Refactored molecule.py, bonds.py, graph.py, and query.py for improved clarity and efficiency. Removed unused methods and redundant code, consolidated bond handling logic, and replaced lists with sets for tracking changes.

Simplify the molecule structure by removing redundant charge and radical attributes and streamline the backup procedure by utilizing the copy method. Improved bond copying with added stereo support, and refined element creation from atomic data.

Updated MoleculeContainer to retain stereo information during atom/bond operations by introducing conditions in the fix_labels method. Expanded substructure method allowing customizable mark settings and improved copy methods in Bond and QueryElement to optionally retain stereo data.

Centralize chemical attributes like charge and radicals within the `atom` object. Simplify stereo data management by directly setting stereochemistry on atom and bond objects and remove unnecessary lookups. Add `ExtendedQuery` to public API and streamline related imports.

Implemented delta_isotope to manage isotopic modifications and added corresponding mdl_isotope properties for multiple elements. Removed common_isotopes and updated relevant assertions for consistent isotope handling. Also updated copyright years for multiple files.

simplified stereo in queries. now it's users problem to set it right.
query isomorphism reduced to query to atom.

no need for queries. dropped.

Renamed '_mdl' directory to 'mdl' and updated all corresponding import statements. This change improves code readability and aligns directory naming conventions across the project.

unpacking WIP

Removed redundant `__hash__` implementations from query elements.
Morgan hashes refactored. Will affect generated smiles strings.
Implemented rings_graph as next level of skin graph.

stereo isomorphism for molecule to molecule implemented

smarts atom stereo parsing implemented. single @ always treated as True label, thus, violates smiles stereo rules.
simple cis-trans parsing supported now. smarts generation is broken now.

dropped smarts generation.
smarts notation complexity reduced.

# Conflicts:
#	chython/algorithms/calculate2d/__init__.py

still not full coverage of conditions.

…phism

no need for multipython tests.

minimal tests added.
test pipeline dropped. doesn't work at all.

tests added.