MoleditPy 4.10.3__tar.gz → 4.11.1__tar.gz

{moleditpy-4.10.3 → moleditpy-4.11.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 4.10.3
+Version: 4.11.1
 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
@@ -729,10 +729,10 @@ Dynamic: license-file
 
 -----
 <p align="center">
-  <img src="img/icon.png" width="500" alt="MoleditPy Icon">
+  <img src="https://hiroyokoyama.github.io/python_molecular_editor/img/icon.png" width="500" alt="MoleditPy Icon">
 </p>
 
-![](img/screenshot.png)
+![MoleditPy screenshot](https://hiroyokoyama.github.io/python_molecular_editor/img/screenshot.png)
 
 
 ## Overview
@@ -846,7 +846,7 @@ moleditpy
 
 ## License & Disclaimer
 
-This project is licensed under the GNU General Public License v3.0 (GPLv3) - see the [LICENSE](LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
+This project is licensed under the GNU General Public License v3.0 (GPLv3) - see the [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
 
 ## Citation
 
@@ -982,7 +982,7 @@ moleditpy
 
 ## ライセンス & 免責事項
 
-このプロジェクトは GNU General Public License v3.0 (GPLv3) のもとでライセンスされています。詳細は [LICENSE](LICENSE) ファイルを参照してください。オープンソースソフトウェアとして、本ソフトウェアは「現状のまま」提供され、いかなる明示または黙示の保証も行いません。また、本ソフトウェアを使用した結果について、作者は一切の責任や義務を負いません。出力結果は慎重に検証されていますが、学術論文の作成など重要な用途においては、ユーザーご自身で結果を独立して確認および検証することを強くお勧めします。バグに遭遇した場合は、Issueを作成してください。
+このプロジェクトは GNU General Public License v3.0 (GPLv3) のもとでライセンスされています。詳細は [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/LICENSE) ファイルを参照してください。オープンソースソフトウェアとして、本ソフトウェアは「現状のまま」提供され、いかなる明示または黙示の保証も行いません。また、本ソフトウェアを使用した結果について、作者は一切の責任や義務を負いません。出力結果は慎重に検証されていますが、学術論文の作成など重要な用途においては、ユーザーご自身で結果を独立して確認および検証することを強くお勧めします。バグに遭遇した場合は、Issueを作成してください。
 
 ## 引用
 

{moleditpy-4.10.3 → moleditpy-4.11.1}/README.md

@@ -25,10 +25,10 @@
 
 -----
 <p align="center">
-  <img src="img/icon.png" width="500" alt="MoleditPy Icon">
+  <img src="https://hiroyokoyama.github.io/python_molecular_editor/img/icon.png" width="500" alt="MoleditPy Icon">
 </p>
 
-![](img/screenshot.png)
+![MoleditPy screenshot](https://hiroyokoyama.github.io/python_molecular_editor/img/screenshot.png)
 
 
 ## Overview
@@ -142,7 +142,7 @@ moleditpy
 
 ## License & Disclaimer
 
-This project is licensed under the GNU General Public License v3.0 (GPLv3) - see the [LICENSE](LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
+This project is licensed under the GNU General Public License v3.0 (GPLv3) - see the [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
 
 ## Citation
 
@@ -278,7 +278,7 @@ moleditpy
 
 ## ライセンス & 免責事項
 
-このプロジェクトは GNU General Public License v3.0 (GPLv3) のもとでライセンスされています。詳細は [LICENSE](LICENSE) ファイルを参照してください。オープンソースソフトウェアとして、本ソフトウェアは「現状のまま」提供され、いかなる明示または黙示の保証も行いません。また、本ソフトウェアを使用した結果について、作者は一切の責任や義務を負いません。出力結果は慎重に検証されていますが、学術論文の作成など重要な用途においては、ユーザーご自身で結果を独立して確認および検証することを強くお勧めします。バグに遭遇した場合は、Issueを作成してください。
+このプロジェクトは GNU General Public License v3.0 (GPLv3) のもとでライセンスされています。詳細は [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/LICENSE) ファイルを参照してください。オープンソースソフトウェアとして、本ソフトウェアは「現状のまま」提供され、いかなる明示または黙示の保証も行いません。また、本ソフトウェアを使用した結果について、作者は一切の責任や義務を負いません。出力結果は慎重に検証されていますが、学術論文の作成など重要な用途においては、ユーザーご自身で結果を独立して確認および検証することを強くお勧めします。バグに遭遇した場合は、Issueを作成してください。
 
