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environment.yml
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environment.yml
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name: LatentDiff
channels:
- bioconda
- pytorch
- plotly
- anaconda
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- absl-py=1.1.0=pyhd8ed1ab_0
- aiohttp=3.8.1=py310h7f8727e_1
- aiosignal=1.2.0=pyhd3eb1b0_0
- anyio=3.6.1=py310hff52083_0
- argon2-cffi=21.3.0=pyhd8ed1ab_0
- argon2-cffi-bindings=21.2.0=py310h5764c6d_2
- asttokens=2.0.5=pyhd8ed1ab_0
- astunparse=1.6.3=pyhd8ed1ab_0
- async-timeout=4.0.1=pyhd3eb1b0_0
- atk-1.0=2.36.0=h3371d22_4
- attrs=21.4.0=pyhd3eb1b0_0
- babel=2.10.3=pyhd8ed1ab_0
- backcall=0.2.0=pyh9f0ad1d_0
- backports=1.0=py_2
- backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
- beautifulsoup4=4.11.1=pyha770c72_0
- biopython=1.79=py310h5764c6d_2
- biotite=0.34.1=py310hde88566_1
- blas=1.0=mkl
- bleach=5.0.1=pyhd8ed1ab_0
- blessings=1.7=py310h06a4308_1002
- blinker=1.4=py310h06a4308_0
- blosc=1.21.1=h83bc5f7_3
- brotli=1.0.9=h166bdaf_7
- brotli-bin=1.0.9=h166bdaf_7
- brotlipy=0.7.0=py310h7f8727e_1002
- bzip2=1.0.8=h7b6447c_0
- c-ares=1.18.1=h7f8727e_0
- ca-certificates=2023.5.7=hbcca054_0
- cached-property=1.5.2=hd8ed1ab_1
- cached_property=1.5.2=pyha770c72_1
- cachetools=4.2.2=pyhd3eb1b0_0
- cairo=1.16.0=ha61ee94_1011
- certifi=2023.5.7=pyhd8ed1ab_0
- cffi=1.15.0=py310hd667e15_1
- cftime=1.6.1=py310hde88566_0
- charset-normalizer=2.0.4=pyhd3eb1b0_0
- click=8.0.4=py310h06a4308_0
- colorama=0.4.5=pyhd8ed1ab_0
- cryptography=37.0.1=py310h9ce1e76_0
- cudatoolkit=11.3.1=h2bc3f7f_2
- curl=7.82.0=h7f8727e_0
- cycler=0.11.0=pyhd8ed1ab_0
- dataclasses=0.8=pyh6d0b6a4_7
- debugpy=1.6.0=py310hd8f1fbe_0
- decorator=5.1.1=pyhd8ed1ab_0
- defusedxml=0.7.1=pyhd8ed1ab_0
- docker-pycreds=0.4.0=py_0
- entrypoints=0.4=pyhd8ed1ab_0
- executing=0.8.3=pyhd8ed1ab_0
- expat=2.4.8=h27087fc_0
- fasteners=0.17.3=pyhd8ed1ab_0
- ffmpeg=4.2.2=h20bf706_0
- fftw=3.3.10=nompi_h77c792f_102
- flit-core=3.7.1=pyhd8ed1ab_0
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=hab24e00_0
- fontconfig=2.14.0=h8e229c2_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- fonttools=4.33.3=py310h5764c6d_0
- freetype=2.11.0=h70c0345_0
- fribidi=1.0.10=h36c2ea0_0
- frozenlist=1.2.0=py310h7f8727e_1
- gdk-pixbuf=2.42.8=hff1cb4f_0
- gettext=0.19.8.1=h73d1719_1008
- ghostscript=9.54.0=h27087fc_2
- giflib=5.2.1=h7b6447c_0
- gitdb=4.0.9=pyhd8ed1ab_0
- gitpython=3.1.27=pyhd8ed1ab_0
- gmp=6.2.1=h295c915_3
- gnutls=3.6.15=he1e5248_0
- google-auth=2.6.0=pyhd3eb1b0_0
- google-auth-oauthlib=0.4.4=pyhd3eb1b0_0
- gpustat=0.6.0=pyhd8ed1ab_1
- gputil=1.4.0=pyh9f0ad1d_0
- graphite2=1.3.13=h58526e2_1001
- graphviz=5.0.0=h5abf519_0
- griddataformats=1.0.1=pyhd8ed1ab_0
- grpcio=1.42.0=py310hce63b2e_0
- gsd=2.5.3=py310hde88566_0
- gtk2=2.24.33=h90689f9_2
- gts=0.7.6=h64030ff_2
- h5py=3.7.0=nompi_py310h06dffec_100
- harfbuzz=4.4.1=hf9f4e7c_0
- hdf4=4.2.15=h10796ff_3
- hdf5=1.12.1=nompi_h2750804_100
- icu=70.1=h27087fc_0
- idna=3.3=pyhd3eb1b0_0
- imageio=2.22.0=pyhfa7a67d_0
- imagemagick=7.1.0.43=pl5321h2098167_0
- importlib-metadata=4.11.3=py310h06a4308_0
- importlib_resources=5.8.0=pyhd8ed1ab_0
- intel-openmp=2021.4.0=h06a4308_3561
- ipykernel=6.9.1=py310h06a4308_0
- ipython=8.4.0=py310hff52083_0
- ipython_genutils=0.2.0=py_1
- ipywidgets=7.7.1=pyhd8ed1ab_0
- jbig=2.1=h7f98852_2003
- jedi=0.18.1=py310hff52083_1
- jinja2=3.1.2=pyhd8ed1ab_1
- joblib=1.1.0=pyhd8ed1ab_0
- jpeg=9e=h7f8727e_0
- json5=0.9.5=pyh9f0ad1d_0
- jsonschema=4.6.1=pyhd8ed1ab_0
- jupyter_client=7.3.4=pyhd8ed1ab_0
- jupyter_core=4.10.0=py310hff52083_0
- jupyter_server=1.18.1=pyhd8ed1ab_0
- jupyterlab=3.4.3=pyhd8ed1ab_0
- jupyterlab_pygments=0.2.2=pyhd8ed1ab_0
- jupyterlab_server=2.12.0=py310h06a4308_0
- jupyterlab_widgets=1.1.1=pyhd8ed1ab_0
- keyutils=1.6.1=h166bdaf_0
- kiwisolver=1.4.3=py310hbf28c38_0
- krb5=1.19.3=h3790be6_0
- lame=3.100=h7b6447c_0
- lcms2=2.12=h3be6417_0
- ld_impl_linux-64=2.38=h1181459_1
- lerc=3.0=h9c3ff4c_0
- libblas=3.9.0=12_linux64_mkl
- libbrotlicommon=1.0.9=h166bdaf_7
- libbrotlidec=1.0.9=h166bdaf_7
- libbrotlienc=1.0.9=h166bdaf_7
- libcblas=3.9.0=12_linux64_mkl
- libcurl=7.82.0=h0b77cf5_0
- libdeflate=1.12=h166bdaf_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libevent=2.1.10=h9b69904_4
- libffi=3.4.2=h7f98852_5
- libgcc-ng=12.1.0=h8d9b700_16
- libgd=2.3.3=h18fbbfe_3
- libgfortran-ng=12.1.0=h69a702a_16
- libgfortran5=12.1.0=hdcd56e2_16
- libglib=2.70.2=h174f98d_4
- libgomp=12.1.0=h8d9b700_16
- libiconv=1.16=h516909a_0
- libidn2=2.3.2=h7f8727e_0
- liblapack=3.9.0=12_linux64_mkl
- libnetcdf=4.8.1=nompi_hb3fd0d9_101
- libnghttp2=1.46.0=hce63b2e_0
- libnsl=2.0.0=h7f98852_0
- libopus=1.3.1=h7b6447c_0
- libpng=1.6.37=hbc83047_0
- libprotobuf=3.20.1=h4ff587b_0
- librsvg=2.54.4=h7abd40a_0
- libsodium=1.0.18=h36c2ea0_1
- libssh2=1.10.0=ha56f1ee_2
- libstdcxx-ng=12.1.0=ha89aaad_16
- libtasn1=4.16.0=h27cfd23_0
- libtiff=4.4.0=hc85c160_1
- libtool=2.4.6=h9c3ff4c_1008
- libunistring=0.9.10=h27cfd23_0
- libuuid=2.32.1=h7f98852_1000
- libuv=1.40.0=h7b6447c_0
- libvpx=1.7.0=h439df22_0
- libwebp=1.2.2=h55f646e_0
- libwebp-base=1.2.2=h7f8727e_0
- libxcb=1.13=h7f98852_1004
- libxml2=2.9.14=h22db469_3
- libzip=1.8.0=h5cef20c_0
- libzlib=1.2.12=h166bdaf_1
- lz4-c=1.9.3=h295c915_1
- lzo=2.10=h516909a_1000
- markdown=3.3.4=py310h06a4308_0
- markupsafe=2.1.1=py310h5764c6d_1
