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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,369 @@ | ||
| name: cfold | ||
| channels: | ||
| - conda-forge | ||
| - defaults | ||
| dependencies: | ||
| - _libgcc_mutex=0.1=conda_forge | ||
| - _openmp_mutex=4.5=2_gnu | ||
| - ambertools=23.3=py312h1577c9a_6 | ||
| - annotated-types=0.6.0=pyhd8ed1ab_0 | ||
| - anyio=4.1.0=pyhd8ed1ab_0 | ||
| - argon2-cffi=23.1.0=pyhd8ed1ab_0 | ||
| - argon2-cffi-bindings=21.2.0=py312h98912ed_4 | ||
| - arpack=3.8.0=nompi_h0baa96a_101 | ||
| - arrow=1.3.0=pyhd8ed1ab_0 | ||
| - asttokens=2.4.1=pyhd8ed1ab_0 | ||
| - astunparse=1.6.3=pyhd8ed1ab_0 | ||
| - async-lru=2.0.4=pyhd8ed1ab_0 | ||
| - attrs=23.1.0=pyh71513ae_1 | ||
| - babel=2.14.0=pyhd8ed1ab_0 | ||
| - beautifulsoup4=4.12.2=pyha770c72_0 | ||
| - blas=1.0=mkl | ||
| - bleach=6.1.0=pyhd8ed1ab_0 | ||
| - blosc=1.21.5=h0f2a231_0 | ||
| - brotli=1.1.0=hd590300_1 | ||
| - brotli-bin=1.1.0=hd590300_1 | ||
| - brotli-python=1.1.0=py312h30efb56_1 | ||
| - bson=0.5.9=py_0 | ||
| - bzip2=1.0.8=h7b6447c_0 | ||
| - c-ares=1.23.0=hd590300_0 | ||
| - c-blosc2=2.11.3=hb4ffafa_0 | ||
| - ca-certificates=2023.11.17=hbcca054_0 | ||
| - cached-property=1.5.2=hd8ed1ab_1 | ||
| - cached_property=1.5.2=pyha770c72_1 | ||
| - cachetools=5.3.2=pyhd8ed1ab_0 | ||
| - cairo=1.18.0=h3faef2a_0 | ||
| - certifi=2023.11.17=py312h06a4308_0 | ||
| - cffi=1.16.0=py312hf06ca03_0 | ||
| - charset-normalizer=3.3.2=pyhd8ed1ab_0 | ||
| - chex=0.1.85=pyhd8ed1ab_0 | ||
| - colorama=0.4.6=pyhd8ed1ab_0 | ||
| - comm=0.1.4=pyhd8ed1ab_0 | ||
| - contourpy=1.2.0=py312h8572e83_0 | ||
| - cuda-version=11.8=h70ddcb2_2 | ||
| - cudatoolkit=11.8.0=h6a678d5_0 | ||
| - cudnn=8.9.2.26=cuda11_0 | ||
| - cycler=0.12.1=pyhd8ed1ab_0 | ||
| - debugpy=1.8.0=py312h30efb56_1 | ||
| - decorator=5.1.1=pyhd8ed1ab_0 | ||
| - defusedxml=0.7.1=pyhd8ed1ab_0 | ||
| - dm-tree=0.1.7=py312h6a678d5_1 | ||
| - entrypoints=0.4=pyhd8ed1ab_0 | ||
| - exceptiongroup=1.2.0=pyhd8ed1ab_0 | ||
| - executing=2.0.1=pyhd8ed1ab_0 | ||
| - expat=2.5.0=h6a678d5_0 | ||
| - fftw=3.3.10=nompi_hc118613_108 | ||
| - 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=h77eed37_1 | ||
| - fontconfig=2.14.2=h14ed4e7_0 | ||
| - fonts-conda-ecosystem=1=0 | ||
| - fonts-conda-forge=1=0 | ||
| - fonttools=4.46.0=py312h98912ed_0 | ||
