MoleditPy 4.8.3__tar.gz → 4.9.1__tar.gz

{moleditpy-4.8.3 → moleditpy-4.9.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 4.8.3
+Version: 4.9.1
 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
@@ -710,7 +710,7 @@ 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)
-[![Overall Coverage](https://img.shields.io/badge/coverage->80%25-green)](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/tests/coverage_report.md)
+[![codecov](https://codecov.io/gh/HiroYokoyama/python_molecular_editor/graph/badge.svg)](https://codecov.io/gh/HiroYokoyama/python_molecular_editor)
 [![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/tests/MANUAL_CHECKLIST.md)
 [![Pylint Score](https://img.shields.io/badge/pylint->9%2F10-brightgreen)](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/tests/pylint-score.txt)
 [![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)

{moleditpy-4.8.3 → moleditpy-4.9.1}/README.md

@@ -6,7 +6,7 @@
 [![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)
-[![Overall Coverage](https://img.shields.io/badge/coverage->80%25-green)](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/tests/coverage_report.md)
+[![codecov](https://codecov.io/gh/HiroYokoyama/python_molecular_editor/graph/badge.svg)](https://codecov.io/gh/HiroYokoyama/python_molecular_editor)
 [![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/tests/MANUAL_CHECKLIST.md)
 [![Pylint Score](https://img.shields.io/badge/pylint->9%2F10-brightgreen)](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/tests/pylint-score.txt)
 [![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)

{moleditpy-4.8.3 → moleditpy-4.9.1}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "4.8.3"
+version = "4.9.1"
 
 license = {file = "LICENSE"}
 

{moleditpy-4.8.3 → moleditpy-4.9.1}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 4.8.3
+Version: 4.9.1
 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
@@ -710,7 +710,7 @@ 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)
-[![Overall Coverage](https://img.shields.io/badge/coverage->80%25-green)](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/tests/coverage_report.md)
+[![codecov](https://codecov.io/gh/HiroYokoyama/python_molecular_editor/graph/badge.svg)](https://codecov.io/gh/HiroYokoyama/python_molecular_editor)
 [![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/tests/MANUAL_CHECKLIST.md)
 [![Pylint Score](https://img.shields.io/badge/pylint->9%2F10-brightgreen)](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/tests/pylint-score.txt)
 [![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)

{moleditpy-4.8.3 → moleditpy-4.9.1}/src/MoleditPy.egg-info/SOURCES.txt

@@ -69,6 +69,7 @@ src/moleditpy/ui/user_template_dialog.py
 src/moleditpy/ui/view_3d_logic.py
 src/moleditpy/ui/zoomable_view.py
 src/moleditpy/ui/settings_tabs/__init__.py
+src/moleditpy/ui/settings_tabs/settings_2d_cleanup_tab.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

{moleditpy-4.8.3 → moleditpy-4.9.1}/src/moleditpy/core/mol_geometry.py

@@ -591,12 +591,63 @@ def _identify_problems_rdkit(
         return None
 
 
-def optimize_2d_coords(mol: Chem.Mol) -> Dict[int, Tuple[float, float]]:
+_TARGET_BOND_LENGTH = 1.5  # matches RDKit's default (non-CoordGen) bond length
+
+
+def _normalize_bond_length(mol: Chem.Mol, target_length: float) -> None:
+    """Rescale a molecule's 2D conformer so its average bond length matches target_length."""
+    if mol.GetNumBonds() == 0:
+        return
+    conf = mol.GetConformer()
+    total_len = 0.0
+    for bond in mol.GetBonds():
+        p1 = conf.GetAtomPosition(bond.GetBeginAtomIdx())
+        p2 = conf.GetAtomPosition(bond.GetEndAtomIdx())
+        total_len += ((p1.x - p2.x) ** 2 + (p1.y - p2.y) ** 2) ** 0.5
+    avg_len = total_len / mol.GetNumBonds()
+    if avg_len <= 1e-6:
+        return
+    factor = target_length / avg_len
+    for i in range(mol.GetNumAtoms()):
+        pos = conf.GetAtomPosition(i)
+        conf.SetAtomPosition(i, (pos.x * factor, pos.y * factor, pos.z))
+
+
+def optimize_2d_coords(
+    mol: Chem.Mol,
+    prefer_coordgen: bool = False,
+    canonical_orientation: bool = True,
+    use_ring_templates: bool = False,
+    straighten_bonds: bool = False,
+    avoid_clashes: bool = False,
+) -> Dict[int, Tuple[float, float]]:
     """Generate 2D coordinates using RDKit and return a map of (x, y) tuples."""
     from rdkit.Chem import rdDepictor
 
