PROTAC-Degradation-Predictor / environment.yml
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Updated README and Conda environment configuration file
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name: env-protac-degradation-predictor
channels:
- pyg
- anaconda
- pytorch
- huggingface
- nvidia
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=main
- _openmp_mutex=5.1=1_gnu
- _py-xgboost-mutex=2.0=cpu_0
- abseil-cpp=20211102.0=h27087fc_1
- absl-py=1.4.0=pyhd8ed1ab_0
- accelerate=0.21.0=pyhd8ed1ab_0
- aiohttp=3.8.3=py310h5eee18b_0
- aiosignal=1.2.0=pyhd8ed1ab_0
- alembic=1.12.0=pyhd8ed1ab_0
- anyio=3.7.1=pyhd8ed1ab_0
- arrow=1.2.3=pyhd8ed1ab_0
- arrow-cpp=11.0.0=py310h7516544_0
- async-timeout=4.0.2=pyhd8ed1ab_0
- aws-c-common=0.4.57=he1b5a44_1
- aws-c-event-stream=0.1.6=h72b8ae1_3
- aws-checksums=0.1.9=h346380f_0
- aws-sdk-cpp=1.8.185=hce553d0_0
- backports=1.0=pyhd8ed1ab_3
- backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0
- beautifulsoup4=4.12.2=pyha770c72_0
- binaryornot=0.4.4=py_1
- blas=1.0=mkl
- blessed=1.19.1=pyhe4f9e05_2
- blinker=1.6.2=pyhd8ed1ab_0
- boltons=23.0.0=pyhd8ed1ab_0
- boost-cpp=1.73.0=h7f8727e_12
- bottleneck=1.3.5=py310ha9d4c09_0
- brotlipy=0.7.0=py310h5764c6d_1004
- bzip2=1.0.8=h7f98852_4
- c-ares=1.19.0=h5eee18b_0
- ca-certificates=2023.08.22=h06a4308_0
- cachecontrol=0.12.14=pyhd8ed1ab_0
- certifi=2023.7.22=py310h06a4308_0
- cffi=1.15.1=py310h5eee18b_3
- chardet=5.1.0=py310hff52083_0
- charset-normalizer=2.0.4=pyhd8ed1ab_0
- cleo=2.0.1=pyhd8ed1ab_0
- click=8.0.4=py310hff52083_0
- cmaes=0.10.0=pyhd8ed1ab_0
- colorama=0.4.6=pyhd8ed1ab_0
- colorlog=6.7.0=py310hff52083_1
- conda=23.7.4=py310hff52083_0
- conda-content-trust=0.1.3=pyhd8ed1ab_0
- conda-package-handling=1.9.0=py310h5eee18b_1
- cookiecutter=2.3.0=pyh1a96a4e_0
- crashtest=0.4.1=pyhd8ed1ab_0
- croniter=1.3.15=pyhd8ed1ab_0
- cryptography=38.0.1=py310h9ce1e76_0
- cuda-cudart=11.8.89=0
- cuda-cupti=11.8.87=0
- cuda-libraries=11.8.0=0
- cuda-nvrtc=11.8.89=0
- cuda-nvtx=11.8.86=0
- cuda-runtime=11.8.0=0
- dataclasses=0.8=pyhc8e2a94_3
- datasets=2.14.4=py_0
- dateutils=0.6.12=py_0
- dbus=1.13.0=h4e0c4b3_1000
- deepdiff=6.2.2=pyhd8ed1ab_0
- dill=0.3.6=pyhd8ed1ab_1
- distlib=0.3.7=pyhd8ed1ab_0
- dulwich=0.21.3=py310h5eee18b_0
