE)
 
         # The labels are CIP E/Z; the neighbors picked above are not always
         # the CIP-higher ones.

{moleditpy_linux-4.11.2 → moleditpy_linux-4.11.3}/src/moleditpy_linux/plugins/plugin_manager.py

@@ -16,8 +16,10 @@ import hashlib
 import importlib.util
 import json
 import logging
+import ntpath
 import os
 import shutil
+import stat
 import sys
 import zipfile
 from typing import Any, Callable, Dict, List, Optional, Tuple
@@ -164,6 +166,88 @@ class PluginManager:
         self.ensure_plugin_dir()
         QDesktopServices.openUrl(QUrl.fromLocalFile(self.plugin_dir))
 
+    @staticmethod
+    def _safe_install_path(root: str, name: str) -> str:
+        """Resolve a portable relative path strictly within an install directory."""
+        normalized = name.replace("\\", "/").rstrip("/")
+        parts = normalized.split("/")
+        reserved = {"CON", "PRN", "AUX", "NUL"} | {
+            f"{prefix}{number}" for prefix in ("COM", "LPT") for number in range(1, 10)
+        }
+        if (
+            not normalized
+            or normalized.startswith("/")
+            or ntpath.splitdrive(normalized)[0]
+            or any(
+                part in ("", ".", "..")
+                or part.endswith((".", " "))
+                or any(char in part for char in '<>:"|?*\0')
+                or part.split(".")[0].upper() in reserved
+                for part in parts
+            )
+        ):
+            raise ValueError(f"Unsafe plugin path: {name!r}")
+        destination = os.path.abspath(os.path.join(root, *parts))
+        resolved_root = os.path.normcase(os.path.realpath(root))
+        resolved_destination = os.path.normcase(os.path.realpath(destination))
+        if (
+            resolved_destination == resolved_root
+            or os.path.commonpath([resolved_root, resolved_destination])
+            != resolved_root
+        ):
+            raise ValueError(f"Plugin path escapes install directory: {name!r}")
+        return destination
+
+    def _install_zip(self, file_path: str, filename: str) -> str:
+        """Validate every archive member before removing or writing plugin files."""
+        with zipfile.ZipFile(file_path, "r") as archive:
+            members = []
+            for member in archive.infolist():
+                self._safe_install_path(self.plugin_dir, member.orig_filename)
+                if stat.S_ISLNK(member.external_attr >> 16):
+                    raise ValueError(
+                        "Plugin ZIP archives cannot contain symbolic links"
+                    )
+                members.append((member, member.filename.replace("\\", "/")))
+            if not members:
+                raise ValueError("Plugin ZIP archive is empty")
+
+            roots = {name.split("/")[0] for _, name in members}
+            nested = (
+                len(roots) == 1
+                and any("/" in name for _, name in members)
+                and next(iter(roots)) != "__init__.py"
+            )
+            folder = next(iter(roots)) if nested else os.path.splitext(filename)[0]
+            destination = self._safe_install_path(self.plugin_dir, folder)
+            relative_members = [
+                (member, name.partition("/")[2] if nested else name)
+                for member, name in members
+            ]
+            # Validate against the package boundary as well as the plugin root.
+            for _, name in relative_members:
+                if name:
+                    self._safe_install_path(destination, name)
+
+            if os.path.exists(destination):
+                if os.path.isdir(destination):
+                    shutil.rmtree(destination)
+                else:
+                    os.remove(destination)
+            os.makedirs(destination)
+            for member, name in relative_members:
+                if not name:
+                    continue
+                target = self._safe_install_path(destination, name)
+                if name.endswith("/"):
+                    os.makedirs(target, exist_ok=True)
+                else:
+                    os.makedirs(os.path.dirname(target), exist_ok=True)
+                    with archive.open(member) as source, open(target, "wb") as output:
+                        shutil.copyfileobj(source, output)
+            kind = "ZIP" if nested else "Flat ZIP"
+            return f"Installed package {folder} (from {kind})"
+
     def install_plugin(self, file_path: str) -> Tuple[bool, str]:
         """Copies a plugin file to the plugin directory. Supports .py and .zip."""
         self.ensure_plugin_dir()
@@ -174,7 +258,7 @@ class PluginManager:
 
