MoleditPy 3.0.0a4__tar.gz → 3.0.0a5__tar.gz

{moleditpy-3.0.0a4 → moleditpy-3.0.0a5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a4
+Version: 3.0.0a5
 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-3.0.0a4 → moleditpy-3.0.0a5}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "3.0.0a4"
+version = "3.0.0a5"
 
 license = {file = "LICENSE"}
 

{moleditpy-3.0.0a4 → moleditpy-3.0.0a5}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a4
+Version: 3.0.0a5
 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-3.0.0a4 → moleditpy-3.0.0a5}/src/MoleditPy.egg-info/SOURCES.txt

@@ -23,7 +23,6 @@ src/moleditpy/assets/icon.png
 src/moleditpy/core/__init__.py
 src/moleditpy/core/mol_geometry.py
 src/moleditpy/core/molecular_data.py
-src/moleditpy/modules/__init__.py
 src/moleditpy/plugins/__init__.py
 src/moleditpy/plugins/plugin_interface.py
 src/moleditpy/plugins/plugin_manager.py
@@ -36,32 +35,31 @@ src/moleditpy/ui/analysis_window.py
 src/moleditpy/ui/angle_dialog.py
 src/moleditpy/ui/app_state.py
 src/moleditpy/ui/atom_item.py
+src/moleditpy/ui/base_picking_dialog.py
 src/moleditpy/ui/bond_item.py
 src/moleditpy/ui/bond_length_dialog.py
 src/moleditpy/ui/calculation_worker.py
 src/moleditpy/ui/color_settings_dialog.py
-src/moleditpy/ui/compute_engine.py
 src/moleditpy/ui/compute_logic.py
 src/moleditpy/ui/constrained_optimization_dialog.py
 src/moleditpy/ui/custom_interactor_style.py
 src/moleditpy/ui/custom_qt_interactor.py
 src/moleditpy/ui/dialog_3d_picking_mixin.py
 src/moleditpy/ui/dialog_logic.py
-src/moleditpy/ui/dialog_manager.py
 src/moleditpy/ui/dihedral_dialog.py
 src/moleditpy/ui/edit_3d_logic.py
 src/moleditpy/ui/edit_actions_logic.py
 src/moleditpy/ui/export_logic.py
+src/moleditpy/ui/geometry_base_dialog.py
+src/moleditpy/ui/io_logic.py
 src/moleditpy/ui/main_window.py
 src/moleditpy/ui/main_window_init.py
 src/moleditpy/ui/mirror_dialog.py
-src/moleditpy/ui/molecular_parsers.py
 src/moleditpy/ui/molecular_scene_handler.py
 src/moleditpy/ui/molecule_scene.py
 src/moleditpy/ui/move_group_dialog.py
 src/moleditpy/ui/periodic_table_dialog.py
 src/moleditpy/ui/planarize_dialog.py
-src/moleditpy/ui/project_io.py
 src/moleditpy/ui/settings_dialog.py
 src/moleditpy/ui/sip_isdeleted_safe.py
 src/moleditpy/ui/string_importers.py
@@ -71,7 +69,6 @@ src/moleditpy/ui/translation_dialog.py
 src/moleditpy/ui/ui_manager.py
 src/moleditpy/ui/user_template_dialog.py
 src/moleditpy/ui/view_3d_logic.py
-src/moleditpy/ui/view_loaders.py
 src/moleditpy/ui/zoomable_view.py
 src/moleditpy/ui/settings_tabs/__init__.py
 src/moleditpy/ui/settings_tabs/settings_2d_tab.py
@@ -80,5 +77,6 @@ src/moleditpy/ui/settings_tabs/settings_other_tab.py
 src/moleditpy/ui/settings_tabs/settings_tab_base.py
 src/moleditpy/utils/__init__.py
 src/moleditpy/utils/constants.py
+src/moleditpy/utils/default_settings.py
 src/moleditpy/utils/sip_isdeleted_safe.py
 src/moleditpy/utils/system_utils.py

{moleditpy-3.0.0a4 → moleditpy-3.0.0a5}/src/moleditpy/core/mol_geometry.py

@@ -300,6 +300,70 @@ def calculate_dihedral(positions: Any, i1: int, i2: int, i3: int, i4: int) -> fl
     return float(np.degrees(angle_rad))
 
