Metadata-Version: 2.2
Name: molgr
Version: 0.1.4
Summary: Reconstruct molecular graphs from XYZ coordinates with RDKit and Open Babel.
Keywords: cheminformatics,chemistry,molecular graph,molecular reconstruction,molecular structure,XYZ,RDKit,Open Babel
Author: Ying-zi Luo
Author-Email: Miao-jiong Tang <mj_t@zju.edu.cn>
License:                     GNU GENERAL PUBLIC LICENSE
                                Version 2, June 1991
         
          Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
          51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
          Everyone is permitted to copy and distribute verbatim copies
          of this license document, but changing it is not allowed.
         
                                     Preamble
         
           The licenses for most software are designed to take away your
         freedom to share and change it.  By contrast, the GNU General Public
         License is intended to guarantee your freedom to share and change free
         software--to make sure the software is free for all its users.  This
         General Public License applies to most of the Free Software
         Foundation's software and to any other program whose authors commit to
         using it.  (Some other Free Software Foundation software is covered by
         the GNU Lesser General Public License instead.)  You can apply it to
         your programs, too.
         
           When we speak of free software, we are referring to freedom, not
         price.  Our General Public Licenses are designed to make sure that you
         have the freedom to distribute copies of free software (and charge for
         this service if you wish), that you receive source code or can get it
         if you want it, that you can change the software or use pieces of it
         in new free programs; and that you know you can do these things.
         
           To protect your rights, we need to make restrictions that forbid
         anyone to deny you these rights or to ask you to surrender the rights.
         These restrictions translate to certain responsibilities for you if you
         distribute copies of the software, or if you modify it.
         
           For example, if you distribute copies of such a program, whether
         gratis or for a fee, you must give the recipients all the rights that
         you have.  You must make sure that they, too, receive or can get the
         source code.  And you must show them these terms so they know their
         rights.
         
           We protect your rights with two steps: (1) copyright the software, and
         (2) offer you this license which gives you legal permission to copy,
         distribute and/or modify the software.
         
           Also, for each author's protection and ours, we want to make certain
         that everyone understands that there is no warranty for this free
         software.  If the software is modified by someone else and passed on, we
         want its recipients to know that what they have is not the original, so
         that any problems introduced by others will not reflect on the original
         authors' reputations.
         
           Finally, any free program is threatened constantly by software
         patents.  We wish to avoid the danger that redistributors of a free
         program will individually obtain patent licenses, in effect making the
         program proprietary.  To prevent this, we have made it clear that any
         patent must be licensed for everyone's free use or not licensed at all.
         
           The precise terms and conditions for copying, distribution and
         modification follow.
         
                             GNU GENERAL PUBLIC LICENSE
            TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
         
           0. This License applies to any program or other work which contains
         a notice placed by the copyright holder saying it may be distributed
         under the terms of this General Public License.  The "Program", below,
         refers to any such program or work, and a "work based on the Program"
         means either the Program or any derivative work under copyright law:
         that is to say, a work containing the Program or a portion of it,
         either verbatim or with modifications and/or translated into another
         language.  (Hereinafter, translation is included without limitation in
         the term "modification".)  Each licensee is addressed as "you".
         
         Activities other than copying, distribution and modification are not
         covered by this License; they are outside its scope.  The act of
         running the Program is not restricted, and the output from the Program
         is covered only if its contents constitute a work based on the
         Program (independent of having been made by running the Program).
         Whether that is true depends on what the Program does.
         
           1. You may copy and distribute verbatim copies of the Program's
         source code as you receive it, in any medium, provided that you
         conspicuously and appropriately publish on each copy an appropriate
         copyright notice and disclaimer of warranty; keep intact all the
         notices that refer to this License and to the absence of any warranty;
         and give any other recipients of the Program a copy of this License
         along with the Program.
         
         You may charge a fee for the physical act of transferring a copy, and
         you may at your option offer warranty protection in exchange for a fee.
         
