mirror of
https://github.com/Saoge123/PocketFlow.git
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Merge pull request #6 from yipy0005/master
Replace requirements.txt with environment.yml for easy conda environment creation
This commit is contained in:
Saoge123
GitHub
11
README.md
11
README.md
@@ -2,13 +2,10 @@
|
||||
|
||||
Deep learning-based molecular generation has extensive applications in many fields, particularly drug discovery. However, majority of current deep generative models (DGMs) are ligand-based and do not consider chemical knowledge in molecular generation process, often resulting in a relatively low success rate. We herein propose a structure-based molecular generative framework with chemical knowledge explicitly considered (named PocketFlow), which generates novel ligand molecules inside protein binding pockets. In various computational evaluations, PocketFlow showed a state-of-the-art performance with generated molecules being 100% chemically valid and highly drug-like. Ablation experiments prove a critical role of chemical knowledge in ensuring the validity and drug-likeness of the generated molecules. We applied PocketFlow to two new target proteins that are related to epigenetic regulation, HAT1 and YTHDC1, and successfully obtained wet-lab validated bioactive compounds. The binding modes of the active compounds with target proteins are close to those predicted by molecular docking, and further confirmed by the X-ray crystal structure. All the results suggest that PocketFlow is a useful deep generative model, capable of generating innovative bioactive molecules from scratch given a protein binding pocket.
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Requirements:
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* Python 3.8
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* pytorch 1.12
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* Pytorch_Geometric 2.1.0
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* RDKit
|
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* Openbabel
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* PyMol
|
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### Create the Conda environment
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~~~
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conda env create -f environment.yml
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~~~
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### Molecular generation
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The molecule can be generated by running the following command, where the pocket pdb file and the model parameter file are required, and the rest of the parameters are optional
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32
create_pocket_pdb.py
Normal file
32
create_pocket_pdb.py
Normal file
@@ -0,0 +1,32 @@
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import argparse
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from pathlib import Path
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from pocket_flow import Ligand, Protein, SplitPocket
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def arguments():
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parser = argparse.ArgumentParser()
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parser.add_argument("--protein", type=str, required=True, help="PDB")
