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--- |
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license: artistic-2.0 |
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--- |
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# Install |
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conda create -n druggpt python=3.7 |
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conda activate druggpt |
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pip install datasets |
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pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu117 |
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pip install transformers |
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pip install scipy scikit-learn |
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conda install -c openbabel openbabel |
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# How to use |
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1. Download the drug_generator.py file and bcl2.fasta. |
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2. Activate the druggpt environment using conda activate druggpt. |
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3. Navigate to the directory containing the drug_generator.py file using cd path/to/directory. |
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4. Run the script with the desired arguments, such as the protein sequence, ligand prompt, number of molecules to generate, and output directory. |
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# Example usage: |
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## If you want to input a protein FASTA file, |
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python drug_generator.py -f bcl2.fasta -n 50 |
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## If you want to input the amino acid sequence of the protein, |
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python drug_generator.py -p MAKQPSDVSSECDREGRQLQPAERPPQLRPGAPTSLQTEPQGNPEGNHGGEGDSCPHGSPQGPLAPPASPGPFATRSPLFIFMRRSSLLSRSSSGYFSFDTDRSPAPMSCDKSTQTPSPPCQAFNHYLSAMASMRQAEPADMRPEIWIAQELRRIGDEFNAYYARRVFLNNYQAAEDHPRMVILRLLRYIVRLVWRMH -n 50 |
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## If you want to provide a prompt for the ligand |
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python drug_generator.py -f bcl2.fasta -l COc1ccc(cc1)C(=O) -n 50 |