           2. You may modify your copy or copies of the Program or any portion
         of it, thus forming a work based on the Program, and copy and
         distribute such modifications or work under the terms of Section 1
         above, provided that you also meet all of these conditions:
         
             a) You must cause the modified files to carry prominent notices
             stating that you changed the files and the date of any change.
         
             b) You must cause any work that you distribute or publish, that in
             whole or in part contains or is derived from the Program or any
             part thereof, to be licensed as a whole at no charge to all third
             parties under the terms of this License.
         
             c) If the modified program normally reads commands interactively
             when run, you must cause it, when started running for such
             interactive use in the most ordinary way, to print or display an
             announcement including an appropriate copyright notice and a
             notice that there is no warranty (or else, saying that you provide
             a warranty) and that users may redistribute the program under
             these conditions, and telling the user how to view a copy of this
             License.  (Exception: if the Program itself is interactive but
             does not normally print such an announcement, your work based on
             the Program is not required to print an announcement.)
         
         These requirements apply to the modified work as a whole.  If
         identifiable sections of that work are not derived from the Program,
         and can be reasonably considered independent and separate works in
         themselves, then this License, and its terms, do not apply to those
         sections when you distribute them as separate works.  But when you
         distribute the same sections as part of a whole which is a work based
         on the Program, the distribution of the whole must be on the terms of
         this License, whose permissions for other licensees extend to the
         entire whole, and thus to each and every part regardless of who wrote it.
         
         Thus, it is not the intent of this section to claim rights or contest
         your rights to work written entirely by you; rather, the intent is to
         exercise the right to control the distribution of derivative or
         collective works based on the Program.
         
         In addition, mere aggregation of another work not based on the Program
         with the Program (or with a work based on the Program) on a volume of
         a storage or distribution medium does not bring the other work under
         the scope of this License.
         
           3. You may copy and distribute the Program (or a work based on it,
         under Section 2) in object code or executable form under the terms of
         Sections 1 and 2 above provided that you also do one of the following:
         
             a) Accompany it with the complete corresponding machine-readable
             source code, which must be distributed under the terms of Sections
             1 and 2 above on a medium customarily used for software interchange; or,
         
             b) Accompany it with a written offer, valid for at least three
             years, to give any third party, for a charge no more than your
             cost of physically performing source distribution, a complete
             machine-readable copy of the corresponding source code, to be
             distributed under the terms of Sections 1 and 2 above on a medium
             customarily used for software interchange; or,
         
             c) Accompany it with the information you received as to the offer
             to distribute corresponding source code.  (This alternative is
             allowed only for noncommercial distribution and only if you
             received the program in object code or executable form with such
             an offer, in accord with Subsection b above.)
         
         The source code for a work means the preferred form of the work for
         making modifications to it.  For an executable work, complete source
         code means all the source code for all modules it contains, plus any
         associated interface definition files, plus the scripts used to
         control compilation and installation of the executable.  However, as a
         special exception, the source code distributed need not include
         anything that is normally distributed (in either source or binary
         form) with the major components (compiler, kernel, and so on) of the
         operating system on which the executable runs, unless that component
         itself accompanies the executable.
         
         If distribution of executable or object code is made by offering
         access to copy from a designated place, then offering equivalent
         access to copy the source code from the same place counts as
         distribution of the source code, even though third parties are not
         compelled to copy the source along with the object code.
         
           4. You may not copy, modify, sublicense, or distribute the Program
         except as expressly provided under this License.  Any attempt
         otherwise to copy, modify, sublicense or distribute the Program is
         void, and will automatically terminate your rights under this License.
         However, parties who have received copies, or rights, from you under
         this License will not have their licenses terminated so long as such
         parties remain in full compliance.
         
           5. You are not required to accept this License, since you have not
         signed it.  However, nothing else grants you permission to modify or
         distribute the Program or its derivative works.  These actions are
         prohibited by law if you do not accept this License.  Therefore, by
         modifying or distributing the Program (or any work based on the
         Program), you indicate your acceptance of this License to do so, and
         all its terms and conditions for copying, distributing or modifying
         the Program or works based on it.
         
           6. Each time you redistribute the Program (or any work based on the
         Program), the recipient automatically receives a license from the
         original licensor to copy, distribute or modify the Program subject to
         these terms and conditions.  You may not impose any further
         restrictions on the recipients' exercise of the rights granted herein.
         You are not responsible for enforcing compliance by third parties to
         this License.
         