- matplotlib-base=3.5.2=py310h5701ce4_0
- matplotlib-inline=0.1.3=pyhd8ed1ab_0
- mdanalysis=2.2.0=py310h769672d_0
- mdtraj=1.9.7=py310hd8d60c7_1
- mistune=0.8.4=py310h6acc77f_1005
- mkl=2021.4.0=h06a4308_640
- mkl-service=2.4.0=py310h7f8727e_0
- mkl_fft=1.3.1=py310hd6ae3a3_0
- mkl_random=1.2.2=py310h00e6091_0
- mmtf-python=1.1.2=py_0
- mrcfile=1.3.0=pyh44b312d_0
- msgpack-python=1.0.4=py310hbf28c38_0
- multidict=5.1.0=py310h7f8727e_2
- munkres=1.1.4=pyh9f0ad1d_0
- nbclassic=0.4.3=pyhd8ed1ab_0
- nbclient=0.6.6=pyhd8ed1ab_0
- nbconvert=6.5.0=pyhd8ed1ab_0
- nbconvert-core=6.5.0=pyhd8ed1ab_0
- nbconvert-pandoc=6.5.0=pyhd8ed1ab_0
- nbformat=5.4.0=pyhd8ed1ab_0
- ncurses=6.3=h7f8727e_2
- nest-asyncio=1.5.5=pyhd8ed1ab_0
- netcdf4=1.6.0=nompi_py310h947f774_100
- nettle=3.7.3=hbbd107a_1
- nglview=3.0.3=pyh8a188c0_0
- notebook=6.4.12=pyha770c72_0
- notebook-shim=0.1.0=pyhd8ed1ab_0
- numexpr=2.8.3=py310hcea2de6_0
- numpy=1.22.3=py310hfa59a62_0
- numpy-base=1.22.3=py310h9585f30_0
- nvidia-ml=7.352.0=pyhd3eb1b0_0
- oauthlib=3.1.0=py_0
- ocl-icd=2.3.1=h7f98852_0
- ocl-icd-system=1.0.0=1
- openh264=2.1.1=h4ff587b_0
- openjpeg=2.4.0=hb52868f_1
- openmm=7.7.0=py310hccf1d78_1
- openssl=1.1.1u=hd590300_0
- packaging=21.3=pyhd8ed1ab_0
- pandoc=2.18=ha770c72_0
- pandocfilters=1.5.0=pyhd8ed1ab_0
- pango=1.50.8=hbd2fdc8_0
- parso=0.8.3=pyhd8ed1ab_0
- pathtools=0.1.2=py_1
- patsy=0.5.2=pyhd8ed1ab_0
- pcre=8.45=h9c3ff4c_0
- perl=5.32.1=2_h7f98852_perl5
- pexpect=4.8.0=pyh9f0ad1d_2
- pickleshare=0.7.5=py_1003
- pillow=9.0.1=py310h22f2fdc_0
- pip=21.2.4=py310h06a4308_0
- pixman=0.40.0=h36c2ea0_0
- pkg-config=0.29.2=h36c2ea0_1008
- plotly=5.9.0=py_0
- prometheus_client=0.14.1=pyhd8ed1ab_0
- promise=2.3=py310hff52083_6
- prompt-toolkit=3.0.30=pyha770c72_0
- psutil=5.9.0=py310h5eee18b_0
- pthread-stubs=0.4=h36c2ea0_1001
- ptyprocess=0.7.0=pyhd3deb0d_0
- pure_eval=0.2.2=pyhd8ed1ab_0
- pyasn1=0.4.8=pyhd3eb1b0_0
- pyasn1-modules=0.2.8=py_0
- pycparser=2.21=pyhd3eb1b0_0
- pygments=2.12.0=pyhd8ed1ab_0
- pyjwt=2.4.0=pyhd8ed1ab_0
- pyopenssl=22.0.0=pyhd3eb1b0_0
- pyparsing=3.0.9=pyhd8ed1ab_0
- pyrsistent=0.18.1=py310h5764c6d_1
- pysocks=1.7.1=py310h06a4308_0
- pytables=3.7.0=py310hf5df6ce_0
- python=3.10.5=h582c2e5_0_cpython
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python-fastjsonschema=2.15.3=pyhd8ed1ab_0
- python_abi=3.10=2_cp310
- pytorch=1.11.0=py3.10_cuda11.3_cudnn8.2.0_0
- pytorch-mutex=1.0=cuda
- pytz=2022.1=pyhd8ed1ab_0
- pyyaml=6.0=py310h5764c6d_4
- pyzmq=23.2.0=py310h330234f_0
- readline=8.1.2=h7f8727e_1
- requests=2.28.0=py310h06a4308_0
- requests-oauthlib=1.3.0=py_0
- rsa=4.7.2=pyhd3eb1b0_1
- scikit-learn=1.1.1=py310hffb9edd_0
- scipy=1.8.1=py310h7612f91_0
- seaborn=0.11.2=hd8ed1ab_0
