MoleditPy 3.0.0a2__tar.gz → 3.0.0a4__tar.gz

{moleditpy-3.0.0a2 → moleditpy-3.0.0a4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a2
+Version: 3.0.0a4
 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
@@ -711,7 +711,7 @@ Dynamic: license-file
 [![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-63.83%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-64%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)
 [![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)
@@ -834,6 +834,7 @@ moleditpy
   * **GUI and 2D Drawing (PyQt6):** The editor is built on a `QGraphicsScene`, where custom `AtomItem` and `BondItem` objects are interactively manipulated. The Undo/Redo feature is implemented by serializing the application state.
   * **Chemical Calculations (RDKit / Open Babel):** RDKit is used to generate molecule objects from 2D data, perform 3D coordinate generation, and calculate properties. Open Babel serves as a fallback for 3D conversion. All heavy computations are run on a separate `QThread` to keep the GUI responsive.
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
+  * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
 ## License
 

{moleditpy-3.0.0a2 → moleditpy-3.0.0a4}/README.md

@@ -7,7 +7,7 @@
 [![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-63.83%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-64%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)
 [![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)
@@ -130,6 +130,7 @@ moleditpy
   * **GUI and 2D Drawing (PyQt6):** The editor is built on a `QGraphicsScene`, where custom `AtomItem` and `BondItem` objects are interactively manipulated. The Undo/Redo feature is implemented by serializing the application state.
   * **Chemical Calculations (RDKit / Open Babel):** RDKit is used to generate molecule objects from 2D data, perform 3D coordinate generation, and calculate properties. Open Babel serves as a fallback for 3D conversion. All heavy computations are run on a separate `QThread` to keep the GUI responsive.
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
+  * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
 ## License
 

{moleditpy-3.0.0a2 → moleditpy-3.0.0a4}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "3.0.0a2"
+version = "3.0.0a4"
 
 license = {file = "LICENSE"}
 

{moleditpy-3.0.0a2 → moleditpy-3.0.0a4}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a2
+Version: 3.0.0a4
 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
@@ -711,7 +711,7 @@ Dynamic: license-file
 [![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-63.83%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-64%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)
 [![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)
@@ -834,6 +834,7 @@ moleditpy
   * **GUI and 2D Drawing (PyQt6):** The editor is built on a `QGraphicsScene`, where custom `AtomItem` and `BondItem` objects are interactively manipulated. The Undo/Redo feature is implemented by serializing the application state.
   * **Chemical Calculations (RDKit / Open Babel):** RDKit is used to generate molecule objects from 2D data, perform 3D coordinate generation, and calculate properties. Open Babel serves as a fallback for 3D conversion. All heavy computations are run on a separate `QThread` to keep the GUI responsive.
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
+  * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
 ## License
 

moleditpy-3.0.0a4/src/MoleditPy.egg-info/SOURCES.txt

@@ -0,0 +1,84 @@
+LICENSE
+README.md
+pyproject.toml
+src/MoleditPy.egg-info/PKG-INFO
+src/MoleditPy.egg-info/SOURCES.txt
+src/MoleditPy.egg-info/dependency_links.txt
+src/MoleditPy.egg-info/entry_points.txt
+src/MoleditPy.egg-info/requires.txt
+src/MoleditPy.egg-info/top_level.txt
+src/moleditpy/__init__.py
+src/moleditpy/__main__.py
+src/moleditpy/main.py
+src/moleditpy.egg-info/PKG-INFO
+src/moleditpy.egg-info/SOURCES.txt
+src/moleditpy.egg-info/dependency_links.txt
+src/moleditpy.egg-info/entry_points.txt
+src/moleditpy.egg-info/requires.txt
+src/moleditpy.egg-info/top_level.txt
+src/moleditpy/assets/file_icon.ico
+src/moleditpy/assets/icon.icns
+src/moleditpy/assets/icon.ico
+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
+src/moleditpy/plugins/plugin_manager_window.py
+src/moleditpy/ui/__init__.py
+src/moleditpy/ui/about_dialog.py
+src/moleditpy/ui/align_plane_dialog.py
+src/moleditpy/ui/alignment_dialog.py
+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/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/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
+src/moleditpy/ui/template_preview_item.py
+src/moleditpy/ui/template_preview_view.py
+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
+src/moleditpy/ui/settings_tabs/settings_3d_tabs.py
+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/sip_isdeleted_safe.py
+src/moleditpy/utils/system_utils.py

moleditpy-3.0.0a4/src/moleditpy/__init__.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+MoleditPy — A Python-based molecular editing software
+
+Author: Hiromichi Yokoyama
+License: GPL-3.0 license
+Repo: https://github.com/HiroYokoyama/python_molecular_editor
+DOI: 10.5281/zenodo.17268532
+"""
+
+"""Top-level package for moleditpy."""
+
+import importlib.util
+
+try:
+    OBABEL_AVAILABLE = importlib.util.find_spec("openbabel") is not None
+except ImportError:
+    OBABEL_AVAILABLE = False

{moleditpy-3.0.0a2/src/moleditpy/modules → moleditpy-3.0.0a4/src/moleditpy/core}/mol_geometry.py

@@ -10,12 +10,11 @@ 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.
-"""
+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
 
@@ -23,8 +22,7 @@ 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
@@ -42,7 +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].
@@ -76,7 +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*.
 