 ## 引用
 

{moleditpy-4.10.3 → moleditpy-4.11.1}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "4.10.3"
+version = "4.11.1"
 
 license = {file = "LICENSE"}
 

{moleditpy-4.10.3 → moleditpy-4.11.1}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 4.10.3
+Version: 4.11.1
 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
@@ -729,10 +729,10 @@ Dynamic: license-file
 
 -----
 <p align="center">
-  <img src="img/icon.png" width="500" alt="MoleditPy Icon">
+  <img src="https://hiroyokoyama.github.io/python_molecular_editor/img/icon.png" width="500" alt="MoleditPy Icon">
 </p>
 
-![](img/screenshot.png)
+![MoleditPy screenshot](https://hiroyokoyama.github.io/python_molecular_editor/img/screenshot.png)
 
 
 ## Overview
@@ -846,7 +846,7 @@ moleditpy
 
 ## License & Disclaimer
 
-This project is licensed under the GNU General Public License v3.0 (GPLv3) - see the [LICENSE](LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
+This project is licensed under the GNU General Public License v3.0 (GPLv3) - see the [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
 
 ## Citation
 
@@ -982,7 +982,7 @@ moleditpy
 
 ## ライセンス & 免責事項
 
-このプロジェクトは GNU General Public License v3.0 (GPLv3) のもとでライセンスされています。詳細は [LICENSE](LICENSE) ファイルを参照してください。オープンソースソフトウェアとして、本ソフトウェアは「現状のまま」提供され、いかなる明示または黙示の保証も行いません。また、本ソフトウェアを使用した結果について、作者は一切の責任や義務を負いません。出力結果は慎重に検証されていますが、学術論文の作成など重要な用途においては、ユーザーご自身で結果を独立して確認および検証することを強くお勧めします。バグに遭遇した場合は、Issueを作成してください。
+このプロジェクトは GNU General Public License v3.0 (GPLv3) のもとでライセンスされています。詳細は [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/LICENSE) ファイルを参照してください。オープンソースソフトウェアとして、本ソフトウェアは「現状のまま」提供され、いかなる明示または黙示の保証も行いません。また、本ソフトウェアを使用した結果について、作者は一切の責任や義務を負いません。出力結果は慎重に検証されていますが、学術論文の作成など重要な用途においては、ユーザーご自身で結果を独立して確認および検証することを強くお勧めします。バグに遭遇した場合は、Issueを作成してください。
 
 ## 引用
 

{moleditpy-4.10.3 → moleditpy-4.11.1}/src/MoleditPy.egg-info/SOURCES.txt

@@ -17,6 +17,7 @@ src/moleditpy/assets/icon.png
 src/moleditpy/core/__init__.py
 src/moleditpy/core/mol_geometry.py
 src/moleditpy/core/molecular_data.py
+src/moleditpy/core/stereo_check.py
 src/moleditpy/plugins/__init__.py
 src/moleditpy/plugins/plugin_interface.py
 src/moleditpy/plugins/plugin_manager.py
@@ -35,6 +36,7 @@ src/moleditpy/ui/bond_item.py
 src/moleditpy/ui/bond_length_dialog.py
 src/moleditpy/ui/calculation_worker.py
 src/moleditpy/ui/chain_mixin.py
+src/moleditpy/ui/chirality_warning_dialog.py
 src/moleditpy/ui/color_settings_dialog.py
 src/moleditpy/ui/compute_logic.py
 src/moleditpy/ui/constrained_optimization_dialog.py
@@ -60,6 +62,7 @@ src/moleditpy/ui/periodic_table_dialog.py
 src/moleditpy/ui/planarize_dialog.py
 src/moleditpy/ui/plugin_menu_manager.py
 src/moleditpy/ui/preview_molecule.py
+src/moleditpy/ui/sdf_record_dialog.py
 src/moleditpy/ui/settings_dialog.py
 src/moleditpy/ui/string_importers.py
 src/moleditpy/ui/template_preview_item.py
@@ -73,12 +76,16 @@ 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_labels_tab.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/default_settings.py
+src/moleditpy/utils/finite_float.py
 src/moleditpy/utils/hit_radius.py
+src/moleditpy/utils/label_style.py
+src/moleditpy/utils/sdf_records.py
 src/moleditpy/utils/sip_isdeleted_safe.py
 src/moleditpy/utils/suppress_log.py
 src/moleditpy/utils/system_utils.py

