chore: open-sourcing rxn-neb.

Signed-off-by: Matteo Manica <[email protected]>

.github/workflows/tests.yaml

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+name: "Running tests: ruff stylinh"
+
+on: [push, pull_request]
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    name: Style, mypy, pytest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.8
+    - name: Install poetry
+      run: pip install poetry==1.7.1
+    - name: Install Dependencies
+      run: poetry install
+    - name: Check style
+      run: poetry run ruff check . && poetry run ruff format --check .

.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/
+*.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/
+src/rxn/neb/.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+../.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+conda_env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# PyCharm
+.idea/
+
+# VSCode
+.vscode/
+
+# Pre-commit configuration
+# .pre-commit-config.yaml
+
+# Apple macOS
+.DS_Store
+
+# ruff
+.ruff_cache
+
+# custom
+check_test.py
+retrosynthesis_check_test_ref.json
+test_retro.json
+sandbox
+rxnfp

README.md

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+# rxn-neb
+
+## Setup
+
+To install the package run:
+
+```console
+poetry install
+```
+
+## Pre-process data for running rxn-neb
+
+Here we assume to start from a JSON file reporting synthesis trees characterized by reactions SMILES represented using a pre-order traversal. A sample is provided [here](./sample-data/reaction_trees.json).
+
+Additionally we assume a model for reaction fingerprints compatible with [`rxnfp`](https://github.com/rxn4chemistry/rxnfp) is available (see the repo for instructions on how to train your own on public or proprietary data).
+
+To get the default model used in RXN for Chemistry simply clone the repo:
+
+```console
+git clone https://github.com/rxn4chemistry/rxnfp.git
+```
+
+You can directly use the default model available at `./rxnfp/rxnfp/models/transformers/bert_ft`.
+
+Prepare the fingerprints from available synthesis trees:
+
+```console
+generate-fingerprints --reaction_trees_path "./sample-data/reaction_trees.json" --fingerprints_model_path "./rxnfp/rxnfp/models/transformers/bert_ft" --generated_fingerprints_path "./sandbox/generated_fingerprints.csv"
+```
+
+Prepare the PCA model for fingerprint compression and related indexes:
+
+```console
+generate-pca-compression-and-indices  --reaction_trees_path "./sample-data/reaction_trees.json" --fingerprints_path "./sandbox/generated_fingerprints.csv" --pca_model_filename "./sandbox/pca.pkl" --tree_data_dict_pca_filename "./sandbox/tree_data_dict_pca.pkl"
+```
+
+NOTE: these examples are creating a `sandbox` folder where all outputs are stored.
+
+## Usage
+
+We assume you have a pair of single-step forward and backward model trained using [`rxn-onmt-models`](https://github.com/rxn4chemistry/rxn-onmt-models) (see the repo for a detailed guide on how to train them on public or proprietary data).
+
+```console
+run-neb-retrosynthesis --product "NS(=O)(=O)c1nn(-c2ccccn2)cc1Br" \
+    --forward_model_path "/path/to/forward_model.pt" \
+    --backward_model_path "/path/to/backward_model.pt" \
+    --fingerprints_model_path "./rxnfp/rxnfp/models/transformers/bert_ft"  \
+    --pca_model_filename "./sandbox/pca.pkl" \
+    --tree_data_dict_pca_filename "./sandbox/tree_data_dict_pca.pkl" \
+    --output_path ./test_retro.json
+```