-    rdDepictor.Compute2DCoords(mol)
+    sample_kwargs = (
+        {"nFlipsPerSample": 3, "nSample": 200, "sampleSeed": 0xF00D}
+        if avoid_clashes
+        else {}
+    )
+
+    rdDepictor.SetPreferCoordGen(prefer_coordgen)
+    try:
+        rdDepictor.Compute2DCoords(
+            mol,
+            canonOrient=canonical_orientation,
+            useRingTemplates=use_ring_templates,
+            **sample_kwargs,  # type: ignore[arg-type]  # RDKit's generated overload differs by platform.
+        )
+        if straighten_bonds:
+            rdDepictor.StraightenDepiction(mol)
+    finally:
+        rdDepictor.SetPreferCoordGen(False)
+    # CoordGen and the default generator use different internal bond-length
+    # conventions (~1.0 vs ~1.5), so normalize here to keep the on-screen
+    # scale consistent regardless of which algorithm produced the layout.
+    _normalize_bond_length(mol, _TARGET_BOND_LENGTH)
     conf = mol.GetConformer()
+
     new_positions = {}
     for rdkit_atom in mol.GetAtoms():
         if rdkit_atom.HasProp("_original_atom_id"):

{moleditpy-4.8.3 → moleditpy-4.9.1}/src/moleditpy/ui/atom_item.py

@@ -95,18 +95,18 @@ class AtomItem(QGraphicsItem):
             | QGraphicsItem.GraphicsItemFlag.ItemSendsGeometryChanges
         )
         self.setZValue(1)
+        self.font: QFont = QFont(FONT_FAMILY, 22, FONT_WEIGHT_BOLD)
         self.update_style()
         self.setAcceptHoverEvents(True)
         self.hovered: bool = False
         self.has_problem: bool = False
         self.is_visible: bool = True
-        self.font: QFont = QFont(FONT_FAMILY, 20, FONT_WEIGHT_BOLD)
 
     def update_style(self) -> None:
         """Refresh font, color, and visibility based on current scene settings."""
         if sip_isdeleted_safe(self):
             return
-        font_size = 20
+        font_size = 22
         font_family = FONT_FAMILY
         font_bold = True
         font_italic = False
@@ -114,7 +114,7 @@ class AtomItem(QGraphicsItem):
 
         scene: Any = self.scene()
         if scene is not None:
-            font_size = scene.get_setting("atom_font_size_2d", 20)
+            font_size = scene.get_setting("atom_font_size_2d", 22)
             font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
             font_bold = scene.get_setting("atom_font_bold_2d", True)
             font_italic = scene.get_setting("atom_font_italic_2d", False)
@@ -136,14 +136,14 @@ class AtomItem(QGraphicsItem):
 
     def visual_rect(self) -> QRectF:
         """Return the rectangle the atom draws into; highlights use this."""
-        font_size = 20
+        font_size = 22
         font_family = FONT_FAMILY
         font_bold = True
         font_italic = False
         font_underline = False
         scene: Any = self.scene()
         if scene is not None:
-            font_size = scene.get_setting("atom_font_size_2d", 20)
+            font_size = scene.get_setting("atom_font_size_2d", 22)
             font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
             font_bold = scene.get_setting("atom_font_bold_2d", True)
             font_italic = scene.get_setting("atom_font_italic_2d", False)
@@ -265,14 +265,14 @@ class AtomItem(QGraphicsItem):
         if not self.is_visible:
             return path
 