           7. If, as a consequence of a court judgment or allegation of patent
         infringement or for any other reason (not limited to patent issues),
         conditions are imposed on you (whether by court order, agreement or
         otherwise) that contradict the conditions of this License, they do not
         excuse you from the conditions of this License.  If you cannot
         distribute so as to satisfy simultaneously your obligations under this
         License and any other pertinent obligations, then as a consequence you
         may not distribute the Program at all.  For example, if a patent
         license would not permit royalty-free redistribution of the Program by
         all those who receive copies directly or indirectly through you, then
         the only way you could satisfy both it and this License would be to
         refrain entirely from distribution of the Program.
         
         If any portion of this section is held invalid or unenforceable under
         any particular circumstance, the balance of the section is intended to
         apply and the section as a whole is intended to apply in other
         circumstances.
         
         It is not the purpose of this section to induce you to infringe any
         patents or other property right claims or to contest validity of any
         such claims; this section has the sole purpose of protecting the
         integrity of the free software distribution system, which is
         implemented by public license practices.  Many people have made
         generous contributions to the wide range of software distributed
         through that system in reliance on consistent application of that
         system; it is up to the author/donor to decide if he or she is willing
         to distribute software through any other system and a licensee cannot
         impose that choice.
         
         This section is intended to make thoroughly clear what is believed to
         be a consequence of the rest of this License.
         
           8. If the distribution and/or use of the Program is restricted in
         certain countries either by patents or by copyrighted interfaces, the
         original copyright holder who places the Program under this License
         may add an explicit geographical distribution limitation excluding
         those countries, so that distribution is permitted only in or among
         countries not thus excluded.  In such case, this License incorporates
         the limitation as if written in the body of this License.
         
           9. The Free Software Foundation may publish revised and/or new versions
         of the General Public License from time to time.  Such new versions will
         be similar in spirit to the present version, but may differ in detail to
         address new problems or concerns.
         
         Each version is given a distinguishing version number.  If the Program
         specifies a version number of this License which applies to it and "any
         later version", you have the option of following the terms and conditions
         either of that version or of any later version published by the Free
         Software Foundation.  If the Program does not specify a version number of
         this License, you may choose any version ever published by the Free Software
         Foundation.
         
           10. If you wish to incorporate parts of the Program into other free
         programs whose distribution conditions are different, write to the author
         to ask for permission.  For software which is copyrighted by the Free
         Software Foundation, write to the Free Software Foundation; we sometimes
         make exceptions for this.  Our decision will be guided by the two goals
         of preserving the free status of all derivatives of our free software and
         of promoting the sharing and reuse of software generally.
         
                                     NO WARRANTY
         
           11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
         FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
         OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
         PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
         OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
         MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
         TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
         PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
         REPAIR OR CORRECTION.
         
           12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
         WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
         REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
         INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
         OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
         TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
         YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
         PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
         POSSIBILITY OF SUCH DAMAGES.
         
                              END OF TERMS AND CONDITIONS
         
                     How to Apply These Terms to Your New Programs
         
           If you develop a new program, and you want it to be of the greatest
         possible use to the public, the best way to achieve this is to make it
         free software which everyone can redistribute and change under these terms.
         
           To do so, attach the following notices to the program.  It is safest
         to attach them to the start of each source file to most effectively
         convey the exclusion of warranty; and each file should have at least
         the "copyright" line and a pointer to where the full notice is found.
         
             <one line to give the program's name and a brief idea of what it does.>
             Copyright (C) <year>  <name of author>
         
             This program is free software; you can redistribute it and/or modify
             it under the terms of the GNU General Public License as published by
             the Free Software Foundation; either version 2 of the License, or
             (at your option) any later version.
         
             This program is distributed in the hope that it will be useful,
             but WITHOUT ANY WARRANTY; without even the implied warranty of
             MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
             GNU General Public License for more details.
         