{moleditpy-4.10.3 → moleditpy-4.11.1}/src/moleditpy/core/mol_geometry.py

@@ -720,7 +720,7 @@ def resolve_2d_overlaps(
         return []
 
     # Union-Find for overlap groups
-    parent = {aid: aid for aid in atom_ids}
+    parent = {aid: aid for aid in ids_list}
 
     def find_set(aid: int) -> int:
         """Find representative root for an element in disjoint-set."""
@@ -743,7 +743,7 @@ def resolve_2d_overlaps(
         unite_sets(id1, id2)
 
     groups_by_root: Dict[int, List[int]] = {}
-    for aid in atom_ids:
+    for aid in ids_list:
         root = find_set(aid)
         groups_by_root.setdefault(root, []).append(aid)
 

{moleditpy-4.10.3 → moleditpy-4.11.1}/src/moleditpy/core/molecular_data.py

@@ -14,6 +14,7 @@ from __future__ import annotations
 import logging
 from typing import Any, Dict, List, Optional, Tuple, Union
 from rdkit import Chem
+from rdkit.Chem import rdCIPLabeler
 
 from ..utils.constants import ANGSTROM_PER_PIXEL
 
@@ -117,6 +118,38 @@ def _to_v3000_block(
     return "\n".join(lines) + "\n"
 
 
+def align_ez_to_cip(mol: Chem.Mol, wanted: Dict[int, str]) -> None:
+    """Make labelled double bonds read as the wanted CIP E/Z, flipping if needed.
+
+    *wanted* maps bond index to "E" or "Z". The bonds' STEREOE/STEREOZ is
+    encoded against whichever neighbors were picked as stereo atoms, which
+    need not be the CIP-higher ones (on CH3-C(Cl)=CH-CH3 the methyl is picked
+    over Cl), so a "Z" label could encode E. Ask the CIP labeler what each
+    bond currently means and flip the ones that read the other way. Bonds
+    with no CIP E/Z (two identical substituents on one end) are left alone.
+    """
+    if not wanted:
+        return
+    probe = Chem.Mol(mol)
+    try:
+        rdCIPLabeler.AssignCIPLabels(probe)
+    except (RuntimeError, ValueError) as e:
+        logging.warning("CIP labelling for E/Z labels failed: %s", e)
+        return
+    flipped = {
+        Chem.BondStereo.STEREOZ: Chem.BondStereo.STEREOE,
+        Chem.BondStereo.STEREOE: Chem.BondStereo.STEREOZ,
+    }
+    for bond_idx, label in wanted.items():
+        probe_bond = probe.GetBondWithIdx(bond_idx)
+        if not probe_bond.HasProp("_CIPCode"):
+            continue
+        if probe_bond.GetProp("_CIPCode") != label:
+            bond = mol.GetBondWithIdx(bond_idx)
+            if bond.GetStereo() in flipped:
+                bond.SetStereo(flipped[bond.GetStereo()])
+
+
 class MolecularData:
     """In-memory graph of atoms and bonds, independent of any UI framework."""
 