-        font_size = 20
+        font_size = 22
         font_family = FONT_FAMILY
         font_bold = True
         font_italic = False
         font_underline = False
         scene: Any = self.scene()
         if scene is not None:
-            font_size = scene.get_setting("atom_font_size_2d", 20)
+            font_size = scene.get_setting("atom_font_size_2d", 22)
             font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
             font_bold = scene.get_setting("atom_font_bold_2d", True)
             font_italic = scene.get_setting("atom_font_italic_2d", False)

{moleditpy-4.8.3 → moleditpy-4.9.1}/src/moleditpy/ui/bond_item.py

@@ -254,7 +254,7 @@ class BondItem(QGraphicsItem):
                 else "bond_spacing_double_2d"
             )
             bond_offset = scene.get_setting(key, 3.5)
-            wedge_width = scene.get_setting("bond_wedge_width_2d", 6.0)
+            wedge_width = scene.get_setting("bond_wedge_width_2d", 8.0)
 
         # Qt prunes clicks whose shape() escapes boundingRect().
         extra = (getattr(self, "order", 1) - 1) * bond_offset + 50 + wedge_width
@@ -270,7 +270,7 @@ class BondItem(QGraphicsItem):
             font_size = 20
             font_family = FONT_FAMILY
             if scene is not None:
-                font_size = scene.get_setting("atom_font_size_2d", 20)
+                font_size = scene.get_setting("atom_font_size_2d", 22)
                 font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
 
             font = QFont(font_family, font_size, FONT_WEIGHT_BOLD)
@@ -363,11 +363,11 @@ class BondItem(QGraphicsItem):
                     bond_color = QColor(color_hex)
 
                 # Width and Cap Style
-                bond_width = scene.get_setting("bond_width_2d", 2.0)
+                bond_width = scene.get_setting("bond_width_2d", 3.0)
                 cap_style_str = scene.get_setting("bond_cap_style_2d", "Round")
 
                 # Wedge/Dash settings
-                wedge_width_half = scene.get_setting("bond_wedge_width_2d", 6.0)
+                wedge_width_half = scene.get_setting("bond_wedge_width_2d", 8.0)
                 num_dashes = int(scene.get_setting("bond_dash_count_2d", 8))
 
                 # Cap Style logic
@@ -531,7 +531,7 @@ class BondItem(QGraphicsItem):
                         font_family = FONT_FAMILY
                         _sc: Any = self.scene()
                         if _sc is not None:
-                            font_size = _sc.get_setting("atom_font_size_2d", 20)
+                            font_size = _sc.get_setting("atom_font_size_2d", 22)
                             font_family = _sc.get_setting(
                                 "atom_font_family_2d", FONT_FAMILY
                             )

{moleditpy-4.8.3 → moleditpy-4.9.1}/src/moleditpy/ui/edit_actions_logic.py

@@ -1154,7 +1154,26 @@ class EditActionsManager:
         try:
             from moleditpy.core.mol_geometry import optimize_2d_coords
 
-            new_positions = optimize_2d_coords(mol)
+            scene = self.host.init_manager.scene
+            prefer_coordgen = bool(scene.get_setting("prefer_coordgen_2d", False))
+            canonical_orientation = bool(
+                scene.get_setting("cleanup_canonical_orientation_2d", True)
+            )
+            use_ring_templates = bool(
+                scene.get_setting("cleanup_use_ring_templates_2d", False)
+            )
+            straighten_bonds = bool(
+                scene.get_setting("cleanup_straighten_bonds_2d", False)
+            )
+            avoid_clashes = bool(scene.get_setting("cleanup_avoid_clashes_2d", False))
+            new_positions = optimize_2d_coords(
+                mol,
+                prefer_coordgen,
+                canonical_orientation,
+                use_ring_templates,
+                straighten_bonds,
+                avoid_clashes,
+            )
 
             if not new_positions:
                 self.host.statusBar().showMessage(  # type: ignore[union-attr]

{moleditpy-4.8.3 → moleditpy-4.9.1}/src/moleditpy/ui/io_logic.py

@@ -30,6 +30,7 @@ from PyQt6.QtWidgets import (
     QPushButton,
     QFileDialog,
     QMessageBox,
+    QWidget,
 )
 
 from rdkit import Chem
@@ -109,6 +110,63 @@ class IOManager:
         lines[3] = self.fix_mol_counts_line(lines[3])
         return "\n".join(lines)
 
