MoleditPy 3.0.0a3__tar.gz → 3.0.0a5__tar.gz

{moleditpy-3.0.0a3 → moleditpy-3.0.0a5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a3
+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-3.0.0a3 → moleditpy-3.0.0a5}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "3.0.0a3"
+version = "3.0.0a5"
 
 license = {file = "LICENSE"}
 

{moleditpy-3.0.0a3 → moleditpy-3.0.0a5}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a3
+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-3.0.0a3 → 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
@@ -36,34 +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.py
 src/moleditpy/ui/edit_3d_logic.py
-src/moleditpy/ui/edit_actions.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
@@ -73,7 +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
@@ -82,5 +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-3.0.0a3 → moleditpy-3.0.0a5}/src/moleditpy/core/mol_geometry.py

@@ -10,23 +10,19 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-"""Pure-logic molecular-geometry helpers.
-
-This module is intentionally free of any GUI imports so that it can
-be unit-tested in isolation and shared across dialogs and main-window
-submodules without circular dependencies.
-"""
-
-import numpy as np
+from __future__ import annotations
 import math
+import logging
 from collections import deque
+from typing import Any, Dict, Iterable, List, Optional, Set, Tuple, Union
+
+import numpy as np
 
 # ------------------------------------------------------------------
 # Primitive geometry helpers
 # ------------------------------------------------------------------
 
-
-def calc_distance(pos1, pos2) -> float:
+def calc_distance(pos1: Union[np.ndarray, Tuple[float, float, float], List[float]], pos2: Union[np.ndarray, Tuple[float, float, float], List[float]]) -> float:
     """Return the Euclidean distance between two 3-D positions.
 
     Parameters
@@ -44,7 +40,11 @@ def calc_distance(pos1, pos2) -> float:
     )
 
 
-def calc_angle_deg(pos1, pos2_vertex, pos3) -> float:
+def calc_angle_deg(
+    pos1: Union[np.ndarray, Tuple[float, float, float], List[float]],
+    pos2_vertex: Union[np.ndarray, Tuple[float, float, float], List[float]],
+    pos3: Union[np.ndarray, Tuple[float, float, float], List[float]],
+) -> float:
     """Return the angle pos1–pos2_vertex–pos3 in degrees.
 
     The angle is measured at *pos2_vertex* and is always in [0, 180].
@@ -78,7 +78,7 @@ def calc_angle_deg(pos1, pos2_vertex, pos3) -> float:
 # ------------------------------------------------------------------
 
 
-def get_connected_group(mol, start_atom, exclude=None):
+def get_connected_group(mol: Any, start_atom: int, exclude: Optional[int] = None) -> Set[int]:
     """Return the set of atom indices reachable from *start_atom*
     without passing through *exclude*.
 
@@ -124,7 +124,7 @@ def get_connected_group(mol, start_atom, exclude=None):
 # ------------------------------------------------------------------
 
 
-def rodrigues_rotate(v, axis, angle):
+def rodrigues_rotate(v: np.ndarray, axis: np.ndarray, angle: float) -> np.ndarray:
     """Rotate vector *v* around a unit *axis* by *angle* radians.
 
     Implements Rodrigues' rotation formula:
@@ -151,8 +151,13 @@ def rodrigues_rotate(v, axis, angle):
 
 
 def adjust_bond_angle(
-    positions, idx_a, idx_b, idx_c, target_angle_deg, atom_indices_to_move
-):
+    positions: np.ndarray,
+    idx_a: int,
+    idx_b: int,
+    idx_c: int,
+    target_angle_deg: float,
+    atom_indices_to_move: Iterable[int],
+) -> float:
     """Adjust the A–B–C bond angle to *target_angle_deg* using a
     difference-based rotation.
 
@@ -244,7 +249,7 @@ def adjust_bond_angle(
 # ------------------------------------------------------------------
 
 
-def calculate_dihedral(positions, i1, i2, i3, i4):
+def calculate_dihedral(positions: Any, i1: int, i2: int, i3: int, i4: int) -> float:
     """Compute the dihedral angle defined by four atom indices.
 
     Parameters
@@ -295,6 +300,70 @@ def calculate_dihedral(positions, i1, i2, i3, i4):
     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
 # ------------------------------------------------------------------
@@ -314,7 +383,7 @@ _VALENCE_LIMITS = {
 }
 
 
-def is_problematic_valence(symbol, bond_count, charge=0):
+def is_problematic_valence(symbol: str, bond_count: Union[int, float], charge: int = 0) -> bool:
     """Return ``True`` if the atom's total bond order exceeds its
     typical maximum valence.
 
@@ -406,7 +475,7 @@ def inject_ez_stereo_to_mol_block(mol_block, rdkit_mol, bonds_data):
     return "\n".join(mol_lines)
 
 
-def identify_valence_problems(atoms_data, bonds_data):
+def identify_valence_problems(atoms_data: Dict[int, Any], bonds_data: Dict[Tuple[int, int], Any]) -> List[int]:
     """Identify atoms with problematic valence.
 