 
+def adjust_dihedral(
+    positions: np.ndarray,
+    i1: int,
+    i2: int,
+    i3: int,
+    i4: int,
+    target_dihedral_deg: float,
+    atom_indices_to_move: Iterable[int],
+) -> float:
+    """Adjust the dihedral angle defined by i1-i2-i3-i4 to target_dihedral_deg.
+    The rotation is performed around the i2-i3 bond axis.
+
+    Parameters
+    ----------
+    positions : ndarray, shape (N, 3)
+        Atom coordinates. **Modified in-place.**
+    i1, i2, i3, i4 : int
+        Atom indices defining the dihedral.
+    target_dihedral_deg : float
+        Target dihedral angle in degrees.
+    atom_indices_to_move : iterable of int
+        Indices of atoms to be rotated.
+
+    Returns
+    -------
+    float
+        Applied rotation in radians.
+    """
+    # Current dihedral
+    current_dihedral = calculate_dihedral(positions, i1, i2, i3, i4)
+
+    # Rotation angle needed
+    delta_deg = target_dihedral_deg - current_dihedral
+
+    # Shortest rotation path
+    if delta_deg > 180:
+        delta_deg -= 360
+    elif delta_deg < -180:
+        delta_deg += 360
+
+    delta_rad = np.radians(delta_deg)
+
+    if abs(delta_rad) < 1e-9:
+        return 0.0
+
+    # Rotation axis (i2 -> i3)
+    pos2 = positions[i2]
+    pos3 = positions[i3]
+    axis = pos3 - pos2
+    axis_norm = np.linalg.norm(axis)
+
+    if axis_norm < 1e-12:
+        return 0.0
+
+    axis_unit = axis / axis_norm
+
+    # Rotate each movable atom
+    for idx in atom_indices_to_move:
+        rel = positions[idx] - pos2
+        positions[idx] = pos2 + rodrigues_rotate(rel, axis_unit, delta_rad)
+
+    return float(delta_rad)
+
+
 # ------------------------------------------------------------------
 # Valence sanity check
 # ------------------------------------------------------------------

{moleditpy-3.0.0a4 → moleditpy-3.0.0a5}/src/moleditpy/core/molecular_data.py

@@ -154,6 +154,7 @@ class MolecularData:
             atom.SetFormalCharge(data.get("charge", 0))
             atom.SetNumRadicalElectrons(data.get("radical", 0))
             atom.SetIntProp("_original_atom_id", atom_id)
+            atom.SetNoImplicit(False)  # Allow RDKit to perceive implicit valence
             idx = mol.AddAtom(atom)
             atom_id_to_idx_map[atom_id] = idx
 

{moleditpy-3.0.0a4 → moleditpy-3.0.0a5}/src/moleditpy/plugins/plugin_interface.py

@@ -10,7 +10,7 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-from typing import Any, Callable, Optional
+from typing import Any, Callable, List, Optional, Union
 
 
 class PluginContext:
@@ -75,6 +75,53 @@ class PluginContext:
         """
         return Plugin3DController(self._manager.get_main_window())
 
+    def show_status_message(self, message: str, timeout: int = 3000) -> None:
+        """
+        Display a message in the application status bar.
+        """
+        self._manager.show_status_message(message, timeout)
+
+    def push_undo_checkpoint(self) -> None:
+        """
+        Create an undo checkpoint for the current state.
+        Call this AFTER making modifications to the molecule to ensure the 
+        new state is saved to the undo history.
+        """
+        self._manager.push_undo_checkpoint()
+
+    def refresh_3d_view(self) -> None:
+        """
+        Force a refresh (re-render) of the 3D scene.
+        """
+        self._manager.refresh_3d_view()
+
+    def reset_3d_camera(self) -> None:
+        """
+        Resets the 3D camera to fit the current molecule.
+        """
+        self._manager.reset_3d_camera()
+
+    def get_selected_atom_indices(self) -> List[int]:
+        """
+        Returns a list of RDKit atom indices currently selected in the 2D or 3D view.
+        Note: RDKit indices are returned, which map to the current_mol.
+        """
+        return self._manager.get_selected_atom_indices()
+
+    def register_window(self, window_id: str, window: Any) -> None:
+        """
+        Register a custom plugin window/dialog with the application.
+        This allows the application to manage the window lifecycle.
+        Windows are namespaced by the plugin name automatically.
+        """
+        self._manager.register_window(self._plugin_name, window_id, window)
+
+    def get_window(self, window_id: str) -> Optional[Any]:
+        """
+        Retrieve a previously registered window by its ID.
+        """
+        return self._manager.get_window(self._plugin_name, window_id)
+
     def get_main_window(self) -> Any:
         """
         Returns the raw MainWindow instance.
@@ -83,22 +130,45 @@ class PluginContext:
         return self._manager.get_main_window()
 