+    @staticmethod
+    def _first_sdf_record(sdf_text: str) -> str:
+        """Return the MOL block of the first record in SDF text.
+
+        Chem.SDMolSupplier(file_path) reads the file itself and cannot be
+        given pre-decoded text, so it never sees the encoding fallbacks in
+        _read_text_lines_flexible and mishandles CP932/Shift-JIS SDF files.
+        Extracting the first record's MOL block (everything before the first
+        "$$$$" separator) lets the already-decoded text go through
+        MolFromMolBlock instead, matching the .mol import path. Trailing SDF
+        property tags after "M  END" are harmless — MolFromMolBlock stops
+        reading once it hits the end of the connection table.
+        """
+        record_lines = []
+        for line in sdf_text.splitlines():
+            if line.strip() == "$$$$":
+                break
+            record_lines.append(line)
+        return "\n".join(record_lines)
+
+    def _load_mol_block_text(self, file_path: str) -> str:
+        """Read a .mol/.sdf file flexibly-encoded and return a MolFromMolBlock-ready block.
+
+        Shared by load_mol_file and load_mol_file_for_3d_viewing so the
+        flexible-encoding read, .sdf first-record extraction, and V2000
+        counts-line fix live in one place.
+        """
+        raw = "".join(self._read_text_lines_flexible(file_path))
+        if file_path.lower().endswith(".sdf"):
+            raw = self._first_sdf_record(raw)
+        return self.fix_mol_block(raw)
+
+    @staticmethod
+    def _read_text_lines_flexible(file_path: str) -> list[str]:
+        """Read a text file's lines, tolerating non-UTF-8 encodings.
+
+        XYZ comment lines are free-form and files authored on Japanese
+        (or other non-UTF-8) locales are commonly saved as Shift-JIS/CP932
+        rather than UTF-8, which raises UnicodeDecodeError under a strict
+        utf-8 open(). Fall back through the encodings Windows/macOS/Linux
+        editors actually produce before giving up and replacing the
+        undecodable bytes, so a mojibake comment never blocks the atoms
+        themselves from loading.
+        """
+        # euc_jp must be tried before cp932/shift_jis: cp932 silently accepts
+        # some genuinely EUC-JP byte sequences and decodes them to the wrong
+        # (mojibake) characters instead of raising, so trying cp932 first
+        # would never let euc_jp text reach its correct decoding.
+        for encoding in ("utf-8-sig", "euc_jp", "cp932", "shift_jis"):
+            try:
+                with open(file_path, "r", encoding=encoding) as f:
+                    return f.readlines()
+            except UnicodeDecodeError:
+                continue
+        with open(file_path, "r", encoding="utf-8", errors="replace") as f:
+            return f.readlines()
+
     @staticmethod
     def _is_numeric_token(token: str) -> bool:
         """True if *token* parses as a float."""
@@ -326,7 +384,8 @@ class IOManager:
         if status_bar is not None:
             status_bar.showMessage(message)
         if not os.environ.get("MOLEDITPY_HEADLESS"):
-            QMessageBox.warning(self.host, title, message)
+            parent = self.host if isinstance(self.host, QWidget) else None
+            QMessageBox.warning(parent, title, message)
 
     def load_xyz_file(self, file_path: str) -> Optional[Any]:
         """Load XYZ file and create RDKit Mol with charge prompt and bond determination."""
@@ -334,8 +393,7 @@ class IOManager:
             return None
 
         try:
-            with open(file_path, "r", encoding="utf-8") as f:
-                return self._mol_from_xyz_lines(f.readlines())
+            return self._mol_from_xyz_lines(self._read_text_lines_flexible(file_path))
         except (RuntimeError, TypeError, ValueError, UnicodeDecodeError) as e:
             self.host.statusBar().showMessage(f"Error parsing XYZ file: {e}")
             return None
@@ -777,19 +835,13 @@ class IOManager:
             return
 