@@ -355,6 +388,7 @@ class MolecularData:
             return None
 
         # Overwrite based on labels (E/Z has highest priority) ---
+        ez_wanted: Dict[int, str] = {}
         for bond_idx, info in bond_stereo_info.items():
             stereo_type = info["type"]
             bond = final_mol.GetBondWithIdx(bond_idx)
@@ -402,6 +436,7 @@ class MolecularData:
                     bond.SetStereo(Chem.BondStereo.STEREOZ)
                 elif stereo_type == 4:
                     bond.SetStereo(Chem.BondStereo.STEREOE)
+                ez_wanted[bond_idx] = "Z" if stereo_type == 3 else "E"
 
                 # Clear BondDir (wedge/dash) of adjacent single bonds assigned via coordinates to avoid label conflicts
                 b1 = final_mol.GetBondBetweenAtoms(begin_atom_idx, neigh1_idx)
@@ -411,6 +446,10 @@ class MolecularData:
                 if b2 is not None:
                     b2.SetBondDir(Chem.BondDir.NONE)
 
+        # The labels are CIP E/Z; the neighbors picked above are not always
+        # the CIP-higher ones.
+        align_ez_to_cip(final_mol, ez_wanted)
+
         # Finalization (cache update + stereochemistry reassignment)
         final_mol.UpdatePropertyCache(strict=False)
 

