First commit

.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/
+docs/source/aizynth*
+docs/source/modules.rst
+docs/source/cli_help.txt
+
+# 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/
+
+# PyCharmm idea
+.idea/
+
+#VS Code
+.vscode/
+
+# Pytest coverage output
+coverage/
+
+# Files created by the tool
+smiles.txt
+config_local.yml

CHANGELOG.md

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+# CHANGELOG
+
+## Version 1.0.0 - 2020-06-11
+
+- First public version

LICENSE

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+Copyright 2020 Samuel Genheden and Esben Bjerrum
+
+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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+# aizynthfinder
+
+aizynthfinder is a tool for retrosynthetic planning. The algorithm is based on a Monte Carlo tree search that recursively breaks down a molecule to purchasable precursors. The tree search is guided by a policy that suggests possible precursors by utilizing a neural network trained on a library of known reaction templates.  
+
+## Prerequisites
+
+Before you begin, ensure you have met the following requirements:
+
+* Linux, Windows or Mac platforms are supported - as long as the dependencies are supported on these platforms.
+
+The tool has been developed on a Linux platform, but the software has been tested on Windows 10 and macOS Catalina.
+
+* You have installed anaconda or miniconda with python 3.6 or later
+
+
+## Installation
+
+To install aizynthfinder, follow these steps:
+
+* First, install these conda packages
+
+```
+conda install -c rdkit rdkit -y
+conda install -c anaconda tensorflow>=2.1.0 -y
+conda install graphviz -y
+```
+
+if you have GPU and CUDA libraries enabled on your machine, you can install the ``tensorflow-gpu`` package instead.
+
+* Secondly, install the ``aizynthfinder`` package
+
+```
+python -m pip install https://github.com/MolecularAI/aizynthfinder/archive/v1.0.0.tar.gz
+```
+
+if you want to install the latest version
+
+or
+
+```
+python -m pip install -e .
+```
+
+if you are a developer, using the repository.
+
+## Usage
+
+The tool will install the ``aizynthcli`` and ``aizynthapp`` tools
+as interfaces to the algorithm:
+
+```
+aizynthcli --config config_local.yml --smiles smiles.txt
+aizynthapp --config config_local.yml
+```
+
+Consult the documentation here for more information.
+
+To use tool you need
+
+    1. A stock file
+    2. A trained rollout policy network (including the Keras model and the list of unique templates)
+
+
+### Testing
+
+Tests uses the ``pytest`` package. 
+
+To use, first install the dependencies
+
+```
+python -m pip install -r requirements_dev.txt
+```
+
+and then run the tests using
+
+```
+pytest -v
+```
+
+## Contributing
+
+We welcome contributions, in the form of issues or pull requests.
+
+If you have a question or want to report a bug, please submit an issue.
+
+
+To contribute with code to the project, follow these steps:
+
+1. Fork this repository.
+2. Create a branch: `git checkout -b <branch_name>`.
+3. Make your changes and commit them: `git commit -m '<commit_message>'`
+4. Push to the remote branch: `git push`
+5. Create the pull request.
+
+Please use ``black`` package for formatting, and follow ``pep8`` style guide.
+
+
+## Contributors
+
+* @SGenheden
+* @EBjerrum
+* @A-Thakkar
+
+The contributors have limited time for support questions, but pleae do not hesitate to submit an issue (see above).
+
+## License
+
+The software is licensed under the MIT license (see LICENSE file), and is free and provided as-is.
+
+## References
+
+1. Thakkar A, Kogej T, Reymond J-L, et al (2019) Datasets and their influence on the development of computer assisted synthesis planning tools in the pharmaceutical domain. Chem Sci. https://doi.org/10.1039/C9SC04944D