- evaluate=0.2.2=pyhd8ed1ab_0
- exceptiongroup=1.1.3=pyhd8ed1ab_0
- expat=2.4.8=h27087fc_0
- fastapi=0.103.1=pyhd8ed1ab_0
- ffmpeg=4.3=hf484d3e_0
- filelock=3.9.0=pyhd8ed1ab_0
- freetype=2.12.1=h4a9f257_0
- frozenlist=1.3.3=py310h5eee18b_0
- fsspec=2023.4.0=pyh1a96a4e_0
- gflags=2.2.2=he1b5a44_1004
- giflib=5.2.1=h36c2ea0_2
- glog=0.5.0=h48cff8f_0
- gmp=6.2.1=h58526e2_0
- gmpy2=2.1.2=py310heeb90bb_0
- gnutls=3.6.15=he1e5248_0
- google-auth-oauthlib=0.4.1=py_2
- greenlet=1.1.2=py310hd8f1fbe_2
- grpc-cpp=1.46.1=h33aed49_1
- grpcio=1.42.0=py310hce63b2e_0
- h11=0.14.0=pyhd8ed1ab_0
- html5lib=1.1=pyh9f0ad1d_0
- huggingface_hub=0.16.4=py_0
- icu=58.2=hf484d3e_1000
- idna=3.4=pyhd8ed1ab_0
- importlib-metadata=6.8.0=pyha770c72_0
- importlib_metadata=6.8.0=hd8ed1ab_0
- importlib_resources=6.0.1=pyhd8ed1ab_0
- inquirer=3.1.3=pyhd8ed1ab_0
- intel-openmp=2023.1.0=hdb19cb5_46305
- itsdangerous=2.1.2=pyhd8ed1ab_0
- jaraco.classes=3.3.0=pyhd8ed1ab_0
- jeepney=0.8.0=pyhd8ed1ab_0
- jinja2=3.1.2=pyhd8ed1ab_1
- joblib=1.2.0=pyhd8ed1ab_0
- jpeg=9e=h166bdaf_1
- jsonpatch=1.32=pyhd8ed1ab_0
- jsonpointer=2.1=pyhd3eb1b0_0
- keyring=23.13.1=py310hff52083_0
- krb5=1.20.1=h568e23c_1
- lame=3.100=h7f98852_1001
- lcms2=2.12=h3be6417_0
- ld_impl_linux-64=2.38=h1181459_1
- lerc=3.0=h9c3ff4c_0
- libboost=1.73.0=h28710b8_12
- libbrotlicommon=1.0.9=h166bdaf_7
- libbrotlidec=1.0.9=h166bdaf_7
- libbrotlienc=1.0.9=h166bdaf_7
- libcublas=11.11.3.6=0
- libcufft=10.9.0.58=0
- libcufile=1.7.1.12=0
- libcurand=10.3.3.129=0
- libcurl=8.1.1=h91b91d3_2
- libcusolver=11.4.1.48=0
- libcusparse=11.7.5.86=0
- libdeflate=1.8=h7f98852_0
- libedit=3.1.20221030=h5eee18b_0
- libev=4.33=h516909a_1
- libevent=2.1.12=h8f2d780_0
- libffi=3.4.2=h7f98852_5
- libgcc-ng=11.2.0=h1234567_1
- libgfortran-ng=11.2.0=h00389a5_1
- libgfortran5=11.2.0=h1234567_1
- libgomp=11.2.0=h1234567_1
- libiconv=1.16=h516909a_0
- libidn2=2.3.4=h5eee18b_0
- libnghttp2=1.52.0=ha637b67_1
- libnpp=11.8.0.86=0
- libnvjpeg=11.9.0.86=0
- libpng=1.6.39=h5eee18b_0
- libprotobuf=3.20.3=he621ea3_0
- libssh2=1.10.0=ha56f1ee_2
- libstdcxx-ng=11.2.0=he4da1e4_16
- libtasn1=4.19.0=h5eee18b_0
- libthrift=0.15.0=h0d84882_2
- libtiff=4.5.0=hecacb30_0
- libunistring=0.9.10=h7f98852_0
- libuuid=1.41.5=h5eee18b_0