moleditpy-4.11.1/src/moleditpy/core/stereo_check.py

@@ -0,0 +1,237 @@
+#!/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 __future__ import annotations
+
+import logging
+from dataclasses import dataclass
+from typing import Dict, FrozenSet, List, Optional, Tuple
+
+from rdkit import Chem
+from rdkit.Chem import rdCIPLabeler
+
+from .molecular_data import MolecularData
+
+
+@dataclass(frozen=True)
+class ChiralityMismatch:
+    """A stereocenter whose 3D configuration differs from the 2D drawing."""
+
+    atom_id: int
+    symbol: str
+    rdkit_index: Optional[int]
+    drawn: str
+    actual: Optional[str]
+
+
+@dataclass(frozen=True)
+class EZMismatch:
+    """A labelled double bond whose 3D configuration differs from the label."""
+
+    atom_ids: Tuple[int, int]
+    symbols: Tuple[str, str]
+    rdkit_bond_index: Optional[int]
+    rdkit_atom_indices: Optional[Tuple[int, int]]
+    drawn: str
+    actual: Optional[str]
+
+
+def _cip_labels_by_atom_id(mol: Chem.Mol) -> Dict[int, str]:
+    """Map editor atom IDs to CIP labels ('R'/'S') for every labelled center."""
+    rdCIPLabeler.AssignCIPLabels(mol)
+    labels: Dict[int, str] = {}
+    for atom in mol.GetAtoms():
+        if atom.HasProp("_CIPCode") and atom.HasProp("_original_atom_id"):
+            labels[atom.GetIntProp("_original_atom_id")] = atom.GetProp("_CIPCode")
+    return labels
+
+
+def drawn_chirality(data: MolecularData) -> Dict[int, str]:
+    """CIP labels of the stereocenters the 2D drawing specifies with wedges."""
+    # Nothing is specified without a wedge or hash; skip CIP labelling.
+    if not any(bond.get("stereo") in (1, 2) for bond in data.bonds.values()):
+        return {}
+    mol = data.to_rdkit_mol(use_2d_stereo=False)
+    if mol is None:
+        return {}
+    Chem.AssignChiralTypesFromBondDirs(mol)
+    Chem.AssignStereochemistry(mol, cleanIt=True, force=True)
+    return _cip_labels_by_atom_id(mol)
+
+
+def actual_chirality(mol_3d: Chem.Mol) -> Dict[int, str]:
+    """CIP labels of the stereocenters in a 3D structure, read from coordinates."""
+    if mol_3d.GetNumConformers() == 0:
+        return {}
+    mol = Chem.Mol(mol_3d)
+    Chem.AssignStereochemistryFrom3D(mol)
+    return _cip_labels_by_atom_id(mol)
+
+
+def find_chirality_mismatches(
+    data: MolecularData, mol_3d: Chem.Mol
+) -> List[ChiralityMismatch]:
+    """Stereocenters drawn in 2D whose configuration the 3D structure does not keep.
+
+    Only centers the drawing specifies (wedge or hash) are compared; an
+    unspecified center can come out either way. A center that is no longer a
+    stereocenter in 3D is reported with ``actual`` None.
+    """
+    try:
+        drawn = drawn_chirality(data)
+        if not drawn:
+            return []
+        actual = actual_chirality(mol_3d)
+    except (RuntimeError, ValueError) as e:
+        logging.warning("Chirality check failed: %s", e)
+        return []
+
+    index_of = {
+        atom.GetIntProp("_original_atom_id"): atom.GetIdx()
+        for atom in mol_3d.GetAtoms()
+        if atom.HasProp("_original_atom_id")
+    }
+    return [
+        ChiralityMismatch(
+            atom_id=atom_id,
+            symbol=str(data.atoms[atom_id]["symbol"]),
+            rdkit_index=index_of.get(atom_id),
+            drawn=label,
+            actual=actual.get(atom_id),
+        )
+        for atom_id, label in sorted(drawn.items())
+        if actual.get(atom_id) != label and atom_id in data.atoms
+    ]
+
+
+def _bond_cip_by_atom_ids(
+    mol: Chem.Mol,
+) -> Dict[FrozenSet[int], Tuple[int, str]]:
+    """Map editor atom-ID pairs to (bond index, CIP E/Z) for every labelled bond.
+
+    Expects CIP labels already assigned on *mol*.
+    """
+    out: Dict[FrozenSet[int], Tuple[int, str]] = {}
+    for bond in mol.GetBonds():
+        begin, end = bond.GetBeginAtom(), bond.GetEndAtom()
+        if not (
+            bond.HasProp("_CIPCode")
+            and begin.HasProp("_original_atom_id")
+            and end.HasProp("_original_atom_id")
+        ):
+            continue
+        key = frozenset(
+            (begin.GetIntProp("_original_atom_id"), end.GetIntProp("_original_atom_id"))
+        )
+        out[key] = (bond.GetIdx(), bond.GetProp("_CIPCode"))
+    return out
+
+
+def drawn_ez(data: MolecularData) -> Dict[Tuple[int, int], str]:
+    """E/Z labels ("E"/"Z") of the drawn double bonds that have a CIP E/Z.
+
+    A label on a bond with two identical groups at one end is dropped: that
+    bond has no E/Z, so the label cannot be checked.
+    """
+    labelled = {
+        (id1, id2): ("Z" if bond["stereo"] == 3 else "E")
+        for (id1, id2), bond in data.bonds.items()
+        if bond.get("stereo") in (3, 4)
+    }
+    if not labelled:
+        return {}
+    drawn_mol = data.to_rdkit_mol(use_2d_stereo=False)
+    if drawn_mol is None:
+        return {}
+    rdCIPLabeler.AssignCIPLabels(drawn_mol)
+    comparable = _bond_cip_by_atom_ids(drawn_mol)
+    return {
+        pair: label for pair, label in labelled.items() if frozenset(pair) in comparable
+    }
+
+
+def actual_ez(mol_3d: Chem.Mol) -> Dict[int, str]:
+    """CIP E/Z ("E"/"Z") of every stereo double bond in a 3D structure.
+
+    Keyed by RDKit bond index and read from the coordinates, with the same
+    labeller as find_ez_mismatches, so a label and the check always agree.
+    """
+    if mol_3d.GetNumConformers() == 0:
+        return {}
+    probe = Chem.Mol(mol_3d)
+    Chem.AssignStereochemistryFrom3D(probe)
+    rdCIPLabeler.AssignCIPLabels(probe)
+    return {
+        bond.GetIdx(): bond.GetProp("_CIPCode")
+        for bond in probe.GetBonds()
+        if bond.HasProp("_CIPCode") and bond.GetProp("_CIPCode") in ("E", "Z")
+    }
+
+
+def find_ez_mismatches(data: MolecularData, mol_3d: Chem.Mol) -> List[EZMismatch]:
+    """Double bonds labelled E or Z in 2D whose 3D configuration differs.
+
+    Only bonds with a CIP E/Z are compared (see drawn_ez).
+    """
+    if mol_3d.GetNumConformers() == 0:
+        return []
+    try:
+        drawn = drawn_ez(data)
+        if not drawn:
+            return []
+        probe = Chem.Mol(mol_3d)
+        Chem.AssignStereochemistryFrom3D(probe)
+        rdCIPLabeler.AssignCIPLabels(probe)
+        actual = _bond_cip_by_atom_ids(probe)
+    except (RuntimeError, ValueError) as e:
+        logging.warning("E/Z check failed: %s", e)
+        return []
+
+    bond_of: Dict[FrozenSet[int], Chem.Bond] = {
+        frozenset(
+            (
+                b.GetBeginAtom().GetIntProp("_original_atom_id"),
+                b.GetEndAtom().GetIntProp("_original_atom_id"),
+            )
+        ): b
+        for b in mol_3d.GetBonds()
+        if b.GetBeginAtom().HasProp("_original_atom_id")
+        and b.GetEndAtom().HasProp("_original_atom_id")
+    }
+    mismatches: List[EZMismatch] = []
+    for (id1, id2), label in sorted(drawn.items()):
+        if id1 not in data.atoms or id2 not in data.atoms:
+            continue
+        key = frozenset((id1, id2))
+        got = actual.get(key)
+        got_label = got[1] if got else None
+        if got_label == label:
+            continue
+        bond = bond_of.get(key)
+        mismatches.append(
+            EZMismatch(
+                atom_ids=(id1, id2),
+                symbols=(
+                    str(data.atoms[id1]["symbol"]),
+                    str(data.atoms[id2]["symbol"]),
+                ),
+                rdkit_bond_index=bond.GetIdx() if bond is not None else None,
+                rdkit_atom_indices=(
+                    (bond.GetBeginAtomIdx(), bond.GetEndAtomIdx())
+                    if bond is not None
+                    else None
+                ),
+                drawn=label,
+                actual=got_label,
+            )
+        )
+    return mismatches