             if os.path.isdir(file_path):
                 # Copy entire directory
-                dest_path = os.path.join(self.plugin_dir, filename)
+                dest_path = self._safe_install_path(self.plugin_dir, filename)
                 if os.path.exists(dest_path):
                     # Option 1: Overwrite (remove then copy) - safer for clean install
                     if os.path.isdir(dest_path):
@@ -190,63 +274,10 @@ class PluginManager:
                 )
                 msg = f"Installed package {filename}"
             elif filename.lower().endswith(".zip"):
-                # Extract ZIP contents
-                with zipfile.ZipFile(file_path, "r") as zf:
-                    # Smart Extraction: Check if ZIP has a single top-level folder
-                    # Fix for paths with backslashes on Windows if zip was created on Windows
-                    roots = set()
-                    root_is_dir = False
-                    for name in zf.namelist():
-                        # Normalize path separators to forward slash for consistent check
-                        name = name.replace("\\", "/")
-                        parts = name.split("/")
-                        if parts[0]:
-                            roots.add(parts[0])
-                            # Sub-entries prove the root is a folder
-                            if len(parts) > 1:
-                                root_is_dir = True
-
-                    is_nested = len(roots) == 1 and root_is_dir
-
-                    if is_nested:
-                        # Case A: ZIP contains a single folder (e.g. MyPlugin/init.py)
-                        top_folder = list(roots)[0]
-
-                        # A root named __init__.py always needs a wrapper folder
-                        if top_folder == "__init__.py":
-                            is_nested = False
-
-                    if is_nested:
-                        # Case A (Confirmed): Extract directly
-                        dest_path = os.path.join(self.plugin_dir, top_folder)
-
-                        # Clean Install: Remove existing folder to prevent stale files
-                        if os.path.exists(dest_path):
-                            if os.path.isdir(dest_path):
-                                shutil.rmtree(dest_path)
-                            else:
-                                os.remove(dest_path)
-
-                        zf.extractall(self.plugin_dir)
-                        msg = f"Installed package {top_folder} (from ZIP)"
-                    else:
-                        # Case B: ZIP is flat (e.g. file1.py, file2.py or just __init__.py)
-                        # Extract into a new folder named after the ZIP file
-                        folder_name = os.path.splitext(filename)[0]
-                        dest_path = os.path.join(self.plugin_dir, folder_name)
-
-                        if os.path.exists(dest_path):
-                            if os.path.isdir(dest_path):
-                                shutil.rmtree(dest_path)
-                            else:
-                                os.remove(dest_path)
-
-                        os.makedirs(dest_path)
-                        zf.extractall(dest_path)
-                        msg = f"Installed package {folder_name} (from Flat ZIP)"
+                msg = self._install_zip(file_path, filename)
             else:
                 # Standard file copy
-                dest_path = os.path.join(self.plugin_dir, filename)
+                dest_path = self._safe_install_path(self.plugin_dir, filename)
                 if os.path.exists(dest_path):
                     if os.path.isdir(dest_path):
                         shutil.rmtree(dest_path)
@@ -265,7 +296,9 @@ class PluginManager:
             OSError,
             ImportError,
             SyntaxError,
+            zipfile.BadZipFile,
         ) as e:
+            logging.warning("Plugin installation failed: %s", e, exc_info=True)
             return False, str(e)
 
     def discover_plugins(self, parent: Any = None) -> List[Dict[str, Any]]:

{moleditpy_linux-4.11.2 → moleditpy_linux-4.11.3}/src/moleditpy_linux/ui/compute_logic.py

@@ -58,6 +58,7 @@ class ComputeManager:
         """Initialize ComputeManager with reference to host window."""
         self._calculating_text_actor: Any = None
         self.original_atom_properties: Dict[int, int] = {}
+        self._worker_atom_properties: Dict[int, Dict[int, int]] = {}
         self.host = host
         self.last_successful_optimization_method: Optional[str] = None
         self._active_calc_threads: List[QThread] = []
@@ -270,6 +271,7 @@ class ComputeManager:
         self.next_conversion_id = run_id + 1
         self.active_worker_ids.add(run_id)
         self._conversion_run_ids.add(run_id)
+        self._worker_atom_properties[run_id] = self.original_atom_properties.copy()
 
         # The worker only runs built-in force fields. If the selected method is a
         # plugin optimizer, pre-optimize with MMFF (RDKit) in the worker (which
@@ -336,6 +338,7 @@ class ComputeManager:
             self.halt_ids.update(wids_to_halt)
         self.active_worker_ids.clear()
         self._pending_plugin_opt.clear()
+        self._worker_atom_properties.clear()
         getattr(self, "_conversion_run_ids", set()).clear()
 
         self._restore_button_ui()
@@ -394,6 +397,11 @@ class ComputeManager:
         run_id = int(getattr(self, "next_conversion_id", 1))
         self.next_conversion_id = run_id + 1
         options["worker_id"] = run_id
+        self._worker_atom_properties[run_id] = {
+            atom.GetIdx(): atom.GetIntProp("_original_atom_id")
+            for atom in self.host.view_3d_manager.current_mol.GetAtoms()
+            if atom.HasProp("_original_atom_id")
+        }
 
         self.active_worker_ids.add(run_id)
 
@@ -601,9 +609,14 @@ class ComputeManager:
         self.host.set_current_molecule(mol)
         self.host.is_xyz_derived = False
 
-        # Restore properties
+        # MOL blocks omit custom atom properties; restore the submitting molecule's IDs.
+        atom_properties = (
+            self._worker_atom_properties.pop(worker_id, {})
+            if worker_id is not None
+            else self.original_atom_properties
+        )
         if mol:
-            for i, orig_id in self.original_atom_properties.items():
+            for i, orig_id in atom_properties.items():
                 if i < mol.GetNumAtoms():
                     mol.GetAtomWithIdx(i).SetIntProp("_original_atom_id", orig_id)
 
@@ -713,11 +726,10 @@ class ComputeManager:
         # Accept either a string or (worker_id, message) tuple from the worker signal
         if isinstance(message, tuple) and len(message) == 2:
             worker_id, msg = message
+            self._worker_atom_properties.pop(worker_id, None)
             getattr(self, "_conversion_run_ids", set()).discard(worker_id)
             if worker_id not in self.active_worker_ids:
-                # Still cleanup overlay/buttons even if stale
-                self._remove_calculating_text()
-                self._restore_button_ui()
+                # A stale worker must not reset the current calculation's UI.
                 # If it was a halt or error from a stale worker, show with ID
                 if msg == "Halt" or msg == "Halted":
                     self.host.statusBar().showMessage(  # type: ignore[union-attr]

{moleditpy_linux-4.11.2 → moleditpy_linux-4.11.3}/src/moleditpy_linux/ui/edit_actions_logic.py

@@ -93,7 +93,7 @@ class Rotate2DDialog(QDialog):
 
         # Slider
         self.slider = QSlider(Qt.Orientation.Horizontal)
-        self.slider.setRange(-180, 180)
+        self.slider.setRange(-360, 360)
         self.slider.setValue(int(initial_angle))
         self.slider.setTickPosition(QSlider.TickPosition.TicksBelow)
         self.slider.setTickInterval(15)
@@ -240,6 +240,9 @@ class EditActionsManager:
             finally:
                 self.host.is_restoring_state = False
 
+            self.host.set_has_unsaved_changes(True)
+            self.host.state_manager.update_window_title()
+
             # Re-evaluate menu states based on 3D structure after Undo
             if (
                 self.host.view_3d_manager.current_mol
@@ -265,6 +268,9 @@ class EditActionsManager:
             finally:
                 self.host.is_restoring_state = False
 
+            self.host.set_has_unsaved_changes(True)
+            self.host.state_manager.update_window_title()
+
             # Re-evaluate menu states based on 3D structure after Redo
             if (
                 self.host.view_3d_manager.current_mol
@@ -954,6 +960,8 @@ class EditActionsManager:
                 # Cancel if requested
                 return False
 
+        # Invalidate outstanding results before replacing the document.
+        self.host.compute_manager.halt_conversion()
         self.host.ui_manager.restore_ui_for_editing()
 
         # Reset 3D mode

{moleditpy_linux-4.11.2 → moleditpy_linux-4.11.3}/src/moleditpy_linux/ui/io_logic.py

@@ -16,6 +16,8 @@ import logging
 import os
 import json
 import pickle
+import stat
+import tempfile
 import unicodedata
 from ..utils.suppress_log import suppress_log
 from typing import Any, Callable, List, Optional, Tuple
@@ -606,6 +608,42 @@ class IOManager:
 
         return len(bonds_added)
 
+    @staticmethod
+    def _write_project_json(file_path: str, data: dict[str, Any]) -> None:
+        """Replace a project only after its complete JSON has been written."""
+        # Resolve symlinks so os.replace updates the linked project rather
+        # than swapping the link itself for a regular file.
+        destination = os.path.realpath(file_path)
+        try:
+            existing_mode = stat.S_IMODE(os.stat(destination).st_mode)
+        except FileNotFoundError:
+            existing_mode = None
+        temporary_path = None
+        try:
+            with tempfile.NamedTemporaryFile(
+                mode="w",
+                encoding="utf-8",
+                dir=os.path.dirname(destination),
+                prefix=f".{os.path.basename(destination)}.",
+                suffix=".tmp",
+                delete=False,
+            ) as stream:
+                temporary_path = stream.name
+                json.dump(data, stream, indent=2, ensure_ascii=False)
+                stream.flush()
+                os.fsync(stream.fileno())
+            if existing_mode is not None:
+                # NamedTemporaryFile is owner-only; keep the project's access.
+                os.chmod(temporary_path, existing_mode)
+            os.replace(temporary_path, destination)
+            temporary_path = None
+        finally:
+            if temporary_path is not None:
+                try:
+                    os.unlink(temporary_path)
+                except OSError:
+                    logging.exception("Failed to remove temporary project file")
+
     def save_project(self) -> None:
         """Save (Ctrl+S) - Defaults to PMEPRJ format."""
         if (
@@ -627,8 +665,7 @@ class IOManager:
         if current_path and current_path.lower().endswith(".pmeprj"):
             try:
                 json_data = self.host.state_manager.create_json_data()
-                with open(current_path, "w", encoding="utf-8") as f:
-                    json.dump(json_data, f, indent=2, ensure_ascii=False)
+                self._write_project_json(current_path, json_data)
 
                 self.host.set_has_unsaved_changes(False)
                 self.host.state_manager.update_window_title()
@@ -669,8 +706,7 @@ class IOManager:
 
         try:
             json_data = self.host.state_manager.create_json_data()
-            with open(file_path, "w", encoding="utf-8") as f:
-                json.dump(json_data, f, indent=2, ensure_ascii=False)
+            self._write_project_json(file_path, json_data)
 
             self.host.set_has_unsaved_changes(False)
             self.host.set_current_file_path(file_path)
@@ -740,8 +776,7 @@ class IOManager:
                 file_path += ".pmeprj"
 
             json_data = self.host.state_manager.create_json_data()
-            with open(file_path, "w", encoding="utf-8") as f:
-                json.dump(json_data, f, indent=2, ensure_ascii=False)
+            self._write_project_json(file_path, json_data)
 
             self.host.set_has_unsaved_changes(False)
             self.host.set_current_file_path(file_path)