     @property
-    def current_molecule(self) -> Any:
+    def current_mol(self) -> Any:
         """
-        Get or set the current molecule (RDKit Mol object).
+        Get or set the current molecule (RDKit Mol object). Shortcut for current_molecule.
         """
-        mw = self._manager.get_main_window()
+        mw = self.get_main_window()
+        return mw.current_mol if mw else None
+
+    @current_mol.setter
+    def current_mol(self, mol: Any):
+        mw = self.get_main_window()
         if mw:
-            return mw.current_mol
-        return None
+            mw.current_mol = mol
+            if hasattr(mw.view_3d_manager, "draw_molecule_3d"):
+                mw.view_3d_manager.draw_molecule_3d(mol)
+
+    @property
+    def current_molecule(self) -> Any:
+        """Alias for current_mol for backward compatibility."""
+        return self.current_mol
 
     @current_molecule.setter
     def current_molecule(self, mol: Any):
-        mw = self._manager.get_main_window()
-        if mw:
-            mw.current_mol = mol
-            if hasattr(mw, "draw_molecule_3d"):
-                mw.draw_molecule_3d(mol)
+        self.current_mol = mol
+
+    @property
+    def plotter(self) -> Any:
+        """
+        Returns the PyVista plotter from the MainWindow.
+        """
+        mw = self.get_main_window()
+        return mw.plotter if mw else None
+
+    @property
+    def scene(self) -> Any:
+        """
+        Returns the 2D MoleculeScene from the MainWindow.
+        """
+        mw = self.get_main_window()
+        return mw.scene if mw else None
 
     def add_export_action(self, label: str, callback: Callable):
         """
@@ -202,6 +272,10 @@ class Plugin3DController:
     def __init__(self, main_window):
         self._mw = main_window
 
+    def _get_v3d(self):
+        """Helper to get the 3D manager."""
+        return getattr(self._mw, "view_3d_manager", None)
+
     def set_atom_color(self, atom_index: int, color_hex: str):
         """
         Set the color of a specific atom in the 3D view.
@@ -209,11 +283,11 @@ class Plugin3DController:
             atom_index: RDKit atom index.
             color_hex: Hex string e.g., "#FF0000".
         """
-        if hasattr(self._mw, "main_window_view_3d"):
-            self._mw.main_window_view_3d.update_atom_color_override(
-                atom_index, color_hex
-            )
-            self._mw.plotter.render()
+        v3d = self._get_v3d()
+        if v3d:
+            v3d.update_atom_color_override(atom_index, color_hex)
+            if hasattr(self._mw, "plotter") and self._mw.plotter:
+                self._mw.plotter.render()
 
     def set_bond_color(self, bond_index: int, color_hex: str):
         """
@@ -223,8 +297,25 @@ class Plugin3DController:
              bond_index: RDKit bond index.
              color_hex: Hex string e.g., "#00FF00".
         """
-        if hasattr(self._mw, "main_window_view_3d"):
-            self._mw.main_window_view_3d.update_bond_color_override(
-                bond_index, color_hex
-            )
-            self._mw.plotter.render()
+        v3d = self._get_v3d()
+        if v3d:
+            v3d.update_bond_color_override(bond_index, color_hex)
+            if hasattr(self._mw, "plotter") and self._mw.plotter:
+                self._mw.plotter.render()
+
+    def set_bond_color_by_atoms(self, atom_idx1: int, atom_idx2: int, color_hex: str):
+        """
+        Set the color of the bond between two atoms.
+
+        Args:
+            atom_idx1: First RDKit atom index.
+            atom_idx2: Second RDKit atom index.
+            color_hex: Hex string e.g., "#00FF00".
+        """
+        mol = getattr(self._mw, "current_mol", None)
+        if not mol:
+            return
+
+        bond = mol.GetBondBetweenAtoms(atom_idx1, atom_idx2)
+        if bond:
+            self.set_bond_color(bond.GetIdx(), color_hex)