| - fqdn=1.5.1=pyhd8ed1ab_0 | ||
| - freetype=2.12.1=h267a509_2 | ||
| - freetype-py=2.3.0=pyhd8ed1ab_0 | ||
| - gettext=0.21.1=h27087fc_0 | ||
| - greenlet=3.0.2=py312h30efb56_0 | ||
| - hdf4=4.2.15=h2a13503_7 | ||
| - hdf5=1.14.3=nompi_h4f84152_100 | ||
| - icu=73.2=h59595ed_0 | ||
| - idna=3.6=pyhd8ed1ab_0 | ||
| - importlib-metadata=6.0.0=py312h06a4308_0 | ||
| - importlib_metadata=6.0.0=hd3eb1b0_0 | ||
| - importlib_resources=6.1.1=pyhd8ed1ab_0 | ||
| - intel-openmp=2023.1.0=hdb19cb5_46306 | ||
| - ipykernel=6.26.0=pyhf8b6a83_0 | ||
| - ipython=8.18.1=pyh707e725_3 | ||
| - ipywidgets=8.1.1=pyhd8ed1ab_0 | ||
| - isoduration=20.11.0=pyhd8ed1ab_0 | ||
| - jedi=0.19.1=pyhd8ed1ab_0 | ||
| - jinja2=3.1.2=pyhd8ed1ab_1 | ||
| - joblib=1.3.2=pyhd8ed1ab_0 | ||
| - json5=0.9.14=pyhd8ed1ab_0 | ||
| - jsonpointer=2.4=py312h7900ff3_3 | ||
| - jsonschema=4.20.0=pyhd8ed1ab_0 | ||
| - jsonschema-specifications=2023.11.2=pyhd8ed1ab_0 | ||
| - jsonschema-with-format-nongpl=4.20.0=pyhd8ed1ab_0 | ||
| - jupyter-lsp=2.2.1=pyhd8ed1ab_0 | ||
| - jupyter_client=8.6.0=pyhd8ed1ab_0 | ||
| - jupyter_core=5.5.0=py312h7900ff3_0 | ||
| - jupyter_events=0.9.0=pyhd8ed1ab_0 | ||
| - jupyter_server=2.12.1=pyhd8ed1ab_0 | ||
| - jupyter_server_terminals=0.5.0=pyhd8ed1ab_0 | ||
| - jupyterlab=4.0.9=pyhd8ed1ab_0 | ||
| - jupyterlab_pygments=0.3.0=pyhd8ed1ab_0 | ||
| - jupyterlab_server=2.25.2=pyhd8ed1ab_0 | ||
| - jupyterlab_widgets=3.0.9=pyhd8ed1ab_0 | ||
| - keyutils=1.6.1=h166bdaf_0 | ||
| - kiwisolver=1.4.5=py312h8572e83_1 | ||
| - krb5=1.21.2=h659d440_0 | ||
| - lcms2=2.16=hb7c19ff_0 | ||
| - ld_impl_linux-64=2.38=h1181459_1 | ||
| - lerc=4.0.0=h27087fc_0 | ||
| - libabseil=20230802.1=cxx17_h59595ed_0 | ||
| - libaec=1.1.2=h59595ed_1 | ||
| - libblas=3.9.0=1_h86c2bf4_netlib | ||
| - libboost=1.82.0=h6fcfa73_6 | ||
| - libboost-python=1.82.0=py312hfb10629_6 | ||
| - libbrotlicommon=1.1.0=hd590300_1 | ||
| - libbrotlidec=1.1.0=hd590300_1 | ||
| - libbrotlienc=1.1.0=hd590300_1 | ||
| - libcurl=8.5.0=hca28451_0 | ||
| - libdeflate=1.19=hd590300_0 | ||
| - libedit=3.1.20191231=he28a2e2_2 | ||
| - libev=4.33=hd590300_2 | ||
| - libexpat=2.5.0=hcb278e6_1 | ||
| - libffi=3.4.4=h6a678d5_0 | ||
| - libgcc-ng=13.2.0=h807b86a_3 | ||
| - libgfortran-ng=13.2.0=h69a702a_3 | ||
