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Vignesh Ram Somnath
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‎.github/workflows/pre-commit.yaml‎

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# Based on https://github.com/pre-commit/action
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name: pre-commit
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on:
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pull_request:
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push:
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branches: [main]
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jobs:
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pre-commit:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v3
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- uses: pre-commit/action@v3.0.0

‎.gitignore‎

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homework
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inference_out_dir_not_specified
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.plotly_cache
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.DS_store
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renew.sh
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tmux_renew.sh
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commit.sh
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images
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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.so3_*
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# pyenv
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.python-version
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# celery beat schedule file
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celerybeat-schedule
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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slurm*
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*~
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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local_config_inference2.yml
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.vscode/
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*.zip
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.idea/
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#################### Project specific
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.p.npy
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.score.npy
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.torus_p.npy
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.torus_score.npy
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# this ignores everything in data except for the file
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!/data
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/data/*
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!/data/splits
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!/data/protein_ligand_example_csv.csv
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!/data/testset_csv.csv
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!/data/INDEX_general_PL_data.2020
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test_run
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cache
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wandb
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logs
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# temporary files
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.openbabel_cache
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temp/
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bsub*
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stderr*
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stdout*
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!/workdir
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/workdir/*
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!/workdir/paper_confidence_model
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!/workdir/paper_score_model
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runs2
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results
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outputs
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wandb
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# this excludes everything in the runs directory except for that specific run
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!/runs
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/runs/*
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!/runs/rigid_redocking
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!/runs/flexible_self_docking
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local_config.yml
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local_config_inference.yml
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local_config_filtering.yml
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temp1.py
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temp5.py
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temp3.py
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temp4.py
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temp5.py
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temp6.py
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temp7.py
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esm
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data/**
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*.ckpt
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*.pt
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workdir/**
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*.pdb
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*.sdf
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*.pkl
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*.npy
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notebooks/**
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rebuttal/**
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*.yaml
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*.pdf
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*.ipynb
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testing/**
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baselines/**
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*.sh
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misc/**
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*.csv

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:
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- id: end-of-file-fixer
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- id: trailing-whitespace
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- id: check-yaml
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- id: check-toml
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- id: check-json
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- id: check-merge-conflict
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- id: requirements-txt-fixer
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- id: detect-private-key
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- repo: https://github.com/psf/black
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rev: 23.3.0
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hooks:
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- id: black
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exclude: ^legacy
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- repo: https://github.com/charliermarsh/ruff-pre-commit
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# Ruff version.
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rev: 'v0.5.5'
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hooks:
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- id: ruff
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args: [--fix]

‎LICENSE‎

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MIT License
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Copyright (c) 2025 Gabriele Corso, Vignesh Ram Somnath, Noah Getz
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

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