             You should have received a copy of the GNU General Public License along
             with this program; if not, write to the Free Software Foundation, Inc.,
             51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
         
         Also add information on how to contact you by electronic and paper mail.
         
         If the program is interactive, make it output a short notice like this
         when it starts in an interactive mode:
         
             Gnomovision version 69, Copyright (C) year name of author
             Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
             This is free software, and you are welcome to redistribute it
             under certain conditions; type `show c' for details.
         
         The hypothetical commands `show w' and `show c' should show the appropriate
         parts of the General Public License.  Of course, the commands you use may
         be called something other than `show w' and `show c'; they could even be
         mouse-clicks or menu items--whatever suits your program.
         
         You should also get your employer (if you work as a programmer) or your
         school, if any, to sign a "copyright disclaimer" for the program, if
         necessary.  Here is a sample; alter the names:
         
           Yoyodyne, Inc., hereby disclaims all copyright interest in the program
           `Gnomovision' (which makes passes at compilers) written by James Hacker.
         
           <signature of Ty Coon>, 1 April 1989
           Ty Coon, President of Vice
         
         This General Public License does not permit incorporating your program into
         proprietary programs.  If your program is a subroutine library, you may
         consider it more useful to permit linking proprietary applications with the
         library.  If this is what you want to do, use the GNU Lesser General
         Public License instead of this License.
         
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: C++
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Typing :: Typed
Project-URL: Homepage, https://github.com/gentle1999/MolGR
Project-URL: Repository, https://github.com/gentle1999/MolGR
Project-URL: Documentation, https://github.com/gentle1999/MolGR/tree/main/docs
Project-URL: Issues, https://github.com/gentle1999/MolGR/issues
Requires-Python: >=3.8
Requires-Dist: rdkit>=2023.9.6
Requires-Dist: openbabel-wheel==3.1.1.22; python_version < "3.9" and sys_platform == "win32"
Requires-Dist: openbabel-wheel; python_version < "3.10" and (sys_platform != "win32" or python_version >= "3.9")
Requires-Dist: openbabel>=3.2.0; python_version >= "3.10"
Requires-Dist: numpy<2; python_version == "3.8"
Requires-Dist: numpy<2,>=1.26; python_version == "3.9"
Requires-Dist: numpy<2.3,>=1.26; python_version >= "3.10" and python_version < "3.13"
Requires-Dist: numpy>=1.26; python_version >= "3.13"
Requires-Dist: typing-extensions>=4.13.2
Description-Content-Type: text/markdown

# MolGR

[English](README.md) | [中文](README.zh-CN.md)

[![CI](https://github.com/gentle1999/MolGR/actions/workflows/ci.yaml/badge.svg)](https://github.com/gentle1999/MolGR/actions/workflows/ci.yaml)
[![PyPI](https://img.shields.io/pypi/v/molgr.svg)](https://pypi.org/project/molgr/)
[![PyPI downloads](https://img.shields.io/pypi/dm/molgr.svg)](https://pypi.org/project/molgr/)
[![Wheel](https://img.shields.io/pypi/wheel/molgr.svg)](https://pypi.org/project/molgr/)
![Platforms](https://img.shields.io/badge/platforms-Linux%20%7C%20macOS%20%7C%20Windows-4C8BF5)
![Python](https://img.shields.io/badge/python-3.8--3.14-3776AB?logo=python&logoColor=white)
![C++](https://img.shields.io/badge/C%2B%2B-17-00599C?logo=cplusplus&logoColor=white)
![Development status](https://img.shields.io/badge/status-active%20development-F59E0B)
![Typing](https://img.shields.io/badge/typing-PEP%20561%20typed-2F74C0)
![Languages](https://img.shields.io/badge/languages-Python%20%7C%20C%2B%2B-00599C)
![Ruff](https://img.shields.io/badge/lint%20%26%20format-Ruff-D7FF64?logo=ruff&logoColor=261230)
[![License](https://img.shields.io/badge/license-GPL--2.0-blue.svg)](LICENSE)

MolGR stands for Moleculer Graph Reconstructor.