         try:
-            if file_path.lower().endswith(".mol"):
-                with open(file_path, "r", encoding="utf-8", errors="replace") as fh:
-                    raw = fh.read()
-                fixed_block = self.fix_mol_block(raw)
-                # Both readers can come back empty on a malformed file; the
-                # stub for MolFromMolBlock does not say so, hence the explicit
-                # declaration. The None check below covers both branches.
-                mol: Optional[Chem.Mol] = Chem.MolFromMolBlock(
-                    fixed_block, sanitize=True, removeHs=False
-                )
-            else:
-                suppl = Chem.SDMolSupplier(file_path, removeHs=False)
-                mol = next(suppl, None)
+            fixed_block = self._load_mol_block_text(file_path)
+            # MolFromMolBlock can come back empty on a malformed file; the
+            # stub does not say so, hence the explicit declaration. The None
+            # check below covers that.
+            mol: Optional[Chem.Mol] = Chem.MolFromMolBlock(
+                fixed_block, sanitize=True, removeHs=False
+            )
 
             if mol is None:
                 raise ValueError("Failed to read molecule from file.")
@@ -991,14 +1043,8 @@ class IOManager:
             if not file_path:
                 return
         try:
-            if file_path.lower().endswith(".sdf"):
-                suppl = Chem.SDMolSupplier(file_path, removeHs=False)
-                mol = next(suppl, None)
-            else:
-                with open(file_path, "r", encoding="utf-8", errors="replace") as fh:
-                    raw = fh.read()
-                fixed_block = self.fix_mol_block(raw)
-                mol = Chem.MolFromMolBlock(fixed_block, sanitize=True, removeHs=False)
+            fixed_block = self._load_mol_block_text(file_path)
+            mol = Chem.MolFromMolBlock(fixed_block, sanitize=True, removeHs=False)
 
             if mol is None:
                 raise ValueError("Failed to load molecule.")

{moleditpy-4.8.3 → moleditpy-4.9.1}/src/moleditpy/ui/main_window_init.py

@@ -225,7 +225,7 @@ class MainInitManager:
         font = None
         if scene is not None:
             family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
-            size = scene.get_setting("atom_font_size_2d", 20)
+            size = scene.get_setting("atom_font_size_2d", 22)
             bold = scene.get_setting("atom_font_bold_2d", True)
             font = QFont(
                 family, size, QFont.Weight.Bold if bold else QFont.Weight.Normal

{moleditpy-4.8.3 → moleditpy-4.9.1}/src/moleditpy/ui/molecular_scene_handler.py

@@ -369,7 +369,7 @@ class TemplateMixin:
             and self.get_setting("template_fusing_enabled_2d", True)
             and not alt_pressed
         ):
-            map_threshold = self.get_setting("template_fusing_distance_2d", 7.0)
+            map_threshold = self.get_setting("template_fusing_distance_2d", 5.0)
             for i, p in enumerate(points):
                 if atom_items[i] is not None:
                     continue
@@ -548,7 +548,7 @@ class TemplateMixin:
             # Snap individual preview vertices to nearby atoms to reflect template fusing visually
             vertex_atoms: List[Optional[AtomItem]] = [None] * len(points)
             if self.get_setting("template_fusing_enabled_2d", True) and not alt_pressed:
-                fuse_dist = self.get_setting("template_fusing_distance_2d", 7.0)
+                fuse_dist = self.get_setting("template_fusing_distance_2d", 5.0)
                 mapped_atoms = set(self.template_context.get("items", []))
                 used_indices = set()
                 click_map_threshold = max(0.5 * bond_len, 8.0)

{moleditpy-4.8.3 → moleditpy-4.9.1}/src/moleditpy/ui/settings_dialog.py

@@ -23,6 +23,7 @@ from PyQt6.QtWidgets import (
 )
 
 from .settings_tabs.settings_2d_tab import Settings2DTab
+from .settings_tabs.settings_2d_cleanup_tab import Settings2DCleanupTab
 from .settings_tabs.settings_3d_tabs import Settings3DSceneTab, SettingsModelTab
 from .settings_tabs.settings_other_tab import SettingsOtherTab
 