{moleditpy-4.10.3 → moleditpy-4.11.1}/src/moleditpy/main.py

@@ -166,6 +166,9 @@ def _read_startup_log_settings() -> tuple[bool, bool]:
     try:
         with open(settings_path, encoding="utf-8") as f:
             data = json.load(f)
+        # Valid JSON that is not an object ([] or null) must not stop startup.
+        if not isinstance(data, dict):
+            return False, False
         return bool(data.get("log_to_file", False)), bool(
             data.get("log_level_debug", False)
         )
@@ -265,10 +268,9 @@ def main() -> None:
             print(f"Error: Plugin path not found: {plugin_path}")
             sys.exit(1)
 
-        try:
-            from moleditpy.plugins.plugin_manager import PluginManager
-        except ImportError:
-            from .plugins.plugin_manager import PluginManager
+        # Relative: an absolute "moleditpy" import would pick up the other
+        # package when both the main and Linux builds are installed.
+        from .plugins.plugin_manager import PluginManager
 
         pm = PluginManager()
         sha256 = pm.compute_sha256(plugin_path)
@@ -299,9 +301,15 @@ def main() -> None:
         print(f" SHA-256:     {sha256}")
         print("=" * 40)
 
-        confirm = (
-            input("\nDo you want to proceed with installation? (y/N): ").strip().lower()
-        )
+        try:
+            confirm = (
+                input("\nDo you want to proceed with installation? (y/N): ")
+                .strip()
+                .lower()
+            )
+        except EOFError:
+            # No terminal to answer from (piped or scripted run): treat as No.
+            confirm = ""
         if confirm == "y":
             success, msg = pm.install_plugin(plugin_path)
             if success:
@@ -321,8 +329,6 @@ def main() -> None:
 
     if sys.platform == "win32":
         try:
-            from PyQt6.QtCore import QTimer
-
             QTimer.singleShot(100, lambda: window.setWindowIcon(window.windowIcon()))
         except (
             Exception