MoleditPy-linux 4.4.0__tar.gz → 4.5.0__tar.gz

{moleditpy_linux-4.4.0 → moleditpy_linux-4.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.4.0
+Version: 4.5.0
 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
@@ -757,7 +757,7 @@ This application combines a modern GUI built with **PyQt6**, powerful cheminform
       * **Mirror:** Create a mirror image of the molecule across a selected plane (XY, XZ, or YZ).
       * **Set Bond Length, Angle, & Dihedral Angle:** Set precise numerical values for distances, angles, and torsional angles.
       * **Constrained Optimization:** Perform force field optimization (MMFF/UFF) while applying fixed constraints to specific distances, angles, or dihedral angles.
-  * **3D Measurement Tools:** A dedicated "Measure" mode allows you to click on atoms in the 3D view to instantly measure and display:
+  * **3D Measurement Tools:** The "Select" mode allows you to click on atoms in the 3D view to instantly measure and display:
       * **Distance** (between 2 atoms)
       * **Angle** (between 3 atoms)
       * **Dihedral Angle** (between 4 atoms)
@@ -893,7 +893,7 @@ Additionally, please cite the plugins you used.
       * **鏡像作成:** 選択した平面 (XY, XZ, YZ) に対して分子の鏡像を作成します。
       * **結合長・角度・二面角:** 原子を選択し、目標値を入力することで、距離、角度、ねじれ角を正確に設定します。
       * **制約付き最適化:** 特定の距離、角度、二面角を固定したまま、力場計算 (MMFF/UFF) による構造最適化を実行します。
-  * **3D測定ツール:** 専用の「Measure」モードで3Dビュー内の原子をクリックするだけで、以下の値を即座に測定・表示します。
+  * **3D測定ツール:** 「Select」モードで3Dビュー内の原子をクリックするだけで、以下の値を即座に測定・表示します。
       * **距離** (2原子間)
       * **角度** (3原子間)
       * **二面角** (4原子間)

{moleditpy_linux-4.4.0 → moleditpy_linux-4.5.0}/README.md

@@ -54,7 +54,7 @@ This application combines a modern GUI built with **PyQt6**, powerful cheminform
       * **Mirror:** Create a mirror image of the molecule across a selected plane (XY, XZ, or YZ).
       * **Set Bond Length, Angle, & Dihedral Angle:** Set precise numerical values for distances, angles, and torsional angles.
       * **Constrained Optimization:** Perform force field optimization (MMFF/UFF) while applying fixed constraints to specific distances, angles, or dihedral angles.
-  * **3D Measurement Tools:** A dedicated "Measure" mode allows you to click on atoms in the 3D view to instantly measure and display:
+  * **3D Measurement Tools:** The "Select" mode allows you to click on atoms in the 3D view to instantly measure and display:
       * **Distance** (between 2 atoms)
       * **Angle** (between 3 atoms)
       * **Dihedral Angle** (between 4 atoms)
@@ -190,7 +190,7 @@ Additionally, please cite the plugins you used.
       * **鏡像作成:** 選択した平面 (XY, XZ, YZ) に対して分子の鏡像を作成します。
       * **結合長・角度・二面角:** 原子を選択し、目標値を入力することで、距離、角度、ねじれ角を正確に設定します。
       * **制約付き最適化:** 特定の距離、角度、二面角を固定したまま、力場計算 (MMFF/UFF) による構造最適化を実行します。
-  * **3D測定ツール:** 専用の「Measure」モードで3Dビュー内の原子をクリックするだけで、以下の値を即座に測定・表示します。
+  * **3D測定ツール:** 「Select」モードで3Dビュー内の原子をクリックするだけで、以下の値を即座に測定・表示します。
       * **距離** (2原子間)
       * **角度** (3原子間)
       * **二面角** (4原子間)