@@ -35,6 +36,7 @@ class SettingsDialog(QDialog):
     def __init__(self, current_settings: Any, parent: Any = None) -> None:
         super().__init__(parent)
         self.tab_2d: Any = None
+        self.tab_2d_cleanup: Any = None
         self.tab_bs: Any = None
         self.tab_cpk: Any = None
         self.tab_other: Any = None
@@ -57,6 +59,7 @@ class SettingsDialog(QDialog):
 
         # Instantiate Tabs
         self.tab_2d = Settings2DTab(self.default_settings, self)
+        self.tab_2d_cleanup = Settings2DCleanupTab(self.default_settings, self)
         self.tab_scene = Settings3DSceneTab(self.default_settings, self)
         self.tab_bs = SettingsModelTab(
             "ball_stick",
@@ -86,6 +89,7 @@ class SettingsDialog(QDialog):
 
         # Add Tabs to Widget
         self.tab_widget.addTab(self.tab_2d, "2D Settings")
+        self.tab_widget.addTab(self.tab_2d_cleanup, "2D Cleanup")
         self.tab_widget.addTab(self.tab_scene, "3D Scene")
         self.tab_widget.addTab(self.tab_bs, "Ball & Stick")
         self.tab_widget.addTab(self.tab_cpk, "CPK (Space-filling)")