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parser.add_argument("--ligand", type=str, required=True, help="SDF")
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args = parser.parse_args()
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return args
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|
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def main():
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args = arguments()
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output_path = f"{Path(args.protein).parent}/pocket.pdb"
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pro = Protein(args.protein)
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lig = Ligand(args.ligand)
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dist_cutoff = 10
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pocket_block, _ = SplitPocket._split_pocket_with_surface_atoms(
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pro, lig, dist_cutoff
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)
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open(output_path, "w").write(pocket_block)
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if __name__ == "__main__":
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main()
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337
environment.yml
Normal file
337
environment.yml
Normal file
@@ -0,0 +1,337 @@
|
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name: pocketflow
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channels:
|
||||
- pyg
|
||||
- schrodinger
|
||||
- pytorch
|
||||
- nvidia
|
||||
- defaults
|
||||
- conda-forge
|
||||
dependencies:
|
||||
- _libgcc_mutex=0.1
|
||||
- _openmp_mutex=4.5
|
||||
- alabaster=0.7.12
|
||||
- apbs=1.5
|
||||
- asttokens=2.0.5
|
||||
- babel=2.11.0
|
||||
- backcall=0.2.0
|
||||
- backports=1.0
|
||||
- backports.functools_lru_cache=2.0.0
|
||||
- blas=1.0
|
||||
- boost=1.70.0
|
||||
- boost-cpp=1.70.0
|
||||
- brotli-python=1.0.9
|
||||
- brotlipy=0.7.0
|
||||
- bzip2=1.0.8
|
||||
- c-ares=1.19.0
|
||||
- ca-certificates=2024.2.2
|
||||
- cairo=1.16.0
|
||||
- certifi=2024.2.2
|
||||
- cffi=1.15.1
|
||||
- charset-normalizer=2.0.4
|
||||
- colorama=0.4.6
|
||||
- comm=0.1.2
|
||||
- cryptography=39.0.1
|
||||
- cuda-cudart=11.7.99
|
||||
- cuda-cupti=11.7.101
|
||||
- cuda-libraries=11.7.1
|
||||
- cuda-nvrtc=11.7.99
|
||||
- cuda-nvtx=11.7.91
|
||||
- cuda-runtime=11.7.1
|
||||
- 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
|
||||
- ffmpeg=4.3
|
||||
- fontconfig=2.14.1
|
||||
- freemol=1.158
|
||||
- freetype=2.12.1
|
||||
- giflib=5.2.1
|
||||
- glew=2.0.0
|
||||
- glib=2.69.1
|
||||
- gmp=6.2.1
|
||||
- gnutls=3.6.13
|
||||
- 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
|
||||
- lame=3.100
|
||||
- lcms2=2.12
|
||||
- ld_impl_linux-64=2.38
|
||||
- lerc=3.0
|
||||
- libblas=3.9.0
|
||||
- libcblas=3.9.0
|
||||
- libclang=10.0.1
|
||||
- libcublas=11.10.3.66
|
||||
- libcufft=10.7.2.124
|
||||
- libcufile=1.9.1.3
|
||||
- libcurand=10.3.5.147
|
||||
- libcurl=7.88.1
|
||||
- libcusolver=11.4.0.1
|
||||
- libcusparse=11.7.4.91
|
||||
- libdeflate=1.17
|
||||
- libedit=3.1.20221030
|
||||
- libev=4.33
|
||||
- libevent=2.1.12
|
||||
- libffi=3.4.4
|
||||
- libgcc-ng=13.2.0
|
||||
- libgfortran-ng=7.5.0
|
||||
- libgfortran4=7.5.0
|
||||
- libglu=9.0.0
|
||||
- libgomp=13.2.0
|
||||
- libholoplaycore=0.1.0_rc4
|
||||