{moleditpy_linux-4.4.0 → moleditpy_linux-4.5.0}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "4.4.0"
+version = "4.5.0"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-4.4.0 → moleditpy_linux-4.5.0}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.4.0
+Version: 4.5.0
 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
@@ -757,7 +757,7 @@ This application combines a modern GUI built with **PyQt6**, powerful cheminform
       * **Mirror:** Create a mirror image of the molecule across a selected plane (XY, XZ, or YZ).
       * **Set Bond Length, Angle, & Dihedral Angle:** Set precise numerical values for distances, angles, and torsional angles.
       * **Constrained Optimization:** Perform force field optimization (MMFF/UFF) while applying fixed constraints to specific distances, angles, or dihedral angles.
-  * **3D Measurement Tools:** A dedicated "Measure" mode allows you to click on atoms in the 3D view to instantly measure and display:
+  * **3D Measurement Tools:** The "Select" mode allows you to click on atoms in the 3D view to instantly measure and display:
       * **Distance** (between 2 atoms)
       * **Angle** (between 3 atoms)
       * **Dihedral Angle** (between 4 atoms)
@@ -893,7 +893,7 @@ Additionally, please cite the plugins you used.
       * **鏡像作成:** 選択した平面 (XY, XZ, YZ) に対して分子の鏡像を作成します。
       * **結合長・角度・二面角:** 原子を選択し、目標値を入力することで、距離、角度、ねじれ角を正確に設定します。
       * **制約付き最適化:** 特定の距離、角度、二面角を固定したまま、力場計算 (MMFF/UFF) による構造最適化を実行します。
-  * **3D測定ツール:** 専用の「Measure」モードで3Dビュー内の原子をクリックするだけで、以下の値を即座に測定・表示します。
+  * **3D測定ツール:** 「Select」モードで3Dビュー内の原子をクリックするだけで、以下の値を即座に測定・表示します。
       * **距離** (2原子間)
       * **角度** (3原子間)
       * **二面角** (4原子間)

{moleditpy_linux-4.4.0 → moleditpy_linux-4.5.0}/src/moleditpy_linux/plugins/plugin_interface.py

@@ -11,7 +11,7 @@ DOI: 10.5281/zenodo.17268532
 """
 
 import logging
-from typing import Any, Callable, List, Optional, Union
+from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 
 
 class PluginContext:
@@ -353,6 +353,28 @@ class PluginContext:
         """
         self._manager.register_document_reset_handler(self._plugin_name, callback)
 
+    def register_atom_drag_handler(
+        self,
+        callback: Callable[
+            [str, List[int], Dict[int, Tuple[float, float, float]]], None
+        ],
+    ) -> None:
+        """Register a handler called during 3D atom or group dragging.
+
+        The callback receives:
+            event_type (str): ``"start"``, ``"move"``, or ``"end"``.
+            atom_indices (List[int]): RDKit atom indices being dragged.
+            positions (dict[int, tuple[float, float, float]]):
+                Current 3D positions of the dragged atoms.
+                Empty dict on ``"start"``.
+        """
+        self._manager.register_atom_drag_handler(self._plugin_name, callback)
+
+    @property
+    def is_dragging_atom(self) -> bool:
+        """Return True if an atom or group is currently being dragged in 3D."""
+        return self._manager.is_dragging_atom()  # type: ignore[no-any-return]
+
     def get_setting(self, key: str, default: Any = None) -> Any:
         """
         Get a plugin-specific persistent setting.

{moleditpy_linux-4.4.0 → moleditpy_linux-4.5.0}/src/moleditpy_linux/plugins/plugin_manager.py

@@ -23,8 +23,9 @@ from typing import Any, Callable, Dict, List, Optional, Tuple
 
 from PyQt6.QtCore import QUrl
 from PyQt6.QtGui import QDesktopServices
-from PyQt6.QtWidgets import QMessageBox
+from PyQt6.QtWidgets import QApplication, QMessageBox
 
+from ..utils.constants import MOVE_DIALOG_TYPES
 from .plugin_interface import PluginContext
 
 
@@ -95,6 +96,7 @@ class PluginManager:
         self.load_handlers: Dict[str, Callable] = {}
         self.custom_3d_styles: Dict[str, Dict[str, Any]] = {}
         self.document_reset_handlers: List[Dict[str, Any]] = []
+        self.atom_drag_handlers: List[Dict[str, Any]] = []
         self.plugin_windows: Dict[
             str, Dict[str, Any]
         ] = {}  # Map of plugin_name -> {window_id -> window}
@@ -247,6 +249,7 @@ class PluginManager:
         self.load_handlers = {}
         self.custom_3d_styles = {}
         self.document_reset_handlers = []
+        self.atom_drag_handlers = []
 
         if not os.path.exists(self.plugin_dir):
             return []
@@ -558,6 +561,10 @@ class PluginManager:
             {"plugin": plugin_name, "callback": callback}
         )
 
