Having trouble with requirements.txt

[yipy0005]

Hi,

Thank you so much for publishing the code, it must have been a lot of work writing the code. I am very keen to try out the repository, but I'm having troubles with installing the requirements.txt file because most of the packages seem to be local to the computer that the repository was developed.

Could you provide a clean conda env file via conda env export --no-builds?

Also, could you let me know what is the CUDA driver that works with the repository?

Thank you so much and I look forward to your reply. 😁

Best regards, Yew Mun

[Saoge123]

name: PocketFlow channels:

• conda-forge
• schrodinger
• defaults dependencies:
• _libgcc_mutex=0.1
• _openmp_mutex=5.1
• alabaster=0.7.12
• apbs=1.5
• asttokens=2.0.5
• babel=2.11.0
• backcall=0.2.0
• blas=1.0
• boost=1.70.0
• boost-cpp=1.70.0
• brotlipy=0.7.0
• bzip2=1.0.8
• c-ares=1.19.0
• ca-certificates=2023.7.22
• cairo=1.16.0
• certifi=2023.7.22
• cffi=1.15.1
• charset-normalizer=2.0.4
• colorama=0.4.6
• comm=0.1.2
• cryptography=39.0.1
• curl=7.88.1
• dbus=1.13.18
• debugpy=1.5.1
• decorator=5.1.1
• docutils=0.18.1
• executing=0.8.3
• expat=2.4.9
• fontconfig=2.14.1
• freemol=1.158
• freetype=2.12.1
• giflib=5.2.1
• glew=2.0.0
• glib=2.69.1
• gst-plugins-base=1.14.1
• gstreamer=1.14.1
• h5py=3.7.0
• hdf4=4.2.13
• hdf5=1.10.6
• icu=58.2
• idna=3.4
• imagesize=1.4.1
• importlib_metadata=6.0.0
• intel-openmp=2023.1.0
• ipykernel=6.19.2
• ipython=8.12.0
• ipywidgets=8.0.7
• jedi=0.18.1
• jinja2=3.1.2
• jpeg=9e
• jupyter_client=8.1.0
• jupyter_core=5.3.0
• jupyterlab_widgets=3.0.8
• krb5=1.20.1
• lcms2=2.12
• ld_impl_linux-64=2.38
• lerc=3.0
• libclang=10.0.1
• libcurl=7.88.1
• libdeflate=1.17
• libedit=3.1.20221030
• libev=4.33
• libevent=2.1.12
• libffi=3.4.4
• libgcc-ng=11.2.0
• libgfortran-ng=7.5.0
• libgfortran4=7.5.0
• libglu=9.0.0
• libgomp=11.2.0
• libholoplaycore=0.1.0_rc4
• libllvm10=10.0.1
• libnetcdf=4.8.1
• libnghttp2=1.52.0
• libopenblas=0.3.18
• libpng=1.6.39
• libpq=12.15
• libsodium=1.0.18
• libssh2=1.10.0
• libstdcxx-ng=11.2.0
• libtiff=4.5.0
• libuuid=1.41.5
• libwebp=1.2.4
• libwebp-base=1.2.4
• libxcb=1.15
• libxkbcommon=1.0.1
• libxml2=2.9.14
• libxslt=1.1.35
• libzip=1.8.0
• lz4-c=1.9.4
• matplotlib-inline=0.1.6
• mengine=1
• mkl=2023.1.0
• mkl-service=2.4.0
• mkl_fft=1.3.6
• mkl_random=1.2.2
• mpeg_encode=1
• mtz2ccp4_px=1.0
• ncurses=6.4
• nest-asyncio=1.5.6
• nspr=4.35
• nss=3.89.1
• openbabel=3.1.1
• openssl=3.0.10
• packaging=23.0
• pandas=1.4.2
• parso=0.8.3
• pcre=8.45
• pdb2pqr=2.1.2+pymol
• pexpect=4.8.0
• pickleshare=0.7.5
• pillow=9.4.0
• pixman=0.40.0
• platformdirs=2.5.2
• ply=3.11
• pmw=2.0.1+3
• prompt-toolkit=3.0.36
• ptyprocess=0.7.0
• pure_eval=0.2.2
• pycairo=1.21.0
• pycparser=2.21
• pygments=2.15.1
• pymol=2.4.1
• pyopenssl=23.0.0
• pyqt=5.15.7
• pyqt5-sip=12.11.0
• pysocks=1.7.1
• python=3.8.12
• python-dateutil=2.8.2
• python-lmdb=1.3.0
• python_abi=3.8
• pytz=2023.3
• pyzmq=25.1.0
• qt-main=5.15.2
• qt-webengine=5.15.9
• qtwebkit=5.212
• rdkit=2019.09.3
• readline=8.2
• rigimol=1.3
• setuptools=67.8.0
• sip=6.6.2
• six=1.16.0
• snowballstemmer=2.2.0
• sphinx=5.0.2
• sphinx_rtd_theme=1.1.1
• sphinxcontrib-applehelp=1.0.2
• sphinxcontrib-devhelp=1.0.2
• sphinxcontrib-htmlhelp=2.0.0
• sphinxcontrib-jsmath=1.0.1
• sphinxcontrib-qthelp=1.0.3
• sphinxcontrib-serializinghtml=1.1.5
• sqlite=3.41.2
• stack_data=0.2.0
• tbb=2021.8.0
• tk=8.6.12
• toml=0.10.2