- libwebp=1.2.4=h11a3e52_1
- libwebp-base=1.2.4=h5eee18b_1
- libxgboost=1.5.1=cpu_h3d145d1_2
- lightning=2.0.4=pyhd8ed1ab_0
- lightning-cloud=0.5.38=pyhd8ed1ab_0
- lightning-utilities=0.9.0=pyhd8ed1ab_0
- lockfile=0.12.2=py_1
- lz4-c=1.9.4=h6a678d5_0
- mako=1.2.4=pyhd8ed1ab_0
- markdown=3.4.4=pyhd8ed1ab_0
- markdown-it-py=3.0.0=pyhd8ed1ab_0
- markupsafe=2.1.1=py310h5764c6d_1
- mdurl=0.1.0=pyhd8ed1ab_0
- mkl=2023.1.0=h213fc3f_46343
- mkl-service=2.4.0=py310h5eee18b_1
- mkl_fft=1.3.6=py310h1128e8f_1
- mkl_random=1.2.2=py310h1128e8f_1
- more-itertools=10.1.0=pyhd8ed1ab_0
- mpc=1.1.0=h04dde30_1009
- mpfr=4.0.2=he80fd80_1
- mpmath=1.3.0=pyhd8ed1ab_0
- msgpack-python=1.0.3=py310hbf28c38_1
- multidict=6.0.2=py310h5764c6d_1
- multiprocess=0.70.14=py310h06a4308_0
- ncurses=6.3=h27087fc_1
- nettle=3.7.3=hbbd107a_1
- networkx=3.1=pyhd8ed1ab_0
- numexpr=2.8.4=py310h85018f9_1
- numpy=1.25.2=py310h5f9d8c6_0
- numpy-base=1.25.2=py310hb5e798b_0
- oauthlib=3.2.2=pyhd8ed1ab_0
- openh264=2.1.1=h780b84a_0
- openssl=1.1.1w=h7f8727e_0
- optuna=3.3.0=pyhd8ed1ab_0
- orc=1.7.4=hb3bc3d3_1
- ordered-set=4.1.0=pyhd8ed1ab_0
- packaging=23.0=pyhd8ed1ab_0
- pandas=1.5.3=py310h1128e8f_0
- pexpect=4.8.0=pyh1a96a4e_2
- pillow=9.4.0=py310h6a678d5_0
- pip=22.3.1=pyhd8ed1ab_0
- pkginfo=1.9.6=pyhd8ed1ab_0
- pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1
- platformdirs=2.6.2=pyhd8ed1ab_0
- poetry=1.4.2=linux_pyhd8ed1ab_0
- poetry-core=1.5.2=pyhd8ed1ab_0
- poetry-plugin-export=1.3.1=pyhd8ed1ab_0
- protobuf=3.20.3=py310h6a678d5_0
- psutil=5.9.0=py310h5764c6d_1
- ptyprocess=0.7.0=pyhd3deb0d_0
- py-xgboost=1.5.1=cpu_py310hd1aba9c_2
- pyarrow=11.0.0=py310h468efa6_0
- pyasn1=0.4.8=py_0
- pyasn1-modules=0.2.7=py_0
- pycosat=0.6.4=py310h5eee18b_0
- pycparser=2.21=pyhd8ed1ab_0
- pydantic=1.9.1=py310h5764c6d_0
- pyg=2.3.1=py310_torch_2.0.0_cu118
- pygments=2.16.1=pyhd8ed1ab_0
- pyjwt=2.8.0=pyhd8ed1ab_0
- pyopenssl=22.0.0=pyhd8ed1ab_1
- pyparsing=3.0.9=py310h06a4308_0
- pyproject_hooks=1.0.0=pyhd8ed1ab_0
- pyrsistent=0.18.1=py310h5764c6d_1
- pysocks=1.7.1=pyha2e5f31_6
- python=3.10.8=h7a1cb2a_1
- python-build=0.10.0=pyhd8ed1ab_1
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python-editor=1.0.4=py_0
- python-installer=0.7.0=pyhd8ed1ab_0