+    def register_atom_drag_handler(self, plugin_name: str, callback: Callable) -> None:
+        """Register a handler called during 3D atom/group dragging."""
+        self.atom_drag_handlers.append({"plugin": plugin_name, "callback": callback})
+
     # --- New API Implementation ---
     def show_status_message(self, message: str, timeout: int = 3000) -> None:
         """Display a message in the MainWindow status bar."""
@@ -653,6 +660,48 @@ class PluginManager:
                     exc_info=True,
                 )
 
+    def invoke_atom_drag_handlers(
+        self,
+        event_type: str,
+        atom_indices: List[int],
+        positions: Dict[int, tuple],
+    ) -> None:
+        """Call all registered atom drag handlers."""
+        for handler in self.atom_drag_handlers:
+            try:
+                handler["callback"](event_type, atom_indices, positions)
+            except Exception as e:  # plugins have full app access; catch everything to keep the drag alive
+                logging.warning(
+                    "Error in atom drag handler for %s: %s",
+                    handler["plugin"],
+                    e,
+                    exc_info=True,
+                )
+
+    def is_dragging_atom(self) -> bool:
+        """Return True if an atom or group is currently being dragged in 3D."""
+        mw = self.main_window
+        if mw is None:
+            return False
+        if getattr(mw, "dragged_atom_info", None) is not None:
+            return True
+        return self._is_dragging_group()
+
+    @staticmethod
+    def _is_dragging_group() -> bool:
+        """Return True while a Move Group / Move Selected Atoms gesture is active."""
+        try:
+            for widget in QApplication.topLevelWidgets():
+                if type(widget).__name__ not in MOVE_DIALOG_TYPES:
+                    continue
+                if getattr(widget, "is_dragging_group_vtk", False) or getattr(
+                    widget, "is_rotating_group_vtk", False
+                ):
+                    return True
+        except (AttributeError, RuntimeError, TypeError):
+            logging.debug("Suppressed non-critical error", exc_info=True)
+        return False
+
     def get_plugin_info_safe(self, file_path: str) -> Dict[str, str]:
         """Extracts plugin metadata using AST parsing (safe, no execution)."""
         info = {

{moleditpy_linux-4.4.0 → moleditpy_linux-4.5.0}/src/moleditpy_linux/ui/atom_item.py

@@ -63,6 +63,8 @@ class AtomItem(QGraphicsItem):
         self.setFlags(
             QGraphicsItem.GraphicsItemFlag.ItemIsMovable
             | QGraphicsItem.GraphicsItemFlag.ItemIsSelectable
+            # Without this Qt never calls itemChange for moves, so bonds lag.
+            | QGraphicsItem.GraphicsItemFlag.ItemSendsGeometryChanges
         )
         self.setZValue(1)
         self.update_style()

{moleditpy_linux-4.4.0 → moleditpy_linux-4.5.0}/src/moleditpy_linux/ui/compute_logic.py

@@ -455,7 +455,8 @@ class ComputeManager:
                 if item:
                     item.has_problem = True
                     item.update()
-        self.host.init_manager.view_2d.setFocus()
+        # Defer so Qt finishes routing the modal result before restoring focus.
+        QTimer.singleShot(0, self.host.init_manager.view_2d.setFocus)
 
     def _setup_mol_block_for_worker(self, mol: Chem.Mol) -> str:
         mol_block = self.host.state_manager.data.to_mol_block()
@@ -617,6 +618,9 @@ class ComputeManager:
         with suppress_log(TypeError, RuntimeError):
             QMessageBox.critical(self.host, "Calculation Error", msg)
 
+        # Restore 2D editor focus so keyboard shortcuts remain active.
+        QTimer.singleShot(0, self.host.init_manager.view_2d.setFocus)
+
     def create_atom_id_mapping(self) -> None:
         """Map 2D atom IDs to 3D RDKit indices."""
         if not self.host.view_3d_manager.current_mol: