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@@ -16,11 +16,13 @@ Additional requirements for active learning experiments: | |
## Molecule experiments | ||
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Additional requirements: | ||
- `pandas rdkit torch_geometric h5py` | ||
- `pandas rdkit torch_geometric h5py ray` | ||
- a few biochemistry programs, see `mols/Programs/README` | ||
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For `rdkit` in particular we found it to be easier to install through (mini)conda. [`torch_geometric`](https://github.com/rusty1s/pytorch_geometric) has non-trivial installation instructions. | ||
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If you have CUDA 10.1 configured, you can run `pip install -r requirements.txt`. You can also change `requirements.txt` to match your CUDA version. (Replace cu101 to cuXXX, where XXX is your CUDA version). | ||
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We compress the 300k molecule dataset for size. To uncompress it, run `cd mols/data/; gunzip docked_mols.h5.gz`. | ||
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We omit docking routines since they are part of a separate contribution still to be submitted. These are available on demand, please do reach out to [email protected] or [email protected]. |
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mkl-fft==1.3.0 | ||
mkl-random==1.2.2 | ||
mkl-service==2.4.0 | ||
numpy | ||
pandas==1.3.3 | ||
ray==1.1.0 | ||
rdkit-pypi | ||
torch==1.7.0+cu101 -f https://download.pytorch.org/whl/torch_stable.html | ||
torch-geometric==1.6.3 | ||
torch-scatter==2.0.5 -f https://pytorch-geometric.com/whl/torch-1.7.0+cu101.html | ||
torch-sparse==0.6.8 -f https://pytorch-geometric.com/whl/torch-1.7.0+cu101.html | ||
tqdm==4.36.1 |