- python-multipart=0.0.6=pyhd8ed1ab_0
- python-slugify=8.0.1=pyhd8ed1ab_0
- python-xxhash=2.0.2=py310h6acc77f_1
- python_abi=3.10=2_cp310
- pytorch=2.0.1=py3.10_cuda11.8_cudnn8.7.0_0
- pytorch-cuda=11.8=h7e8668a_5
- pytorch-lightning=2.0.9=pyhd8ed1ab_0
- pytorch-mutex=1.0=cuda
- pytz=2022.7.1=pyhd8ed1ab_0
- pyu2f=0.1.5=pyhd8ed1ab_0
- pyyaml=6.0=py310h5764c6d_4
- rapidfuzz=2.13.7=py310h1128e8f_0
- re2=2022.04.01=h27087fc_0
- readchar=4.0.5=pyhd8ed1ab_0
- readline=8.2=h5eee18b_0
- regex=2022.7.9=py310h5eee18b_0
- requests-oauthlib=1.3.1=pyhd8ed1ab_0
- requests-toolbelt=0.10.1=pyhd8ed1ab_0
- responses=0.18.0=pyhd8ed1ab_0
- rich=13.5.1=pyhd8ed1ab_0
- rsa=4.9=pyhd8ed1ab_0
- ruamel.yaml=0.17.21=py310h5764c6d_1
- ruamel.yaml.clib=0.2.6=py310h5764c6d_1
- sacremoses=master=py_0
- scikit-learn=1.2.0=py310h6a678d5_1
- scipy=1.9.3=py310h5f9d8c6_2
- secretstorage=3.3.3=py310hff52083_1
- setuptools=65.5.0=pyhd8ed1ab_0
- shellingham=1.5.3=pyhd8ed1ab_0
- six=1.16.0=pyh6c4a22f_0
- snappy=1.1.9=hbd366e4_1
- sniffio=1.3.0=pyhd8ed1ab_0
- soupsieve=2.5=pyhd8ed1ab_1
- sqlalchemy=1.4.36=py310h5764c6d_0
- sqlite=3.40.0=h5082296_0
- starlette=0.27.0=pyhd8ed1ab_0
- starsessions=1.3.0=pyhd8ed1ab_0
- sympy=1.11.1=pyh04b8f61_3
- tabulate=0.9.0=pyhd8ed1ab_1
- tbb=2021.8.0=hdb19cb5_0
- tensorboard=2.6.0=py_0
- tensorboard-plugin-wit=1.8.1=pyhd8ed1ab_0
- text-unidecode=1.3=py_0
- threadpoolctl=2.2.0=pyh0d69192_0
- tk=8.6.12=h1ccaba5_0
- tokenizers=0.13.2=py310he7d60b5_1
- tomli=2.0.1=pyhd8ed1ab_0
- tomlkit=0.12.1=pyha770c72_0
- toolz=0.12.0=pyhd8ed1ab_0
- torchaudio=2.0.2=py310_cu118
- torchmetrics=1.1.2=pyhd8ed1ab_0
- torchtriton=2.0.0=py310
- torchvision=0.15.2=py310_cu118
- tqdm=4.64.1=pyhd8ed1ab_0
- transformers=4.29.2=pyhd8ed1ab_0
- trove-classifiers=2023.8.7=pyhd8ed1ab_0
- typing-extensions=4.7.1=hd8ed1ab_0
- typing_extensions=4.7.1=pyha770c72_0
- tzdata=2022g=h191b570_0
- unidecode=1.3.6=pyhd8ed1ab_0
- urllib3=1.26.13=pyhd8ed1ab_0
- utf8proc=2.6.1=h27cfd23_0
- uvicorn=0.23.2=py310hff52083_0
- virtualenv=20.21.1=pyhd8ed1ab_0
- wcwidth=0.2.6=pyhd8ed1ab_0
- webencodings=0.5.1=pyhd8ed1ab_2
- websockets=10.3=py310h5764c6d_0
- werkzeug=2.3.6=pyhd8ed1ab_0
- wheel=0.37.1=pyhd8ed1ab_0
- xxhash=0.8.0=h7f98852_3
- xz=5.2.8=h5eee18b_0
- yaml=0.2.5=h7f98852_2