- libiconv=1.17
|
||||
- liblapack=3.9.0
|
||||
- libllvm10=10.0.1
|
||||
- libnetcdf=4.8.1
|
||||
- libnghttp2=1.52.0
|
||||
- libnpp=11.7.4.75
|
||||
- libnvjpeg=11.8.0.2
|
||||
- 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
|
||||
- nettle=3.6
|
||||
- nspr=4.35
|
||||
- nss=3.89.1
|
||||
- openbabel=3.1.1
|
||||
- openh264=2.1.1
|
||||
- openssl=3.3.0
|
||||
- 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
|
||||
- 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
|
||||
- pytorch=1.13.0
|
||||
- pytorch-cluster=1.6.1
|
||||
- pytorch-cuda=11.7
|
||||
- pytorch-mutex=1.0
|
||||
- pytorch-scatter=2.1.1
|
||||
- pytorch-sparse=0.6.17
|
||||
- pytorch-spline-conv=1.2.2
|
||||
- pytz=2023.3.post1
|
||||
- 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
|
||||
- torchaudio=0.13.0
|
||||
- torchvision=0.14.0
|
||||
- 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
|
||||
- xorg-kbproto=1.0.7
|
||||
- xorg-libx11=1.7.2
|
||||
- xorg-libxext=1.3.4
|
||||
- xorg-xextproto=7.3.0
|
||||
- xorg-xproto=7.0.31
|
||||
- xz=5.2.10
|
||||
- zeromq=4.3.4
|
||||
- zlib=1.2.13
|
||||
- zstd=1.5.5
|
||||
- pip
|
||||
- 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
|
||||
- https://data.pyg.org/whl/torch-1.13.0%2Bcu117/pyg_lib-0.2.0%2Bpt113cu117-cp38-cp38-linux_x86_64.whl
|
||||
- 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-geometric==2.3.1
|
||||
- torchdiffeq==0.2.3
|
||||
- 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
|
||||
270
requirements.txt
270
requirements.txt
@@ -1,270 +0,0 @@
|
||||
absl-py @ file:///opt/conda/conda-bld/absl-py_1639803114343/work
|
||||
aiohttp @ file:///tmp/build/80754af9/aiohttp_1637844158574/work
|
||||
aiosignal @ file:///tmp/build/80754af9/aiosignal_1637843061372/work
|
||||
alabaster==0.7.12
|
||||
antlr4-python3-runtime==4.9.3
|
||||
anyio @ file:///tmp/build/80754af9/anyio_1644481698350/work/dist
|
||||
apex==0.1
|
||||
argon2-cffi @ file:///opt/conda/conda-bld/argon2-cffi_1645000214183/work
|
||||
argon2-cffi-bindings @ file:///tmp/build/80754af9/argon2-cffi-bindings_1644569684262/work
|
||||
ase==3.22.1
|
||||
astroid==2.9.3
|
||||
async-timeout @ file:///tmp/build/80754af9/async-timeout_1637851218186/work
|
||||
atom3d==0.2.6
|
||||
attrs @ file:///opt/conda/conda-bld/attrs_1642510447205/work
|
||||
autocommand==2.2.2
|
||||
autopep8==1.6.0
|
||||
Babel @ file:///tmp/build/80754af9/babel_1620871417480/work
|
||||
backcall @ file:///home/ktietz/src/ci/backcall_1611930011877/work
|
||||
biopython==1.79
|
||||
bleach @ file:///opt/conda/conda-bld/bleach_1641577558959/work
|
||||
blinker==1.4
|
||||
Bottleneck==1.3.2
|
||||
brotlipy==0.7.0
|
||||
cachetools @ file:///tmp/build/80754af9/cachetools_1619597386817/work
|
||||
captum==0.2.0
|
||||
certifi==2023.5.7
|
||||
cffi @ file:///opt/conda/conda-bld/cffi_1642701102775/work
|
||||
charset-normalizer @ file:///tmp/build/80754af9/charset-normalizer_1630003229654/work
|
||||
cheroot==9.0.0
|
||||
CherryPy==18.8.0
|
||||
cilog==1.2.3
|
||||
click==8.0.3
|
||||
cloudpickle==2.1.0
|
||||
colour==0.1.5
|
||||
cryptography @ file:///tmp/build/80754af9/cryptography_1633520369403/work
|
||||
cycler @ file:///tmp/build/80754af9/cycler_1637851556182/work
|
||||
debugpy @ file:///tmp/build/80754af9/debugpy_1637091796427/work
|
||||
decorator @ file:///opt/conda/conda-bld/decorator_1643638310831/work
|
||||
defusedxml @ file:///tmp/build/80754af9/defusedxml_1615228127516/work