| - libgfortran5=13.2.0=ha4646dd_3 | ||
| - libglib=2.78.3=h783c2da_0 | ||
| - libgomp=13.2.0=h807b86a_3 | ||
| - libgrpc=1.58.2=he06187c_0 | ||
| - libiconv=1.17=h166bdaf_0 | ||
| - libjpeg-turbo=3.0.0=hd590300_1 | ||
| - liblapack=3.9.0=5_h92ddd45_netlib | ||
| - libnetcdf=4.9.2=nompi_h80fb2b6_112 | ||
| - libnghttp2=1.58.0=h47da74e_1 | ||
| - libnsl=2.0.1=hd590300_0 | ||
| - libpng=1.6.39=h753d276_0 | ||
| - libprotobuf=4.24.3=hf27288f_1 | ||
| - libre2-11=2023.06.02=h7a70373_0 | ||
| - libsodium=1.0.18=h36c2ea0_1 | ||
| - libsqlite=3.44.2=h2797004_0 | ||
| - libssh2=1.11.0=h0841786_0 | ||
| - libstdcxx-ng=13.2.0=h7e041cc_3 | ||
| - libtiff=4.6.0=ha9c0a0a_2 | ||
| - libuuid=2.38.1=h0b41bf4_0 | ||
| - libwebp-base=1.3.2=hd590300_0 | ||
| - libxcb=1.15=h0b41bf4_0 | ||
| - libxml2=2.11.6=h232c23b_0 | ||
| - libxslt=1.1.37=h0054252_1 | ||
| - libzip=1.10.1=h2629f0a_3 | ||
| - libzlib=1.2.13=hd590300_5 | ||
| - lxml=4.9.3=py312he528aba_3 | ||
| - lz4-c=1.9.4=hcb278e6_0 | ||
| - lzo=2.10=h516909a_1000 | ||
| - markupsafe=2.1.3=py312h98912ed_1 | ||
| - matplotlib-base=3.8.2=py312he5832f3_0 | ||
| - matplotlib-inline=0.1.6=pyhd8ed1ab_0 | ||
| - mda-xdrlib=0.2.0=pyhd8ed1ab_0 | ||
| - mdtraj=1.9.9=py312hadb1fa1_1 | ||
| - mistune=3.0.2=pyhd8ed1ab_0 | ||
| - mkl=2023.1.0=h213fc3f_46344 | ||
| - mkl-service=2.4.0=py312h5eee18b_1 | ||
| - mkl_fft=1.3.8=py312h5eee18b_0 | ||
| - mkl_random=1.2.4=py312hdb19cb5_0 | ||
| - ml_dtypes=0.3.1=py312hfb8ada1_2 | ||
| - munkres=1.1.4=pyh9f0ad1d_0 | ||
| - nbclient=0.8.0=pyhd8ed1ab_0 | ||
| - nbconvert-core=7.12.0=pyhd8ed1ab_0 | ||
| - nbformat=5.9.2=pyhd8ed1ab_0 | ||
| - nccl=2.19.4.1=h6103f9b_0 | ||
| - ncurses=6.4=h6a678d5_0 | ||
| - nest-asyncio=1.5.8=pyhd8ed1ab_0 | ||
| - netcdf-fortran=4.6.1=nompi_hacb5139_103 | ||
| - networkx=3.2.1=pyhd8ed1ab_0 | ||
| - notebook=7.0.6=pyhd8ed1ab_0 | ||
| - notebook-shim=0.2.3=pyhd8ed1ab_0 | ||
| - numexpr=2.8.7=py312hf827012_0 | ||
| - numpy=1.26.2=py312hc5e2394_0 | ||
| - numpy-base=1.26.2=py312h0da6c21_0 | ||
| - ocl-icd=2.3.1=h7f98852_0 | ||
| - ocl-icd-system=1.0.0=1 | ||
| - openff-amber-ff-ports=0.0.4=pyhca7485f_0 | ||
| - openff-forcefields=2023.11.0=pyhca7485f_0 | ||
| - openff-interchange=0.3.18=pyhd8ed1ab_0 | ||
| - openff-interchange-base=0.3.18=pyhd8ed1ab_0 | ||
| - openff-models=0.1.1=pyhca7485f_0 | ||