MolGR is a Python package for reconstructing molecular graphs from XYZ coordinates.
It accepts an XYZ block, total charge, and spin multiplicity, and returns an
`rdkit.Chem.Mol` with bond orders, a 3D conformer, optional dative bonds, and optional
stereochemistry.

MolGR currently provides two switchable reconstruction backends:

- `cpp`: the default backend, exposed through `molgr._core`, for regular use and
  performance-sensitive workflows.
- `python`: the Python reference implementation in [`src/molgr/fallback/`](src/molgr/fallback/),
  used for semantic alignment, debugging, and regression tests.

## Quick Usage

The main entrypoint is `molgr.interface.xyz_to_rdmol`:

```python
from molgr.interface import xyz_to_rdmol

xyz = """3
water
O 0.000000 0.000000 0.000000
H 0.758602 0.000000 0.504284
H -0.758602 0.000000 0.504284
"""

mol = xyz_to_rdmol(
    xyz,
    total_charge=0,
    spin_multiplicity=1,
    backend="cpp",  # "python" is also available
)
```

Before reconstruction, MolGR calculates the total electron count as the sum of
the atomic numbers minus `total_charge` and rejects impossible spin
multiplicities. In particular, even-electron systems require odd multiplicities,
while odd-electron systems require even multiplicities. The accepted
`spin_multiplicity` is then normalized as
`total_radical_electrons = spin_multiplicity - 1`. By default, MolGR also
completes possible dative bonds and stereochemistry. Pass
`make_dative_bonds=False` or `make_stereochemistry=False` to disable those
post-processing steps.

## Configuration

Runtime configuration is dataclass-based. The package-level
[`molgr.config.CONFIG`](src/molgr/config.py) object is used by default, and callers may
either mutate that global object or pass an explicit [`MolGRConfig`](src/molgr/config.py)
to `xyz_to_rdmol(..., config=...)`.

```python
from molgr.config import CONFIG

CONFIG.cpp_backend.enable_target_bucket_parallelism = True
CONFIG.cpp_backend.target_bucket_parallel_threshold = 1
CONFIG.cpp_backend.target_bucket_parallel_max_threads = None
```

On Windows, `CONFIG.cpp_backend.max_threads` defaults to `1`. Enabling C++
backend thread parallelism on Windows is not recommended: concurrent Open Babel
reconstruction can cause native access violations that Python cannot catch. Keep
`max_threads=1` unless the complete workload has been validated locally. Linux
and macOS keep the automatic `None` default.

The C++ backend is the default accelerated implementation of the Python fallback
semantics. C++-only switches may change scheduling, caching, or thread-safe vendor
implementations, but they must not change the selected molecule for the same
`MolGRConfig`.

## Installation

MolGR requires Python `>=3.8`. Runtime and build dependencies are declared in
[`pyproject.toml`](pyproject.toml). The default development workflow uses `uv`.

### C++ Build Requirements

Building from source compiles the `molgr._core` extension. The local build environment
must provide:

- CMake `>=3.15`.
- A C++17-capable compiler:
  - Linux: GCC 9+ or Clang 10+.
  - macOS: Apple Clang from a current Xcode Command Line Tools installation.
  - Windows: MSVC Build Tools 2019+ with the C++ workload.
- Python development headers for the active Python interpreter. In virtual environments
  created by `uv`, this is usually provided by the selected Python installation.
- Python build packages from [`pyproject.toml`](pyproject.toml): `scikit-build-core`,
  `pybind11`, `setuptools-scm`, and `openbabel-wheel`.
- A working OpenBabel wheel for the target platform. The CMake build locates OpenBabel
  headers and libraries from the installed `openbabel-wheel` package.

Install from source and build the C++ extension:

```bash
cd MolGR
uv sync --dev
uv pip install -e . -v --no-build-isolation
```

Editable installation builds the C++ extension through `scikit-build-core`, `pybind11`,
and the OpenBabel package available in the current Python environment. After changing C++
code or pybind11 bindings, rebuild before running affected tests:

```bash
make cpp-build
```

To mimic CI-style dependency resolution against PyPI instead of the local mirror configured in
[`pyproject.toml`](pyproject.toml), pass explicit indexes:

```bash
uv sync --dev --index https://pypi.org/simple --default-index https://pypi.org/simple
uv pip install -e . -v --no-build-isolation \
  --index https://pypi.org/simple \
  --default-index https://pypi.org/simple
```

## Project Layout

- [`src/molgr/interface.py`](src/molgr/interface.py): public API, config resolution,
  backend routing, and RDKit post-processing.
- [`src/molgr/fallback/`](src/molgr/fallback/): Python reference implementation.
- [`src/cpp/`](src/cpp/): C++ reconstruction implementation.
- [`src/bindings/`](src/bindings/): pybind11 bindings for `molgr._core`.
- [`src/molgr/utils/`](src/molgr/utils/): conversion, equivalence, and RDKit post-processing utilities.
- [`tests/`](tests/): public behavior tests, fallback tests, converter tests, and C++ parity tests.
- [`benchmarks/`](benchmarks/): benchmark entrypoints, dedicated dependencies, and benchmark docs.
- [`docs/`](docs/): architecture and release documentation.
- [`docs/development/MOLECULE_REVIEW_TOOL.md`](docs/development/MOLECULE_REVIEW_TOOL.md): MolGR reconstruction review and trace tool.

## Algorithm Overview

MolGR treats the Python fallback as the semantic reference and the C++ backend as the accelerated
path. Both backends follow the same high-level reconstruction flow:

1. Parse the XYZ input and determine reconstruction targets from total charge,
   spin multiplicity, and runtime config.
2. Route to `backend="cpp"` or `backend="python"`.
3. For metal-free structures, search neighboring-radical seeds in increasing
   charge-separation discrepancy layers. The layers share resonance deduplication state and stop
   at the first valid layer; deformed-pi and bond-break recovery run only if every primary layer is empty.
4. For metal-containing structures, temporarily strip metals from the organic core, enumerate
   possible metal states, and group those states by the induced organic charge/radical target.
5. Reconstruct each organic target bucket once, then reuse it across corresponding metal candidates.
6. Score organic candidates or combined metal-organic candidates and select the best state.
7. Convert backend output to an RDKit molecule and optionally complete dative bonds and stereochemistry.

See [`docs/architecture/ALGORITHM_ARCHITECTURE.md`](docs/architecture/ALGORITHM_ARCHITECTURE.md)
for the full call graph, metal search, resonance recovery, and C++ optimization notes.

## Development

Create or refresh the development environment:

```bash
uv sync --dev
```

Build the extension in editable mode:

```bash
uv pip install -e . -v --no-build-isolation
```

Common checks:

```bash
uv run ruff check .
uv run ruff format --check .
uv run mypy src
uv run pyright
uv run pytest
```

Build source and wheel distributions:

```bash
uv build
```

The root [`makefile`](makefile) provides common development shortcuts:

- `make format`: run the Ruff formatter; modifies files.
- `make lint`: run `ruff check . --fix`; modifies files.
- `make test`: run pytest.
- `make type-check`: run MyPy and Pyright on `src`.
- `make cpp-build`: rebuild the editable C++ extension and refresh C++ IDE config.
- `make stubs`: regenerate type stubs for the compiled extension.

`make stubs` runs `pybind11-stubgen` against `molgr._core`, keeps the public
`pipeline` stubs and the development/parity helper stubs under
[`src/molgr/_core/dev/`](src/molgr/_core/dev/), then formats and lints the generated
`.pyi` files.

Optional VSCode/clangd C++ configuration:

```bash
uv run python scripts/gen_vscode_config_with_ob.py --build-dir build
```

## Testing

Run the full test suite:

```bash
uv run pytest
```

Useful focused tests during development:

```bash
uv run pytest tests/test_main.py
uv run pytest tests/test_backend_reconstruction_regression.py
uv run pytest tests/test_fallback_resonance.py
uv run pytest tests/test_fallback_get_possible_metal_radicals.py
```

When changing C++, pybind11 bindings, or the `_core` public surface:

1. Rebuild the extension with `make cpp-build`.
2. Run affected C++/Python parity tests, for example
   [`tests/test_backend_reconstruction_regression.py`](tests/test_backend_reconstruction_regression.py)
   [`tests/test_cpp_python_metal_candidate_parity.py`](tests/test_cpp_python_metal_candidate_parity.py),
   [`tests/test_cpp_uff_atom_typing_cache.py`](tests/test_cpp_uff_atom_typing_cache.py),
   and [`tests/test_force_field_scoring_policy.py`](tests/test_force_field_scoring_policy.py).
3. If binding interfaces changed, run `make stubs` and inspect the generated `.pyi` files.