moleditpy-4.9.1/src/moleditpy/ui/settings_tabs/settings_2d_cleanup_tab.py

@@ -0,0 +1,146 @@
+#!/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
+"""
+
+from collections.abc import Mapping
+from typing import Any, Optional
+
+from PyQt6.QtWidgets import (
+    QCheckBox,
+    QFormLayout,
+    QWidget,
+)
+from .settings_tab_base import SettingsTabBase
+
+
+class Settings2DCleanupTab(SettingsTabBase):
+    """Settings tab for the 'Clean Up 2D Structure' layout options."""
+
+    def __init__(
+        self, default_settings: Mapping[str, Any], parent: Optional[QWidget] = None
+    ) -> None:
+        super().__init__(default_settings, parent)
+        self.prefer_coordgen_2d_checkbox: Any = None
+        self.cleanup_canonical_orientation_2d_checkbox: Any = None
+        self.cleanup_use_ring_templates_2d_checkbox: Any = None
+        self.cleanup_straighten_bonds_2d_checkbox: Any = None
+        self.cleanup_avoid_clashes_2d_checkbox: Any = None
+        # (checkbox, base tooltip) pairs for options CoordGen silently ignores.
+        self._coordgen_ignored: list[tuple[Any, str]] = []
+        self._setup_ui()
+
+    def _setup_ui(self) -> None:
+        form_layout = QFormLayout(self)
+
+        self.prefer_coordgen_2d_checkbox = QCheckBox()
+        self.prefer_coordgen_2d_checkbox.setToolTip(
+            "If checked, 'Clean Up 2D Structure' uses RDKit's CoordGen "
+            "algorithm, which typically produces nicer ring layouts than "
+            "the default generator."
+        )
+        form_layout.addRow(
+            "Prefer CoordGen for Cleanup:", self.prefer_coordgen_2d_checkbox
+        )
+
+        canonical_tooltip = (
+            "If checked, 'Clean Up 2D Structure' rotates the result into "
+            "RDKit's canonical orientation. Note that cleanup always "
+            "regenerates coordinates, so unchecking this keeps the "
+            "generator's raw orientation, not the pre-cleanup one."
+        )
+        self.cleanup_canonical_orientation_2d_checkbox = QCheckBox()
+        self.cleanup_canonical_orientation_2d_checkbox.setToolTip(canonical_tooltip)
+        form_layout.addRow(
+            "Canonical Orientation:", self.cleanup_canonical_orientation_2d_checkbox
+        )
+
+        ring_templates_tooltip = (
+            "If checked, 'Clean Up 2D Structure' uses RDKit's built-in "
+            "template shapes for strained polycyclic ring systems. Only a "
+            "small set of ring systems has a template, so most structures "
+            "are unaffected."
+        )
+        self.cleanup_use_ring_templates_2d_checkbox = QCheckBox()
+        self.cleanup_use_ring_templates_2d_checkbox.setToolTip(ring_templates_tooltip)
+        form_layout.addRow(
+            "Use Ring Templates:", self.cleanup_use_ring_templates_2d_checkbox
+        )
+
+        self.cleanup_straighten_bonds_2d_checkbox = QCheckBox()
+        self.cleanup_straighten_bonds_2d_checkbox.setToolTip(
+            "If checked, 'Clean Up 2D Structure' rotates the result so most "
+            "bonds align to 30°/90° angles."
+        )
+        form_layout.addRow(
+            "Straighten Bonds:", self.cleanup_straighten_bonds_2d_checkbox
+        )
+
+        avoid_clashes_tooltip = (
+            "If checked, 'Clean Up 2D Structure' samples extra layouts to "
+            "reduce atom/bond overlap. Mainly affects flexible acyclic "
+            "chains, and can be slower on large molecules."
+        )
+        self.cleanup_avoid_clashes_2d_checkbox = QCheckBox()
+        self.cleanup_avoid_clashes_2d_checkbox.setToolTip(avoid_clashes_tooltip)
+        form_layout.addRow("Avoid Clashes:", self.cleanup_avoid_clashes_2d_checkbox)
+
+        # RDKit's CoordGen algorithm silently ignores canonOrient,
+        # useRingTemplates and the clash-avoidance sampling parameters, so
+        # these are grayed out while it is active. StraightenDepiction runs
+        # afterwards on the finished depiction, so it still applies.
+        self._coordgen_ignored = [
+            (self.cleanup_canonical_orientation_2d_checkbox, canonical_tooltip),
+            (self.cleanup_use_ring_templates_2d_checkbox, ring_templates_tooltip),
+            (self.cleanup_avoid_clashes_2d_checkbox, avoid_clashes_tooltip),
+        ]
+        self.prefer_coordgen_2d_checkbox.toggled.connect(
+            self._update_coordgen_dependent_options
+        )
+
+    def _update_coordgen_dependent_options(self, prefer_coordgen: bool) -> None:
+        suffix = " (not applicable when Prefer CoordGen is checked)"
+        for checkbox, base_tooltip in self._coordgen_ignored:
+            checkbox.setEnabled(not prefer_coordgen)
+            checkbox.setToolTip(base_tooltip + (suffix if prefer_coordgen else ""))
+
+    def update_ui(self, settings_dict: Mapping[str, Any]) -> None:
+        prefer_coordgen = settings_dict.get("prefer_coordgen_2d", False)
+        self.prefer_coordgen_2d_checkbox.setChecked(prefer_coordgen)
+        self._update_coordgen_dependent_options(prefer_coordgen)
+        self.cleanup_canonical_orientation_2d_checkbox.setChecked(
+            settings_dict.get("cleanup_canonical_orientation_2d", True)
+        )
+        self.cleanup_use_ring_templates_2d_checkbox.setChecked(
+            settings_dict.get("cleanup_use_ring_templates_2d", False)
+        )
+        self.cleanup_straighten_bonds_2d_checkbox.setChecked(
+            settings_dict.get("cleanup_straighten_bonds_2d", False)
+        )
+        self.cleanup_avoid_clashes_2d_checkbox.setChecked(
+            settings_dict.get("cleanup_avoid_clashes_2d", False)
+        )
+
+    def get_settings(self) -> dict[str, Any]:
+        return {
+            "prefer_coordgen_2d": self.prefer_coordgen_2d_checkbox.isChecked(),
+            "cleanup_canonical_orientation_2d": (
+                self.cleanup_canonical_orientation_2d_checkbox.isChecked()
+            ),
+            "cleanup_use_ring_templates_2d": (
+                self.cleanup_use_ring_templates_2d_checkbox.isChecked()
+            ),
+            "cleanup_straighten_bonds_2d": (
+                self.cleanup_straighten_bonds_2d_checkbox.isChecked()
+            ),
+            "cleanup_avoid_clashes_2d": (
+                self.cleanup_avoid_clashes_2d_checkbox.isChecked()
+            ),
+        }