| - openff-toolkit=0.14.5=pyhd8ed1ab_1 | ||
| - openff-toolkit-base=0.14.5=pyhd8ed1ab_1 | ||
| - openff-units=0.2.1=pyh1a96a4e_0 | ||
| - openff-utilities=0.1.12=pyhd8ed1ab_0 | ||
| - openjpeg=2.5.0=h488ebb8_3 | ||
| - openmm=8.1.0=py312hc343695_1 | ||
| - openmmforcefields=0.11.2=pyhd8ed1ab_1 | ||
| - openssl=3.2.0=hd590300_1 | ||
| - opt-einsum=3.3.0=hd8ed1ab_2 | ||
| - opt_einsum=3.3.0=pyhd3eb1b0_1 | ||
| - overrides=7.4.0=pyhd8ed1ab_0 | ||
| - packaging=23.2=pyhd8ed1ab_0 | ||
| - packmol=20.010=h86c2bf4_0 | ||
| - pandas=2.1.4=py312hfb8ada1_0 | ||
| - pandocfilters=1.5.0=pyhd8ed1ab_0 | ||
| - panedr=0.7.2=pyhd8ed1ab_0 | ||
| - parmed=4.2.2=py312h30efb56_1 | ||
| - parso=0.8.3=pyhd8ed1ab_0 | ||
| - pbr=6.0.0=pyhd8ed1ab_0 | ||
| - pcre2=10.42=hcad00b1_0 | ||
| - pdbfixer=1.9=pyh1a96a4e_0 | ||
| - perl=5.32.1=4_hd590300_perl5 | ||
| - pexpect=4.8.0=pyh1a96a4e_2 | ||
| - pickleshare=0.7.5=py_1003 | ||
| - pillow=10.1.0=py312hf3581a9_0 | ||
| - pint=0.21=pyhd8ed1ab_0 | ||
| - pip=23.3.1=py312h06a4308_0 | ||
| - pixman=0.42.2=h59595ed_0 | ||
| - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1 | ||
| - platformdirs=4.1.0=pyhd8ed1ab_0 | ||
| - prometheus_client=0.19.0=pyhd8ed1ab_0 | ||
| - prompt-toolkit=3.0.42=pyha770c72_0 | ||
| - psutil=5.9.7=py312h98912ed_0 | ||
| - pthread-stubs=0.4=h36c2ea0_1001 | ||
| - ptyprocess=0.7.0=pyhd3deb0d_0 | ||
| - pure_eval=0.2.2=pyhd8ed1ab_0 | ||
| - py-cpuinfo=9.0.0=pyhd8ed1ab_0 | ||
| - pycairo=1.25.1=py312he48a392_0 | ||
| - pycparser=2.21=pyhd8ed1ab_0 | ||
| - pydantic=2.5.2=pyhd8ed1ab_0 | ||
| - pydantic-core=2.14.5=py312h4b3b743_0 | ||
| - pyedr=0.7.2=pyhd8ed1ab_0 | ||
| - pygments=2.17.2=pyhd8ed1ab_0 | ||
| - pyparsing=3.1.1=pyhd8ed1ab_0 | ||
| - pysocks=1.7.1=pyha2e5f31_6 | ||
| - pytables=3.9.2=py312h5531bb7_1 | ||
| - python=3.12.0=hab00c5b_0_cpython | ||
| - python-constraint=1.4.0=py_0 | ||
| - python-dateutil=2.8.2=pyhd8ed1ab_0 | ||
| - python-fastjsonschema=2.19.0=pyhd8ed1ab_0 | ||
| - python-json-logger=2.0.7=pyhd8ed1ab_0 | ||
| - python-tzdata=2023.3=pyhd8ed1ab_0 | ||
| - python_abi=3.12=4_cp312 | ||
| - pytz=2023.3.post1=pyhd8ed1ab_0 | ||
| - pyyaml=6.0.1=py312h98912ed_1 | ||
| - pyzmq=25.1.2=py312h886d080_0 | ||
| - rdkit=2023.09.3=py312hd93e07f_1 | ||
| - re2=2023.06.02=h2873b5e_0 | ||
| - readline=8.2=h5eee18b_0 | ||