|
||||
dgl-cu113==0.9.0
|
||||
dglgo==0.0.2
|
||||
dgllife==0.2.9
|
||||
dill==0.3.6
|
||||
dive-into-graphs==1.0.0
|
||||
docutils==0.18.1
|
||||
easy-parallel==0.1.6
|
||||
easydict==1.9
|
||||
entrypoints==0.3
|
||||
et-xmlfile==1.1.0
|
||||
faerun==0.4.7
|
||||
fire==0.4.0
|
||||
flake8==4.0.1
|
||||
fonttools==4.25.0
|
||||
freesasa==2.1.0
|
||||
frozenlist @ file:///tmp/build/80754af9/frozenlist_1637767111923/work
|
||||
fsspec==2022.11.0
|
||||
future==0.18.2
|
||||
google-auth @ file:///tmp/build/80754af9/google-auth_1626320605116/work
|
||||
google-auth-oauthlib @ file:///tmp/build/80754af9/google-auth-oauthlib_1617120569401/work
|
||||
googledrivedownloader==0.4
|
||||
graphviz==0.19.2
|
||||
greenlet @ file:///tmp/build/80754af9/greenlet_1628887725296/work
|
||||
grpcio @ file:///tmp/build/80754af9/grpcio_1637590823556/work
|
||||
gym==0.26.2
|
||||
gym-notices==0.0.8
|
||||
h5py==3.7.0
|
||||
hydra-core==1.2.0
|
||||
hyperopt==0.2.7
|
||||
idna @ file:///tmp/build/80754af9/idna_1637925883363/work
|
||||
imagesize==1.4.1
|
||||
importlib-metadata @ file:///tmp/build/80754af9/importlib-metadata_1638542885373/work
|
||||
importlib-resources==5.8.0
|
||||
inflect==6.0.2
|
||||
ipykernel @ file:///tmp/build/80754af9/ipykernel_1633545412716/work/dist/ipykernel-6.4.1-py3-none-any.whl
|
||||
ipympl @ file:///home/conda/feedstock_root/build_artifacts/ipympl_1645174282670/work
|
||||
ipython @ file:///tmp/build/80754af9/ipython_1643818147236/work
|
||||
ipython-genutils @ file:///tmp/build/80754af9/ipython_genutils_1606773439826/work
|
||||
ipywidgets @ file:///home/conda/feedstock_root/build_artifacts/ipywidgets_1660929733321/work
|
||||
isodate==0.6.1
|
||||
isort==5.10.1
|
||||
jaraco.classes==3.2.3
|
||||
jaraco.collections==3.8.0
|
||||
jaraco.context==4.3.0
|
||||
jaraco.functools==3.6.0
|
||||
jaraco.text==3.11.1
|
||||
jedi==0.18.1
|
||||
Jinja2 @ file:///tmp/build/80754af9/jinja2_1635780242639/work
|
||||
joblib==1.1.0
|
||||
json5 @ file:///tmp/build/80754af9/json5_1624432770122/work
|
||||
jsonschema @ file:///Users/ktietz/demo/mc3/conda-bld/jsonschema_1630511932244/work
|
||||
jupyter-client @ file:///opt/conda/conda-bld/jupyter_client_1643638337975/work
|
||||
jupyter-core @ file:///tmp/build/80754af9/jupyter_core_1636524756443/work
|
||||
jupyter-lsp @ file:///home/conda/feedstock_root/build_artifacts/jupyter-lsp-meta_1639326415622/work/jupyter-lsp
|
||||
jupyter-server @ file:///opt/conda/conda-bld/jupyter_server_1644494914632/work
|
||||
jupyterlab @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_1643984239174/work
|
||||
jupyterlab-lsp @ file:///home/conda/feedstock_root/build_artifacts/jupyter-lsp-meta_1641036216377/work/jupyterlab-lsp
|
||||
jupyterlab-pygments @ file:///tmp/build/80754af9/jupyterlab_pygments_1601490720602/work
|
||||
jupyterlab-server @ file:///opt/conda/conda-bld/jupyterlab_server_1644500396812/work
|
||||
jupyterlab-widgets @ file:///tmp/build/80754af9/jupyterlab_widgets_1609884341231/work
|
||||
kiwisolver @ file:///opt/conda/conda-bld/kiwisolver_1638569886207/work
|
||||
lazy-object-proxy==1.7.1
|
||||
lightning-utilities==0.3.0
|
||||
littleutils==0.2.2
|
||||
llvmlite==0.38.0
|
||||
lmdb @ file:///tmp/build/80754af9/python-lmdb_1619708137835/work
|
||||
Markdown @ file:///tmp/build/80754af9/markdown_1614363528767/work
|
||||
MarkupSafe @ file:///tmp/build/80754af9/markupsafe_1621528148836/work