     Parameters
@@ -441,7 +510,7 @@ def identify_valence_problems(atoms_data, bonds_data):
     return problem_atom_ids
 
 
-def optimize_2d_coords(mol):
+def optimize_2d_coords(mol: Any) -> Dict[int, Tuple[float, float]]:
     """Generate 2D coordinates using RDKit and return a map of (x, y) tuples."""
     from rdkit.Chem import AllChem
 
@@ -571,12 +640,12 @@ def resolve_2d_overlaps(
                 rep_id1, rep_id2 = i1, i2
                 break
 
-        if not rep_id1:
+        if rep_id1 is None:
             continue
 
         frag1 = next((f for f in fragments if rep_id1 in f), None)
         frag2 = next((f for f in fragments if rep_id2 in f), None)
-        if not frag1 or not frag2 or frag1 == frag2:
+        if frag1 is None or frag2 is None or frag1 == frag2:
             continue
 
         ids_to_move = frag1 if rep_id1 > rep_id2 else frag2

{moleditpy-3.0.0a3 → moleditpy-3.0.0a5}/src/moleditpy/core/molecular_data.py

@@ -10,7 +10,9 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
+from __future__ import annotations
 import logging
+from typing import Any, Dict, List, Optional, Set, Tuple, Union
 from rdkit import Chem
 
 try:
@@ -22,21 +24,26 @@ except ImportError:
 class PointTuple(tuple):
     """Backward-compatible tuple that allows .x() and .y() access like QPointF."""
 
-    def x(self):
+    def x(self) -> float:
         return self[0]
 
-    def y(self):
+    def y(self) -> float:
         return self[1]
 
 
 class MolecularData:
-    def __init__(self):
+    atoms: Dict[int, Dict[str, Any]]
+    bonds: Dict[Tuple[int, int], Dict[str, Any]]
+    adjacency_list: Dict[int, List[int]]
+    _next_atom_id: int
+
+    def __init__(self) -> None:
         self.atoms = {}
         self.bonds = {}
         self._next_atom_id = 0
         self.adjacency_list = {}
 
-    def add_atom(self, symbol, pos, charge=0, radical=0):
+    def add_atom(self, symbol: str, pos: Union[Any, Tuple[float, float]], charge: int = 0, radical: int = 0) -> int:
         atom_id = self._next_atom_id
         # Internalize position as raw floats to decouple from UI types (QPointF)
         if hasattr(pos, "x") and hasattr(pos, "y"):
@@ -55,7 +62,7 @@ class MolecularData:
         self._next_atom_id += 1
         return atom_id
 
-    def set_atom_pos(self, atom_id, pos):
+    def set_atom_pos(self, atom_id: int, pos: Union[Any, Tuple[float, float]]) -> None:
         """Update atom position using raw floats or QPointF."""
         if atom_id in self.atoms:
             if hasattr(pos, "x") and hasattr(pos, "y"):
@@ -65,7 +72,7 @@ class MolecularData:
             else:
                 self.atoms[atom_id]["pos"] = PointTuple((float(pos[0]), float(pos[1])))
 
-    def add_bond(self, id1, id2, order=1, stereo=0):
+    def add_bond(self, id1: int, id2: int, order: Union[int, float] = 1, stereo: int = 0) -> Tuple[Tuple[int, int], str]:
         # For stereo bonds, do not sort because ID order determines direction.
         # For non-stereo bonds, sort to normalize the key.
         if stereo == 0:
@@ -88,7 +95,7 @@ class MolecularData:
             self.bonds[(id1, id2)] = bond_data
             return (id1, id2), "created"
 
-    def remove_atom(self, atom_id):
+    def remove_atom(self, atom_id: int) -> None:
         if atom_id in self.atoms:
             # Safely get neighbors before deleting the atom's own entry
             neighbors = self.adjacency_list.get(atom_id, [])
@@ -111,7 +118,7 @@ class MolecularData:
             for key in bonds_to_remove:
                 self.bonds.pop(key, None)
 
-    def remove_bond(self, id1, id2):
+    def remove_bond(self, id1: int, id2: int) -> None:
         # Look for directional stereo bonds (forward/reverse) and normalized non-stereo bond keys.
         key_to_remove = None
         if (id1, id2) in self.bonds:
@@ -126,7 +133,7 @@ class MolecularData:
                 self.adjacency_list[id2].remove(id1)
             self.bonds.pop(key_to_remove, None)
 
-    def to_rdkit_mol(self, use_2d_stereo=True):
+    def to_rdkit_mol(self, use_2d_stereo: bool = True) -> Optional[Chem.Mol]:
         """
         use_2d_stereo: True estimates E/Z from 2D coordinates (as before). False prioritizes E/Z labels.
         Call with use_2d_stereo=False for 3D conversion.
@@ -147,6 +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
 
@@ -227,7 +235,7 @@ class MolecularData:
                 )
 
         # Helper: Pick neighbors prioritizing heavy atoms
-        def pick_preferred_neighbor(atom, exclude_idx):
+        def pick_preferred_neighbor(atom: Chem.Atom, exclude_idx: int) -> Optional[int]:
             for nbr in atom.GetNeighbors():
                 if nbr.GetIdx() == exclude_idx:
                     continue
@@ -305,7 +313,7 @@ class MolecularData:
             Chem.AssignStereochemistry(final_mol, cleanIt=False, force=False)
         return final_mol
 
-    def update_ring_info_2d(self):
+    def update_ring_info_2d(self) -> None:
         """Update is_in_ring and ring_center for all BondItems based on 2D topology."""
         if not self.atoms or not self.bonds:
             return
@@ -386,7 +394,7 @@ class MolecularData:
                     # so this is usually correct for 2D drawing.
                     bond_item.ring_center = ring_center
 
-    def to_mol_block(self):
+    def to_mol_block(self) -> Optional[str]:
         mol = self.to_rdkit_mol()
         if mol:
             try:
@@ -449,7 +457,7 @@ class MolecularData:
         mol_block += "M  END\n"
         return mol_block
 
-    def to_template_dict(self, name, version="1.0", application_version=""):
+    def to_template_dict(self, name: str, version: str = "1.0", application_version: str = "") -> Dict[str, Any]:
         """Convert current structure to a dictionary for template storage."""
         import datetime
 

{moleditpy-3.0.0a3 → 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)