| - referencing=0.32.0=pyhd8ed1ab_0 | ||
| - reportlab=4.0.7=py312h98912ed_0 | ||
| - requests=2.31.0=pyhd8ed1ab_0 | ||
| - rfc3339-validator=0.1.4=pyhd8ed1ab_0 | ||
| - rfc3986-validator=0.1.1=pyh9f0ad1d_0 | ||
| - rlpycairo=0.2.0=pyhd8ed1ab_0 | ||
| - rpds-py=0.13.2=py312h4b3b743_0 | ||
| - scipy=1.11.4=py312hc5e2394_0 | ||
| - send2trash=1.8.2=pyh41d4057_0 | ||
| - setuptools=68.0.0=py312h06a4308_0 | ||
| - six=1.16.0=pyh6c4a22f_0 | ||
| - smirnoff99frosst=1.1.0=pyh44b312d_0 | ||
| - snappy=1.1.10=h9fff704_0 | ||
| - sniffio=1.3.0=pyhd8ed1ab_0 | ||
| - soupsieve=2.5=pyhd8ed1ab_1 | ||
| - sqlalchemy=2.0.23=py312h98912ed_0 | ||
| - sqlite=3.41.2=h5eee18b_0 | ||
| - stack_data=0.6.2=pyhd8ed1ab_0 | ||
| - tbb=2021.8.0=hdb19cb5_0 | ||
| - terminado=0.18.0=pyh0d859eb_0 | ||
| - tinycss2=1.2.1=pyhd8ed1ab_0 | ||
| - tinydb=4.8.0=pyhd8ed1ab_0 | ||
| - tk=8.6.13=noxft_h4845f30_101 | ||
| - tomli=2.0.1=pyhd8ed1ab_0 | ||
| - toolz=0.12.0=py312h06a4308_0 | ||
| - tornado=6.3.3=py312h98912ed_1 | ||
| - tqdm=4.66.1=pyhd8ed1ab_0 | ||
| - traitlets=5.14.0=pyhd8ed1ab_0 | ||
| - types-python-dateutil=2.8.19.14=pyhd8ed1ab_0 | ||
| - typing-extensions=4.9.0=hd8ed1ab_0 | ||
| - typing_extensions=4.9.0=pyha770c72_0 | ||
| - typing_utils=0.1.0=pyhd8ed1ab_0 | ||
| - tzdata=2023c=h04d1e81_0 | ||
| - uri-template=1.3.0=pyhd8ed1ab_0 | ||
| - urllib3=2.1.0=pyhd8ed1ab_0 | ||
| - validators=0.18.2=pyhd3eb1b0_0 | ||
| - wcwidth=0.2.12=pyhd8ed1ab_0 | ||
| - webcolors=1.13=pyhd8ed1ab_0 | ||
| - webencodings=0.5.1=pyhd8ed1ab_2 | ||
| - websocket-client=1.7.0=pyhd8ed1ab_0 | ||
| - wheel=0.41.2=py312h06a4308_0 | ||
| - widgetsnbextension=4.0.9=pyhd8ed1ab_0 | ||
| - xmltodict=0.13.0=pyhd8ed1ab_0 | ||
| - xorg-kbproto=1.0.7=h7f98852_1002 | ||
| - xorg-libice=1.1.1=hd590300_0 | ||
| - xorg-libsm=1.2.4=h7391055_0 | ||
| - xorg-libx11=1.8.7=h8ee46fc_0 | ||
| - xorg-libxau=1.0.11=hd590300_0 | ||
| - xorg-libxdmcp=1.1.3=h7f98852_0 | ||
| - xorg-libxext=1.3.4=h0b41bf4_2 | ||
| - xorg-libxrender=0.9.11=hd590300_0 | ||
| - xorg-libxt=1.3.0=hd590300_1 | ||
| - xorg-renderproto=0.11.1=h7f98852_1002 | ||
| - xorg-xextproto=7.3.0=h0b41bf4_1003 | ||
| - xorg-xproto=7.0.31=h7f98852_1007 | ||
| - xz=5.4.5=h5eee18b_0 | ||
| - yaml=0.2.5=h7f98852_2 | ||
| - zeromq=4.3.5=h59595ed_0 | ||
| - zipp=3.11.0=py312h06a4308_0 | ||