• tornado=6.2
• traitlets=5.7.1
• typing_extensions=4.6.3
• urllib3=1.26.16
• wcwidth=0.2.5
• wheel=0.38.4
• widgetsnbextension=4.0.8
• xz=5.2.10
• zeromq=4.3.4
• zlib=1.2.13
• zstd=1.5.5
• pip:
  • absl-py==1.4.0
  • anyio==4.0.0
  • appdirs==1.4.4
  • argon2-cffi==23.1.0
  • argon2-cffi-bindings==21.2.0
  • arrow==1.3.0
  • async-lru==2.0.4
  • attrs==23.1.0
  • beautifulsoup4==4.12.2
  • bleach==6.1.0
  • cachetools==5.3.1
  • click==8.1.7
  • contourpy==1.1.0
  • cycler==0.11.0
  • defusedxml==0.7.1
  • docker-pycreds==0.4.0
  • easydict==1.10
  • et-xmlfile==1.1.0
  • exceptiongroup==1.1.3
  • fastjsonschema==2.18.1
  • fonttools==4.40.0
  • fqdn==1.5.1
  • gitdb==4.0.11
  • gitpython==3.1.40
  • google-auth==2.21.0
  • google-auth-oauthlib==1.0.0
  • grpcio==1.56.0
  • imageio==2.33.1
  • importlib-metadata==6.7.0
  • importlib-resources==5.12.0
  • ipython-genutils==0.2.0
  • isoduration==20.11.0
  • jax==0.4.13
  • jaxlib==0.4.13
  • joblib==1.2.0
  • json5==0.9.14
  • jsonpointer==2.4
  • jsonschema==4.19.2
  • jsonschema-specifications==2023.7.1
  • jupyter==1.0.0
  • jupyter-console==6.6.3
  • jupyter-events==0.8.0
  • jupyter-lsp==2.2.0
  • jupyter-server==2.9.1
  • jupyter-server-terminals==0.4.4
  • jupyterlab==4.0.7
  • jupyterlab-pygments==0.2.2
  • jupyterlab-server==2.25.0
  • kiwisolver==1.4.4
  • markdown==3.4.3
  • markupsafe==2.1.3
  • matplotlib==3.7.1
  • meeko==0.4.0
  • mistune==3.0.2
  • ml-dtypes==0.2.0
  • msgpack==1.0.7
  • nbclient==0.8.0
  • nbconvert==7.10.0
  • nbformat==5.9.2
  • notebook==7.0.6
  • notebook-shim==0.2.3
  • numpy==1.23.0
  • nvidia-cublas-cu11==11.11.3.6
  • nvidia-cufft-cu11==10.9.0.58
  • oauthlib==3.2.2
  • openpyxl==3.1.2
  • opt-einsum==3.3.0
  • overrides==7.4.0
  • pandocfilters==1.5.0
  • pip==23.3.2
  • pkgutil-resolve-name==1.3.10
  • prometheus-client==0.18.0
  • protobuf==4.23.3
  • psutil==5.9.5
  • pyasn1==0.5.0
  • pyasn1-modules==0.3.0
  • pyg-lib==0.2.0+pt113cu117
  • pyparsing==3.1.0
  • python-json-logger==2.0.7
  • pyyaml==6.0
  • qtconsole==5.4.4
  • qtpy==2.4.1
  • referencing==0.30.2
  • requests==2.31.0
  • requests-oauthlib==1.3.1
  • rfc3339-validator==0.1.4
  • rfc3986-validator==0.1.1
  • rpds-py==0.10.6
  • rsa==4.9
  • scikit-learn==1.2.2
  • scipy==1.10.1
  • seaborn==0.12.2
  • send2trash==1.8.2
  • sentry-sdk==1.39.1
  • setproctitle==1.3.3
  • smmap==5.0.1
  • sniffio==1.3.0
  • soupsieve==2.5
  • tensorboard==2.13.0
  • tensorboard-data-server==0.7.1
  • terminado==0.17.1
  • threadpoolctl==3.1.0
  • tinycss2==1.2.1
  • tomli==2.0.1
  • torch==1.13.0+cu117
  • torch-cluster==1.6.1+pt113cu117
  • torch-geometric==2.3.1
  • torch-scatter==2.1.1+pt113cu117
  • torch-sparse==0.6.17+pt113cu117
  • torch-spline-conv==1.2.2+pt113cu117
  • torchaudio==0.13.0+cu117
  • torchdiffeq==0.2.3
  • torchvision==0.14.0+cu117
  • tqdm==4.65.0
  • types-python-dateutil==2.8.19.14
  • uri-template==1.3.0
  • vina==1.2.5
  • wandb==0.16.1
  • webcolors==1.13
  • webencodings==0.5.1
  • websocket-client==1.6.4
  • werkzeug==2.3.6
  • xgboost==1.0.2
  • zipp==3.15.0
  • zuko==1.0.1

[Saoge123]

Hi, thanks for your attention. The code runs on cuda11.3 or 11.7.

[yipy0005]

Hi, I have managed to get the repository to work. In addition, I have submitted a pull request to replace requirements.txt with environment.yml instead. I have also updated the README.md to provide instructions on how to create the conda environment. 😁

Cheers! Yew Mun