MoleditPy 3.0.0a4__tar.gz → 3.0.0a6__tar.gz

{moleditpy-3.0.0a4 → moleditpy-3.0.0a6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a4
+Version: 3.0.0a6
 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
@@ -710,10 +710,10 @@ Dynamic: license-file
 [![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
-![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-64%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-75%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-67%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-8.93%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
 
 [🇯🇵 日本語 (Japanese)](#japanese)

{moleditpy-3.0.0a4 → moleditpy-3.0.0a6}/README.md

@@ -6,10 +6,10 @@
 [![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
-![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-64%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-75%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-67%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-8.93%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
 
 [🇯🇵 日本語 (Japanese)](#japanese)

{moleditpy-3.0.0a4 → moleditpy-3.0.0a6}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "3.0.0a4"
+version = "3.0.0a6"
 
 license = {file = "LICENSE"}
 

{moleditpy-3.0.0a4 → moleditpy-3.0.0a6}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a4
+Version: 3.0.0a6
 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
@@ -710,10 +710,10 @@ Dynamic: license-file
 [![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
-![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-64%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-75%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-67%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-8.93%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
 
 [🇯🇵 日本語 (Japanese)](#japanese)

{moleditpy-3.0.0a4 → moleditpy-3.0.0a6}/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-3.0.0a6}/src/moleditpy/core/mol_geometry.py

@@ -12,7 +12,6 @@ DOI: 10.5281/zenodo.17268532
 
 from __future__ import annotations
 import math
-import logging
 from collections import deque
 from typing import Any, Dict, Iterable, List, Optional, Set, Tuple, Union
 
@@ -22,7 +21,11 @@ import numpy as np
 # Primitive geometry helpers
 # ------------------------------------------------------------------
 
-def calc_distance(pos1: Union[np.ndarray, Tuple[float, float, float], List[float]], pos2: Union[np.ndarray, Tuple[float, float, float], List[float]]) -> 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
@@ -78,7 +81,9 @@ def calc_angle_deg(
 # ------------------------------------------------------------------
 
 
-def get_connected_group(mol: Any, start_atom: int, exclude: Optional[int] = None) -> Set[int]:
+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*.
 
@@ -300,6 +305,70 @@ 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
 # ------------------------------------------------------------------
@@ -319,7 +388,9 @@ _VALENCE_LIMITS = {
 }
 
 
-def is_problematic_valence(symbol: str, bond_count: Union[int, float], charge: int = 0) -> bool:
+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.
 
@@ -411,7 +482,9 @@ def inject_ez_stereo_to_mol_block(mol_block, rdkit_mol, bonds_data):
     return "\n".join(mol_lines)
 
 
-def identify_valence_problems(atoms_data: Dict[int, Any], bonds_data: Dict[Tuple[int, int], Any]) -> List[int]:
+def identify_valence_problems(
+    atoms_data: Dict[int, Any], bonds_data: Dict[Tuple[int, int], Any]
+) -> List[int]:
     """Identify atoms with problematic valence.
 
     Parameters

{moleditpy-3.0.0a4 → moleditpy-3.0.0a6}/src/moleditpy/core/molecular_data.py

@@ -12,7 +12,7 @@ DOI: 10.5281/zenodo.17268532
 
 from __future__ import annotations
 import logging
-from typing import Any, Dict, List, Optional, Set, Tuple, Union
+from typing import Any, Dict, List, Optional, Tuple, Union
 from rdkit import Chem
 
 try:
@@ -43,7 +43,13 @@ class MolecularData:
         self._next_atom_id = 0
         self.adjacency_list = {}
 
-    def add_atom(self, symbol: str, pos: Union[Any, Tuple[float, float]], charge: int = 0, radical: int = 0) -> int:
+    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"):
@@ -72,7 +78,9 @@ class MolecularData:
             else:
                 self.atoms[atom_id]["pos"] = PointTuple((float(pos[0]), float(pos[1])))
 
-    def add_bond(self, id1: int, id2: int, order: Union[int, float] = 1, stereo: int = 0) -> Tuple[Tuple[int, int], str]:
+    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:
@@ -154,6 +162,7 @@ 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
 
@@ -456,7 +465,9 @@ class MolecularData:
         mol_block += "M  END\n"
         return mol_block
 
-    def to_template_dict(self, name: str, version: str = "1.0", application_version: str = "") -> Dict[str, Any]:
+    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-3.0.0a4 → moleditpy-3.0.0a6}/src/moleditpy/main.py

@@ -50,7 +50,6 @@ def setup_logging():
     sys.excepthook = handle_exception
 
 
-
 def main():
     # Setup logging as early as possible
     setup_logging()