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wengong-jin / hgraph2graph

Hierarchical Generation of Molecular Graphs using Structural Motifs

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If anyone has done fine tuning, please share environment.yaml

rokieplayer20 opened this issue · comments

commented

Looking at the issues here, I'm adjusting the environment. If you use chemprop 1.2 or 1.3, it will ask you to install descriptastorus. When I install it, I get an import error because scipy.bigrat is missing.

So when I install the latest chemprop it automatically changes to rdkit 2023. It is difficult to match the version
Please share environment.yaml

commented

Hi, where you able to solve the challenge? Here is my env.yaml for chemprop if needed
name: chemprop
channels:

  • defaults
    dependencies:
  • _libgcc_mutex=0.1=main
  • _openmp_mutex=5.1=1_gnu
  • ca-certificates=2023.05.30=h06a4308_0
  • ld_impl_linux-64=2.38=h1181459_1
  • libffi=3.4.4=h6a678d5_0
  • libgcc-ng=11.2.0=h1234567_1
  • libgomp=11.2.0=h1234567_1
  • libstdcxx-ng=11.2.0=h1234567_1
  • ncurses=6.4=h6a678d5_0
  • openssl=1.1.1t=h7f8727e_0
  • pip=23.0.1=py38h06a4308_0
  • python=3.8.16=h7a1cb2a_3
  • readline=8.2=h5eee18b_0
  • setuptools=67.8.0=py38h06a4308_0
  • sqlite=3.41.2=h5eee18b_0
  • tk=8.6.12=h1ccaba5_0
  • wheel=0.38.4=py38h06a4308_0
  • xz=5.4.2=h5eee18b_0
  • zlib=1.2.13=h5eee18b_0
  • pip:
    • alabaster==0.7.13
    • babel==2.12.1
    • blinker==1.6.2
    • certifi==2023.5.7
    • charset-normalizer==3.1.0
    • chemprop==1.5.2
    • click==8.1.3
    • cloudpickle==2.2.1
    • cmake==3.26.4
    • contourpy==1.0.7
    • cycler==0.11.0
    • docstring-parser==0.15
    • docutils==0.20.1
    • filelock==3.12.0
    • flask==2.3.2
    • fonttools==4.39.4
    • future==0.18.3
    • hyperopt==0.2.7
    • idna==3.4
    • imagesize==1.4.1
    • importlib-metadata==6.6.0
    • importlib-resources==5.12.0
    • itsdangerous==2.1.2
    • jinja2==3.1.2
    • joblib==1.2.0
    • kiwisolver==1.4.4
    • lazy-loader==0.2
    • lit==16.0.5.post0
    • markupsafe==2.1.3
    • matplotlib==3.7.1
    • mpmath==1.3.0
    • mypy-extensions==1.0.0
    • networkx==3.1
    • numpy==1.24.3
    • nvidia-cublas-cu11==11.10.3.66
    • nvidia-cuda-cupti-cu11==11.7.101
    • nvidia-cuda-nvrtc-cu11==11.7.99
    • nvidia-cuda-runtime-cu11==11.7.99
    • nvidia-cudnn-cu11==8.5.0.96
    • nvidia-cufft-cu11==10.9.0.58
    • nvidia-curand-cu11==10.2.10.91
    • nvidia-cusolver-cu11==11.4.0.1
    • nvidia-cusparse-cu11==11.7.4.91
    • nvidia-nccl-cu11==2.14.3
    • nvidia-nvtx-cu11==11.7.91
    • packaging==23.1
    • pandas==2.0.2
    • pandas-flavor==0.5.0
    • pillow==9.5.0
    • protobuf==3.20.3
    • py4j==0.10.9.7
    • pygments==2.15.1
    • pyparsing==3.0.9
    • python-dateutil==2.8.2
    • pytz==2023.3
    • rdkit==2023.3.1
    • requests==2.31.0
    • scikit-learn==1.2.2
    • scipy==1.10.1
    • seaborn==0.12.2
    • six==1.16.0
    • snowballstemmer==2.2.0
    • sphinx==7.0.1
    • sphinxcontrib-applehelp==1.0.4
    • sphinxcontrib-devhelp==1.0.2
    • sphinxcontrib-htmlhelp==2.0.1
    • sphinxcontrib-jsmath==1.0.1
    • sphinxcontrib-qthelp==1.0.3
    • sphinxcontrib-serializinghtml==1.1.5
    • sympy==1.12
    • tensorboardx==2.6
    • threadpoolctl==3.1.0
    • torch==2.0.1
    • tqdm==4.65.0
    • triton==2.0.0
    • typed-argument-parser==1.8.0
    • typing-extensions==4.6.3
    • typing-inspect==0.9.0
    • tzdata==2023.3
    • urllib3==2.0.3
    • werkzeug==2.3.6
    • xarray==2023.1.0
    • zipp==3.15.0
      prefix: /home/aorubuloye/.conda/envs/chemprop