| - zlib=1.2.13=hd590300_5 | ||
| - zlib-ng=2.0.7=h0b41bf4_0 | ||
| - zstd=1.5.5=hfc55251_0 | ||
| - pip: | ||
| - absl-py==2.0.0 | ||
| - amberutils==21.0 | ||
| - biopython==1.81 | ||
| - click==8.1.7 | ||
| - contextlib2==21.6.0 | ||
| - dm-haiku==0.0.11 | ||
| - edgembar==0.2 | ||
| - etils==1.6.0 | ||
| - flatbuffers==23.5.26 | ||
| - flax==0.7.5 | ||
| - fsspec==2023.12.1 | ||
| - gast==0.5.4 | ||
| - google-auth==2.25.2 | ||
| - google-auth-oauthlib==1.1.0 | ||
| - google-pasta==0.2.0 | ||
| - grpcio==1.60.0 | ||
| - h5py==3.10.0 | ||
| - immutabledict==2.0.0 | ||
| - jax==0.4.23 | ||
| - jmp==0.0.4 | ||
| - keras-nightly==3.0.1.dev2023121103 | ||
| - libclang==16.0.6 | ||
| - markdown==3.5.1 | ||
| - markdown-it-py==3.0.0 | ||
| - mdurl==0.1.2 | ||
| - ml-collections==0.1.1 | ||
| - mmpbsa-py==16.0 | ||
| - msgpack==1.0.7 | ||
| - namex==0.0.7 | ||
| - nvidia-cublas-cu12==12.3.4.1 | ||
| - nvidia-cuda-cupti-cu12==12.3.101 | ||
| - nvidia-cuda-nvcc-cu12==12.3.103 | ||
| - nvidia-cuda-nvrtc-cu12==12.3.103 | ||
| - nvidia-cuda-runtime-cu12==12.3.101 | ||
| - nvidia-cudnn-cu12==8.9.7.29 | ||
| - nvidia-cufft-cu12==11.0.12.1 | ||
| - nvidia-cusolver-cu12==11.5.4.101 | ||
| - nvidia-cusparse-cu12==12.2.0.103 | ||
| - nvidia-nccl-cu12==2.19.3 | ||
| - nvidia-nvjitlink-cu12==12.3.101 | ||
| - oauthlib==3.2.2 | ||
| - optax==0.1.4 | ||
| - orbax-checkpoint==0.4.7 | ||
| - packmol-memgen==2023.2.24 | ||
| - pdb4amber==22.0 | ||
| - protobuf==4.25.1 | ||
| - pyasn1==0.5.1 | ||
| - pyasn1-modules==0.3.0 | ||
| - pymsmt==22.0 | ||
| - pytraj==2.0.6 | ||
| - requests-oauthlib==1.3.1 | ||
| - rich==13.7.0 | ||
| - rsa==4.9 | ||
| - sander==22.0 | ||
| - svgwrite==1.4.3 | ||
| - tabulate==0.9.0 | ||
| - tb-nightly==2.16.0a20231211 | ||
| - tensorboard-data-server==0.7.2 | ||
| - tensorstore==0.1.51 | ||
| - termcolor==2.4.0 | ||
| - tf-estimator-nightly==2.14.0.dev2023080308 | ||
| - tf-keras-nightly==2.16.0.dev2023121110 | ||
| - tf-nightly==2.16.0.dev20231211 | ||
| - tree==0.2.4 | ||
| - werkzeug==3.0.1 | ||
| - wrapt==1.14.1 | ||
| prefix: ./envs/ |
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| ## MSA feats | ||
| conda activate cfold | ||
| MSA_DIR=./data/test/ | ||
| OUTDIR=./data/test/ | ||
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