|
||||
matplotlib @ file:///tmp/build/80754af9/matplotlib-suite_1645455682260/work
|
||||
matplotlib-inline @ file:///tmp/build/80754af9/matplotlib-inline_1628242447089/work
|
||||
mccabe==0.6.1
|
||||
meeko==0.4.0
|
||||
mistune==0.8.4
|
||||
mkl-fft==1.3.1
|
||||
mkl-random @ file:///tmp/build/80754af9/mkl_random_1626186064646/work
|
||||
mkl-service==2.4.0
|
||||
more-itertools==9.1.0
|
||||
mpmath==1.2.1
|
||||
msgpack==1.0.4
|
||||
multidict @ file:///opt/conda/conda-bld/multidict_1640703752579/work
|
||||
multipledispatch==0.6.0
|
||||
multiprocess==0.70.14
|
||||
munkres==1.1.4
|
||||
mypy-extensions==0.4.3
|
||||
nbclassic @ file:///opt/conda/conda-bld/nbclassic_1644943264176/work
|
||||
nbclient @ file:///tmp/build/80754af9/nbclient_1645431659072/work
|
||||
nbconvert @ file:///opt/conda/conda-bld/nbconvert_1641309195684/work
|
||||
nbformat @ file:///tmp/build/80754af9/nbformat_1617383369282/work
|
||||
nest-asyncio @ file:///tmp/build/80754af9/nest-asyncio_1613680548246/work
|
||||
netron==5.7.0
|
||||
networkx==2.6.3
|
||||
nglview @ file:///home/conda/feedstock_root/build_artifacts/nglview_1623387107190/work
|
||||
notebook @ file:///tmp/build/80754af9/notebook_1645002536250/work
|
||||
numba==0.55.1
|
||||
numexpr @ file:///tmp/build/80754af9/numexpr_1640704208950/work
|
||||
numpy @ file:///tmp/build/80754af9/numpy_and_numpy_base_1634095647912/work
|
||||
numpydoc==1.4.0
|
||||
oauthlib @ file:///opt/conda/conda-bld/oauthlib_1644332107998/work
|
||||
ogb==1.3.3
|
||||
olefile @ file:///Users/ktietz/demo/mc3/conda-bld/olefile_1629805411829/work
|
||||
omegaconf==2.2.2
|
||||
openpyxl==3.0.10
|
||||
ortools==9.3.10497
|
||||
outdated==0.2.1
|
||||
packaging @ file:///tmp/build/80754af9/packaging_1637314298585/work
|
||||
pandas==1.4.1
|
||||
pandocfilters @ file:///opt/conda/conda-bld/pandocfilters_1643405455980/work
|
||||
parso==0.8.3
|
||||
pathos==0.3.0
|
||||
pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work
|
||||
pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work
|
||||
Pillow==8.4.0
|
||||
platformdirs==2.5.1
|
||||
pluggy==1.0.0
|
||||
Pmw==2.1.1
|
||||
portend==3.1.0
|
||||
pox==0.3.2
|
||||
ppft==1.7.6.6
|
||||
prometheus-client @ file:///opt/conda/conda-bld/prometheus_client_1643788673601/work
|
||||
prompt-toolkit @ file:///tmp/build/80754af9/prompt-toolkit_1633440160888/work
|
||||
protobuf==3.20.1
|
||||
psutil==5.9.1
|
||||
ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
|
||||
py4j==0.10.9.5
|
||||
pyasn1 @ file:///Users/ktietz/demo/mc3/conda-bld/pyasn1_1629708007385/work
|
||||
pyasn1-modules==0.2.8
|
||||
pycairo==1.19.1
|
||||
pycodestyle==2.8.0
|
||||
pycparser @ file:///tmp/build/80754af9/pycparser_1636541352034/work
|
||||
pydantic==1.9.1
|
||||
pydocstyle==6.1.1
|
||||
pyflakes==2.4.0
|
||||
Pygments @ file:///opt/conda/conda-bld/pygments_1644249106324/work
|
||||
PyJWT @ file:///tmp/build/80754af9/pyjwt_1619651636675/work
|
||||
pylint==2.12.2
|
||||
pymol==2.5.0
|
||||
pyOpenSSL @ file:///tmp/build/80754af9/pyopenssl_1635333100036/work
|
||||
pyparsing @ file:///tmp/build/80754af9/pyparsing_1635766073266/work
|
||||
PyQt5==5.12.3
|
||||
PyQt5_sip==4.19.18
|
||||
PyQtChart==5.12
|
||||
PyQtWebEngine==5.12.1
|
||||
pyrr==0.10.3
|
||||
pyrsistent @ file:///tmp/build/80754af9/pyrsistent_1636110947380/work
|
||||
pyscf==1.7.6.post1
|
||||
PySocks @ file:///tmp/build/80754af9/pysocks_1605305779399/work
|
||||
python-dateutil @ file:///tmp/build/80754af9/python-dateutil_1626374649649/work
|
||||
python-dotenv==0.21.0
|
||||
python-lsp-jsonrpc==1.0.0
|
||||
python-lsp-server==1.3.3
|
||||
pytorch-lightning==1.8.3.post1
|
||||
pytz==2021.3
|
||||
PyYAML==6.0
|
||||
pyzmq @ file:///tmp/build/80754af9/pyzmq_1638436375034/work
|
||||
rdflib==6.1.1
|
||||
rdkit-pypi==2022.3.4
|
||||
reportlab==3.5.67
|
||||
requests @ file:///opt/conda/conda-bld/requests_1641824580448/work
|
||||
requests-oauthlib==1.3.0
|
||||
rope==0.23.0
|
||||
rsa @ file:///tmp/build/80754af9/rsa_1614366226499/work
|
||||
ruamel.yaml==0.17.21
|
||||
ruamel.yaml.clib==0.2.6
|
||||
scikit-learn==1.0.2
|
||||
scipy==1.8.0
|
||||
seaborn==0.12.2
|
||||
Send2Trash @ file:///tmp/build/80754af9/send2trash_1632406701022/work
|
||||
shap==0.41.0
|
||||
six @ file:///tmp/build/80754af9/six_1644875935023/work
|
||||
slicer==0.0.7
|
||||
sniffio @ file:///tmp/build/80754af9/sniffio_1614030475067/work
|
||||
snowballstemmer==2.2.0
|
||||
Sphinx==5.0.2
|
||||
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
|
||||
SQLAlchemy @ file:///tmp/build/80754af9/sqlalchemy_1638290671404/work
|
||||
style==1.1.0
|
||||
sympy==1.10
|
||||
tables==3.7.0
|
||||
tabulate==0.8.10
|
||||
tempora==5.2.1
|
||||
tensorboard @ file:///home/conda/feedstock_root/build_artifacts/tensorboard_1644015949874/work/tensorboard-2.8.0-py3-none-any.whl
|
||||
tensorboard-data-server @ file:///tmp/build/80754af9/tensorboard-data-server_1633035064162/work/tensorboard_data_server-0.6.0-py3-none-manylinux2010_x86_64.whl
|
||||
tensorboard-plugin-wit==1.6.0
|
||||
tensorboardX==2.5.1
|
||||
termcolor==2.1.1
|
||||
terminado @ file:///tmp/build/80754af9/terminado_1644322581811/work
|
||||
testpath @ file:///tmp/build/80754af9/testpath_1624638946665/work
|
||||
threadpoolctl==3.1.0
|
||||
tmap==1.0.6
|
||||
toml==0.10.2
|
||||
torch==1.12.1
|
||||
torch-cluster==1.6.0
|
||||
torch-geometric==2.1.0.post1
|
||||
torch-scatter==2.0.9
|
||||
torch-sparse==0.6.15
|
||||
torch-spline-conv==1.2.1
|
||||
torch-tb-profiler==0.4.0
|
||||
torchaudio==0.12.1
|
||||
torchdiffeq==0.2.3
|
||||
torchmetrics==0.11.0
|
||||
torchvision==0.13.1
|
||||
torchviz==0.0.2
|
||||
tornado @ file:///tmp/build/80754af9/tornado_1606942300299/work
|
||||
tqdm==4.63.0
|
||||
traitlets @ file:///tmp/build/80754af9/traitlets_1636710298902/work
|
||||
typed-argument-parser==1.7.2
|
||||
typer==0.6.1
|
||||
typing-inspect==0.7.1
|
||||
typing_extensions==4.4.0
|
||||
ujson==5.1.0
|
||||
update==0.0.1
|
||||
urllib3 @ file:///opt/conda/conda-bld/urllib3_1643638302206/work
|
||||
wcwidth @ file:///Users/ktietz/demo/mc3/conda-bld/wcwidth_1629357192024/work
|
||||
webencodings==0.5.1
|
||||
websocket-client @ file:///tmp/build/80754af9/websocket-client_1614804261064/work
|
||||
Werkzeug @ file:///opt/conda/conda-bld/werkzeug_1645628268370/work
|
||||
widgetsnbextension @ file:///home/conda/feedstock_root/build_artifacts/widgetsnbextension_1655939017940/work
|
||||
wrapt==1.13.3
|
||||
xeus-python==0.13.6
|
||||
xeus-python-shell @ file:///home/conda/feedstock_root/build_artifacts/xeus-python-shell_1642004964212/work
|
||||
XlsxWriter==3.0.3
|
||||
yacs==0.1.8
|
||||
yapf==0.32.0
|
||||
yarl @ file:///tmp/build/80754af9/yarl_1606939922162/work
|
||||
zc.lockfile==3.0.post1
|
||||
zipp @ file:///opt/conda/conda-bld/zipp_1641824620731/work
|
||||
Reference in New Issue
Block a user