{moleditpy-3.0.0a4 → moleditpy-3.0.0a5}/src/moleditpy/plugins/plugin_manager.py

@@ -50,6 +50,7 @@ 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.plugin_windows: Dict[str, Dict[str, Any]] = {} # Map of plugin_name -> {window_id -> window}
 
     def get_main_window(self) -> Any:
         return self.main_window
@@ -454,6 +455,82 @@ class PluginManager:
             {"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."""
+        if self.main_window and hasattr(self.main_window, "statusBar"):
+            status_bar = self.main_window.statusBar()
+            if status_bar:
+                status_bar.showMessage(message, timeout)
+
+    def push_undo_checkpoint(self) -> None:
+        """Triggers an undo checkpoint in the application state."""
+        if self.main_window and hasattr(self.main_window, "state_manager"):
+            self.main_window.state_manager.push_undo_state()
+
+    def refresh_3d_view(self) -> None:
+        """Force a re-render of the 3D scene."""
+        if self.main_window and hasattr(self.main_window, "plotter") and self.main_window.plotter:
+            self.main_window.plotter.render()
+
+    def reset_3d_camera(self) -> None:
+        """Reset the 3D camera to fit the current molecule."""
+        if self.main_window and hasattr(self.main_window, "plotter") and self.main_window.plotter:
+            self.main_window.plotter.reset_camera()
+            self.main_window.plotter.render()
+
+    def get_selected_atom_indices(self) -> List[int]:
+        """Retrieve RDKit atom indices currently selected in the 2D scene."""
+        selected_indices = []
+        if not self.main_window:
+            return []
+
+        # Check 2D selection
+        try:
+            from .plugin_interface import PluginContext
+            # We need to access the scene items.
+            # In MoleditPy, atoms in the scene are AtomItem objects which have an 'atom_id'.
+            # These atom_ids map to entries in state_manager.data.atoms.
+            # RDKit molecule atoms have an '_original_atom_id' property.
+            
+            scene = getattr(self.main_window, "scene", None)
+            if scene:
+                selected_items = scene.selectedItems()
+                selected_atom_ids = set()
+                for item in selected_items:
+                    # Relying on duck-typing for AtomItem
+                    if hasattr(item, "atom_id"):
+                        selected_atom_ids.add(item.atom_id)
+                
+                # Now map these editor IDs to RDKit indices
+                mol = getattr(self.main_window, "current_mol", None)
+                if mol and selected_atom_ids:
+                    for i in range(mol.GetNumAtoms()):
+                        atom = mol.GetAtomWithIdx(i)
+                        if atom.HasProp("_original_atom_id"):
+                            try:
+                                orig_id = atom.GetIntProp("_original_atom_id")
+                                if orig_id in selected_atom_ids:
+                                    selected_indices.append(i)
+                            except (RuntimeError, ValueError, TypeError):
+                                continue
+        except ImportError:
+            pass
+        except Exception as e:
+            logging.error(f"Error retrieving selected atom indices: {e}")
+
+        return selected_indices
+
+    def register_window(self, plugin_name: str, window_id: str, window: Any) -> None:
+        """Register a plugin window to keep it alive and manageable."""
+        if plugin_name not in self.plugin_windows:
+            self.plugin_windows[plugin_name] = {}
+        self.plugin_windows[plugin_name][window_id] = window
+
+    def get_window(self, plugin_name: str, window_id: str) -> Optional[Any]:
+        """Retrieve a registered plugin window."""
+        return self.plugin_windows.get(plugin_name, {}).get(window_id)
+
     def invoke_document_reset_handlers(self) -> None:
         """Call all registered document reset handlers."""
         for handler in self.document_reset_handlers: