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.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+**/models/*.txt
+local/
+*ipynb
+query/

.pre-commit-config.yaml

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+default_language_version:
+    python: python3
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: check-added-large-files
+  # - repo: https://github.com/astral-sh/ruff-pre-commit
+  #   rev: "v0.0.270"
+  #   hooks:
+  #     - id: ruff
+  #       args: [ --fix, --exit-non-zero-on-fix ]
+  - repo: https://github.com/psf/black
+    rev: "23.3.0"
+    hooks:
+      - id: black
+        language_version: python3
+  - repo: https://github.com/PyCQA/isort
+    rev: "5.12.0"
+    hooks:
+      - id: isort
+        args: [--profile=black, "--skip=__init__.py", "--filter-files"]

LICENSE

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+MIT License
+
+Copyright (c) 2023 White Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+[![tests](https://github.com/ur-whitelab/chemcrow-public/actions/workflows/tests.yml/badge.svg)](https://github.com/ur-whitelab/chemcrow-public)
+[![PyPI](https://img.shields.io/pypi/v/chemcrow)](https://img.shields.io/pypi/v/chemcrow)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/chemcrow)](https://img.shields.io/pypi/pyversions/chemcrow)
+[![DOI:10.1101/2020.07.15.204701](https://zenodo.org/badge/DOI/10.48550/arXiv.2304.05376.svg)](https://doi.org/10.48550/arXiv.2304.05376)
+[![DOI](https://zenodo.org/badge/649361700.svg)](https://zenodo.org/doi/10.5281/zenodo.10884638)
+
+
+
+
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="assets/chemcrow_dark_bold.png" width='100%'>
+  <source media="(prefers-color-scheme: light)" srcset="assets/chemcrow_light_bold.png" width='100%'>
+  <img alt="ChemCrow logo" src="/assets/" width="100%">
+</picture>
+
+
+<br></br>
+
+
+ChemCrow is an open source package for the accurate solution of reasoning-intensive chemical tasks.
+
+Built with Langchain, it uses a collection of chemical tools including RDKit, paper-qa, as well as some relevant databases in chemistry, like Pubchem and chem-space.
+
+## 🤗 Try it out in [HuggingFace](https://huggingface.co/spaces/doncamilom/ChemCrow)!
+
+[![ChemCrow Demo](assets/hf-demo.png)](https://huggingface.co/spaces/doncamilom/ChemCrow)
+
+
+## ⚠️ Note
+
+This package does not contain all the tools described in the [ChemCrow paper](https://arxiv.org/abs/2304.05376) because
+of API usage restrictions. This repo will not give the same results as that paper.
+
+All the experiments have been released under [ChemCrow runs](https://github.com/ur-whitelab/chemcrow-runs).
+
+
+## 👩‍💻 Installation
+
+```
+pip install chemcrow
+```
+
+## 🔥 Usage
+First set up your API keys in your environment.
+```
+export OPENAI_API_KEY=your-openai-api-key
+```
+
+You can optionally use Serp API:
+
+```
+export SERP_API_KEY=your-serpapi-api-key
+```
+
+In a Python session:
+```python
+from chemcrow.agents import ChemCrow
+
+chem_model = ChemCrow(model="gpt-4-0613", temp=0.1, streaming=False)
+chem_model.run("What is the molecular weight of tylenol?")
+```
+
+## ✅ Citation
+Bran, Andres M., et al. "ChemCrow: Augmenting large-language models with chemistry tools." arXiv preprint arXiv:2304.05376 (2023).
+
+```bibtex
+@article{bran2023chemcrow,
+      title={ChemCrow: Augmenting large-language models with chemistry tools},
+      author={Andres M Bran and Sam Cox and Oliver Schilter and Carlo Baldassari and Andrew D White and Philippe Schwaller},
+      year={2023},
+      eprint={2304.05376},
+      archivePrefix={arXiv},
+      primaryClass={physics.chem-ph},
+      publisher={arXiv}
+}
+```

dev-requirements.txt

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+pre-commit
+python-dotenv

setup.py

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+from setuptools import find_packages, setup
+
+exec(open("chemcrow/version.py").read())
+
+with open("README.md", "r", encoding="utf-8") as fh:
+    long_description = fh.read()
+
+setup(
+    name="chemcrow",
+    python_requires=">=3.9, <3.12",  # this temporarily fixes molbloom install, which breaks with 3.12
+    version=__version__,
+    description="Accurate solution of reasoning-intensive chemical tasks, powered by LLMs.",
+    author="Andres M Bran, Sam Cox, Andrew White, Philippe Schwaller",
+    author_email="andrew.white@rochester.edu",
+    url="https://github.com/ur-whitelab/chemcrow-public",
+    license="MIT",
+    packages=find_packages(),
+    package_data={"chemcrow": ["data/chem_wep_smi.csv"]},
+    install_requires=[
+        "ipython",
+        "python-dotenv",
+        "rdkit",
+        "synspace",
+        "openai==0.27.8",
+        "molbloom",
+        "paper-qa==1.1.1",
+        "google-search-results",
+        "langchain>=0.0.234,<=0.0.275",
+        "langchain_core==0.0.1",
+        "nest_asyncio",
+        "tiktoken",
+        "rmrkl",
+        #"paper-scraper@git+https://github.com/blackadad/paper-scraper.git",
+        "streamlit",
+        "rxn4chemistry",
+        "duckduckgo-search",
+        "wikipedia",
+    ],
+    test_suite="tests",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    classifiers=[
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+)