The C++ backend is an acceleration of the Python fallback semantics. Keep the
backend parity guardrails in
[`docs/architecture/ALGORITHM_ARCHITECTURE.md`](docs/architecture/ALGORITHM_ARCHITECTURE.md#cpppython-parity-guardrails)
in sync when changing SMARTS matching, UFF setup state, resonance selection,
or C++-only acceleration switches.

Some tests depend on OpenBabel. They may be skipped when the dependency is unavailable.

## Benchmark

Benchmark dependencies live in [`benchmarks/pyproject.toml`](benchmarks/pyproject.toml), separate
from the release dependency graph and the root [`uv.lock`](uv.lock). Benchmarks use a dedicated environment:
default path `.venv-benchmark`, default Python executable `python3.10`.

Create or refresh the benchmark environment:

```bash
bash scripts/benchmark_env.sh create
```

Run the SMILES/XYZ benchmark:

```bash
bash scripts/benchmark_env.sh run python benchmarks/smiles_xyz_benchmark/run.py \
  --input tests/test_cases.csv \
  --limit 10 \
  --out benchmarks/_runs/smiles-demo
```

Run the Molfile/SDF benchmark:

```bash
bash scripts/benchmark_env.sh run python benchmarks/molfile_xyz_benchmark/run.py \
  --input tests/data/sdf/MoNNMo.sdf \
  --limit 1 \
  --out benchmarks/_runs/molfile-demo
```

Run a tmQMg backend parity subset:

```bash
bash scripts/benchmark_env.sh run python benchmarks/tmqmg_xyz_benchmark/run.py \
  --csv /path/to/tmqmg.csv \
  --xyz-dir /path/to/xyz \
  --limit 1000 \
  --out benchmarks/_runs/tmqmg-parity \
  --case-timeout-seconds 1.0 \
  --cpp-accelerations all \
  --methods molgr_cpp,molgr_fallback
```

For repeated benchmark commands, switch the current shell environment:

```bash
eval "$(bash scripts/benchmark_env.sh env)"
```

Restore the default project environment:

```bash
unset UV_PROJECT UV_PROJECT_ENVIRONMENT UV_PYTHON
```

See [`benchmarks/README.md`](benchmarks/README.md) or
[`benchmarks/README.zh-CN.md`](benchmarks/README.zh-CN.md) for details.

## Documentation

- [`docs/README.md`](docs/README.md): English documentation index.
- [`docs/README.zh-CN.md`](docs/README.zh-CN.md): Chinese documentation index.
- [`docs/architecture/ALGORITHM_ARCHITECTURE.md`](docs/architecture/ALGORITHM_ARCHITECTURE.md):
  English algorithm architecture.
- [`docs/architecture/ALGORITHM_ARCHITECTURE.zh-CN.md`](docs/architecture/ALGORITHM_ARCHITECTURE.zh-CN.md):
  Chinese algorithm architecture.
- [`docs/release/DEVELOPMENT_RELEASE_GUIDE.md`](docs/release/DEVELOPMENT_RELEASE_GUIDE.md):
  English development and release guide.
- [`docs/release/DEVELOPMENT_RELEASE_GUIDE.zh-CN.md`](docs/release/DEVELOPMENT_RELEASE_GUIDE.zh-CN.md):
  Chinese development and release guide.
- [`benchmarks/README.md`](benchmarks/README.md): English benchmark environment, commands, and outputs.
- [`benchmarks/README.zh-CN.md`](benchmarks/README.zh-CN.md): Chinese benchmark environment, commands, and outputs.

## License

MolGR is released under the GNU General Public License v2. See [`LICENSE`](LICENSE).