@@ -122,7 +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:
@@ -149,8 +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.
 
@@ -242,7 +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
@@ -312,7 +319,7 @@ _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.
 
@@ -404,7 +411,7 @@ 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
@@ -437,3 +444,148 @@ def identify_valence_problems(atoms_data, bonds_data):
             problem_atom_ids.append(atom_id)
 
     return problem_atom_ids
+
+
+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
+
+    AllChem.Compute2DCoords(mol)
+    conf = mol.GetConformer()
+    new_positions = {}
+    for rdkit_atom in mol.GetAtoms():
+        if rdkit_atom.HasProp("_original_atom_id"):
+            original_id = rdkit_atom.GetIntProp("_original_atom_id")
+            pos = conf.GetAtomPosition(rdkit_atom.GetIdx())
+            new_positions[original_id] = (pos.x, pos.y)
+    return new_positions
+
+
+def calculate_best_fit_plane_projection(centered_positions, normal, centroid):
+    """Project centered points orthogonally onto the plane defined by normal and centroid."""
+    projections = centered_positions - np.outer(
+        np.dot(centered_positions, normal), normal
+    )
+    return projections + centroid
+
+
+def rotate_2d_points(points_map, center_x, center_y, angle_degrees):
+    """Rotate 2D points (atom_id -> (x, y)) around a center."""
+    rad = math.radians(angle_degrees)
+    cos_a = math.cos(rad)
+    sin_a = math.sin(rad)
+    new_positions = {}
+    for atom_id, (x, y) in points_map.items():
+        dx = x - center_x
+        dy = y - center_y
+        new_dx = dx * cos_a - dy * sin_a
+        new_dy = dx * sin_a + dy * cos_a
+        new_positions[atom_id] = (center_x + new_dx, center_y + new_dy)
+    return new_positions
+
+
+def resolve_2d_overlaps(
+    atom_ids,
+    positions_map,
+    adjacency_list,
+    overlap_threshold=0.5,
+    move_distance=20,
+    has_bond_check_func=None,
+):
+    """Detect and resolve overlapping atom groups in 2D.
+
+    Returns list of (atom_ids_set, translation_vector_tuple).
+    """
+    overlapping_pairs = []
+    ids_list = list(atom_ids)
+    for i in range(len(ids_list)):
+        for j in range(i + 1, len(ids_list)):
+            id1 = ids_list[i]
+            id2 = ids_list[j]
+
+            # Skip directly bonded pairs
+            if has_bond_check_func and has_bond_check_func(id1, id2):
+                continue
+
+            p1 = positions_map[id1]
+            p2 = positions_map[id2]
+            dist = math.sqrt((p1[0] - p2[0]) ** 2 + (p1[1] - p2[1]) ** 2)
+            if dist < overlap_threshold:
+                overlapping_pairs.append((id1, id2))
+
+    if not overlapping_pairs:
+        return []
+
+    # Union-Find for overlap groups
+    parent = {aid: aid for aid in atom_ids}
+
+    def find_set(aid):
+        if parent[aid] == aid:
+            return aid
+        parent[aid] = find_set(parent[aid])
+        return parent[aid]
+
+    def unite_sets(aid1, aid2):
+        root1 = find_set(aid1)
+        root2 = find_set(aid2)
+        if root1 != root2:
+            parent[root2] = root1
+
+    for id1, id2 in overlapping_pairs:
+        unite_sets(id1, id2)
+
+    groups_by_root = {}
+    for aid in atom_ids:
+        root = find_set(aid)
+        groups_by_root.setdefault(root, []).append(aid)
+
+    move_operations = []
+    processed_roots = set()
+
+    for root_id, group_ids in groups_by_root.items():
+        if root_id in processed_roots or len(group_ids) < 2:
+            continue
+        processed_roots.add(root_id)
+
+        # Split into fragments via BFS
+        fragments = []
+        visited = set()
+        group_set = set(group_ids)
+        for aid in group_ids:
+            if aid not in visited:
+                frag = set()
+                q = deque([aid])
+                visited.add(aid)
+                frag.add(aid)
+                while q:
+                    curr = q.popleft()
+                    for neighbor in adjacency_list.get(curr, []):
+                        if neighbor in group_set and neighbor not in visited:
+                            visited.add(neighbor)
+                            frag.add(neighbor)
+                            q.append(neighbor)
+                fragments.append(frag)
+
+        if len(fragments) < 2:
+            continue
+
+        # Find representative pair
+        rep_id1, rep_id2 = None, None
+        for i1, i2 in overlapping_pairs:
+            if find_set(i1) == root_id:
+                rep_id1, rep_id2 = i1, i2
+                break
+
+        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 frag1 is None or frag2 is None or frag1 == frag2:
+            continue
+
+        ids_to_move = frag1 if rep_id1 > rep_id2 else frag2
+        # Move vector (-move_distance, move_distance)
+        move_operations.append((ids_to_move, (-move_distance, move_distance)))
+
+    return move_operations