- seaborn-base=0.11.2=pyhd8ed1ab_0
- send2trash=1.8.0=pyhd8ed1ab_0
- sentry-sdk=1.9.10=pyhd8ed1ab_0
- setproctitle=1.3.2=py310h5764c6d_0
- setuptools=61.2.0=py310h06a4308_0
- shortuuid=1.0.9=pyha770c72_1
- six=1.16.0=pyhd3eb1b0_1
- smmap=3.0.5=pyh44b312d_0
- snappy=1.1.9=hbd366e4_1
- sniffio=1.2.0=py310hff52083_3
- soupsieve=2.3.1=pyhd8ed1ab_0
- sqlite=3.38.5=hc218d9a_0
- stack_data=0.3.0=pyhd8ed1ab_0
- statsmodels=0.13.2=py310hde88566_0
- tenacity=8.0.1=py310h06a4308_0
- tensorboard=2.9.0=pyhd8ed1ab_0
- tensorboard-data-server=0.6.0=py310hca6d32c_0
- tensorboard-plugin-wit=1.6.0=py_0
- terminado=0.15.0=py310hff52083_0
- threadpoolctl=3.1.0=pyh8a188c0_0
- tidynamics=1.0.0=py_0
- tinycss2=1.1.1=pyhd8ed1ab_0
- tk=8.6.12=h1ccaba5_0
- tmalign=20170708=h1107714_4
- tmux=3.3=h385fc29_0
- torchaudio=0.11.0=py310_cu113
- torchvision=0.12.0=py310_cu113
- tornado=6.2=py310h5764c6d_0
- tqdm=4.64.0=pyhd8ed1ab_0
- traitlets=5.3.0=pyhd8ed1ab_0
- tree=2.1.1=hd590300_0
- typing-extensions=4.1.1=hd3eb1b0_0
- typing_extensions=4.1.1=pyh06a4308_0
- tzdata=2022a=hda174b7_0
- unicodedata2=14.0.0=py310h5764c6d_1
- urllib3=1.26.9=py310h06a4308_0
- wandb=0.13.1=pyhd8ed1ab_0
- wcwidth=0.2.5=pyh9f0ad1d_2
- webencodings=0.5.1=py_1
- websocket-client=1.3.3=pyhd8ed1ab_0
- werkzeug=2.0.3=pyhd3eb1b0_0
- wheel=0.37.1=pyhd3eb1b0_0
- widgetsnbextension=3.6.1=pyha770c72_0
- x264=1!157.20191217=h7b6447c_0
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.0.10=h7f98852_0
- xorg-libsm=1.2.3=hd9c2040_1000
- xorg-libx11=1.7.2=h7f98852_0
- xorg-libxau=1.0.9=h7f98852_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h7f98852_1
- xorg-libxrender=0.9.10=h7f98852_1003
- xorg-libxt=1.2.1=h7f98852_2
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h7f98852_1002
- xorg-xproto=7.0.31=h7f98852_1007
- xz=5.2.5=h7f8727e_1
- yaml=0.2.5=h7f98852_2
- yarl=1.6.3=py310h7f8727e_1
- zeromq=4.3.4=h9c3ff4c_1
- zipp=3.8.0=py310h06a4308_0
- zlib=1.2.12=h166bdaf_1
- zstd=1.5.2=ha4553b6_0
- pip:
- contextlib2==21.6.0
- dgl==1.1.1
- dm-tree==0.1.6
- e3nn==0.5.0
- flatbuffers==1.12
- gast==0.4.0
- google-pasta==0.2.0
- googledrivedownloader==0.4
- isodate==0.6.1
- jax==0.4.13
- jaxlib==0.4.13+cuda11.cudnn86
- keras==2.9.0
- keras-preprocessing==1.1.2
- libclang==14.0.1
- ml-collections==0.1.1
- ml-dtypes==0.2.0
- mpmath==1.2.1
- networkx==2.8.3
- opt-einsum==3.3.0
- opt-einsum-fx==0.1.4
- pandas==1.4.2
- protobuf==3.19.4
- python-louvain==0.16
- rdflib==6.1.1
- sympy==1.11.1
- tensorflow==2.9.1
- tensorflow-estimator==2.9.0
- tensorflow-io-gcs-filesystem==0.26.0
- termcolor==1.1.0
- torch-cluster==1.6.0
- torch-geometric==2.1.0.post1
- torch-scatter==2.0.9
- torch-sparse==0.6.13
- wget==3.2
- wrapt==1.14.1
- yacs==0.1.8