{moleditpy-4.8.3 → moleditpy-4.9.1}/src/moleditpy/ui/settings_tabs/settings_2d_tab.py

@@ -170,6 +170,7 @@ class Settings2DTab(SettingsTabBase):
         self.atom_font_underline_2d_btn.setFont(underline_font)
 
         style_row = QHBoxLayout()
+        style_row.setContentsMargins(0, 0, 0, 0)
         style_row.setSpacing(4)
         style_row.addWidget(self.atom_font_bold_2d_btn)
         style_row.addWidget(self.atom_font_italic_2d_btn)
@@ -301,13 +302,13 @@ class Settings2DTab(SettingsTabBase):
         self._update_color_buttons()
 
         self.bond_width_2d_slider.setValue(
-            int(settings_dict.get("bond_width_2d", 2.0) * 10)
+            int(settings_dict.get("bond_width_2d", 3.0) * 10)
         )
         self.bond_spacing_double_2d_slider.setValue(
-            int(settings_dict.get("bond_spacing_double_2d", 3.5) * 10)
+            int(settings_dict.get("bond_spacing_double_2d", 5.0) * 10)
         )
         self.bond_spacing_triple_2d_slider.setValue(
-            int(settings_dict.get("bond_spacing_triple_2d", 3.5) * 10)
+            int(settings_dict.get("bond_spacing_triple_2d", 6.0) * 10)
         )
 
         cap_style = settings_dict.get("bond_cap_style_2d", "Round")
@@ -316,7 +317,7 @@ class Settings2DTab(SettingsTabBase):
             self.bond_cap_style_2d_combo.setCurrentIndex(idx)
 
         self.bond_wedge_width_2d_slider.setValue(
-            int(settings_dict.get("bond_wedge_width_2d", 6.0) * 10)
+            int(settings_dict.get("bond_wedge_width_2d", 8.0) * 10)
         )
         self.bond_dash_count_2d_slider.setValue(
             settings_dict.get("bond_dash_count_2d", 8)
@@ -326,7 +327,7 @@ class Settings2DTab(SettingsTabBase):
         self.atom_font_family_2d_combo.setCurrentFont(QFont(font_family))
 
         self.atom_font_size_2d_slider.setValue(
-            settings_dict.get("atom_font_size_2d", 20)
+            settings_dict.get("atom_font_size_2d", 22)
         )
         self.atom_font_bold_2d_btn.setChecked(
             settings_dict.get("atom_font_bold_2d", True)

{moleditpy-4.8.3 → moleditpy-4.9.1}/src/moleditpy/utils/default_settings.py

@@ -66,22 +66,27 @@ DEFAULT_SETTINGS = {
     "bond_color": "#808080",
     "cpk_colors": {},
     # --- 2D Settings ---
-    "bond_width_2d": 2.0,
-    "bond_spacing_double_2d": 3.5,
-    "bond_spacing_triple_2d": 3.5,
-    "atom_font_size_2d": 20,
+    "bond_width_2d": 3.0,
+    "bond_spacing_double_2d": 5.0,
+    "bond_spacing_triple_2d": 6.0,
+    "atom_font_size_2d": 22,
     "background_color_2d": "#FFFFFF",
     "bond_color_2d": "#222222",
     "atom_use_bond_color_2d": False,
     "bond_cap_style_2d": "Round",
-    "bond_wedge_width_2d": 6.0,
+    "bond_wedge_width_2d": 8.0,
     "bond_dash_count_2d": 8,
     "atom_font_family_2d": "Arial",
     "atom_font_bold_2d": True,
     "atom_font_italic_2d": False,
     "atom_font_underline_2d": False,
     "template_fusing_enabled_2d": True,
-    "template_fusing_distance_2d": 7.0,
+    "template_fusing_distance_2d": 5.0,
     "template_snapping_distance_2d": 14.0,
     "bond_snapping_distance_2d": 14.0,
+    "prefer_coordgen_2d": False,
+    "cleanup_canonical_orientation_2d": True,
+    "cleanup_use_ring_templates_2d": False,
+    "cleanup_straighten_bonds_2d": False,
+    "cleanup_avoid_clashes_2d": False,
 }