- yarl=1.8.1=py310h5eee18b_0
- zipp=3.16.2=pyhd8ed1ab_0
- zlib=1.2.13=h5eee18b_0
- zstd=1.5.2=ha4553b6_0
- pip:
- appdirs==1.4.4
- argon2-cffi==23.1.0
- argon2-cffi-bindings==21.2.0
- asttokens==2.4.1
- async-lru==2.0.4
- attrs==23.2.0
- babel==2.14.0
- bleach==6.1.0
- cachetools==4.2.4
- comm==0.2.2
- contourpy==1.2.1
- cycler==0.12.1
- debugpy==1.8.1
- decorator==5.1.1
- defusedxml==0.7.1
- docker-pycreds==0.4.0
- docstring-parser==0.15
- executing==2.0.1
- fastjsonschema==2.19.1
- fonttools==4.51.0
- fqdn==1.5.1
- gitdb==4.0.11
- gitpython==3.1.42
- google-auth==1.35.0
- h5py==3.10.0
- httpcore==1.0.5
- httpx==0.27.0
- imbalanced-learn==0.12.0
- iniconfig==2.0.0
- ipykernel==6.29.4
- ipython==8.23.0
- ipywidgets==8.1.2
- isoduration==20.11.0
- jedi==0.19.1
- json5==0.9.25
- jsonargparse==4.23.1
- jsonschema==4.21.1
- jsonschema-specifications==2023.12.1
- jupyter==1.0.0
- jupyter-client==8.6.1
- jupyter-console==6.6.3
- jupyter-core==5.7.2
- jupyter-events==0.10.0
- jupyter-lsp==2.2.5
- jupyter-server==2.14.0
- jupyter-server-terminals==0.5.3
- jupyterlab==4.1.6
- jupyterlab-pygments==0.3.0
- jupyterlab-server==2.26.0
- jupyterlab-widgets==3.0.10
- kiwisolver==1.4.5
- llvmlite==0.42.0
- matplotlib==3.8.4
- matplotlib-inline==0.1.7
- mistune==3.0.2
- nbclient==0.10.0
- nbconvert==7.16.3
- nbformat==5.10.4
- nest-asyncio==1.6.0
- nltk==3.8.1
- notebook==7.1.3
- notebook-shim==0.2.4
- numba==0.59.1
- overrides==7.7.0
- pandocfilters==1.5.1
- parso==0.8.4
- pluggy==1.5.0
- prometheus-client==0.20.0
- prompt-toolkit==3.0.43
- pure-eval==0.2.2
- pynndescent==0.5.12
- pynvml==11.5.0
- pytest==8.1.1
- python-json-logger==2.0.7
- pyzmq==26.0.1
- qtconsole==5.5.1
- qtpy==2.4.1
- rdkit==2023.9.5
- rdkit-pypi==2022.9.5
- referencing==0.34.0
- requests==2.31.0
- rfc3339-validator==0.1.4
- rfc3986-validator==0.1.1
- rouge-score==0.1.2
- rpds-py==0.18.0
- seaborn==0.13.2
- send2trash==1.8.3
- sentry-sdk==1.41.0
- setproctitle==1.3.3
- smmap==5.0.1
- stack-data==0.6.3
- tensorboard-data-server==0.6.1
- terminado==0.18.1
- tinycss2==1.2.1
- tornado==6.4
- traitlets==5.14.3
- typeshed-client==2.3.0
- umap-learn==0.5.6
- uri-template==1.3.0
- wandb==0.16.4
- webcolors==1.13
- websocket-client==1.7.0
- widgetsnbextension==4.0.10