<jupyter_start><jupyter_text>Get AF2 embeddings of 'single' representations 3/28/2022: 181297 cif files in /data/ga122/alphafold/pdb_mmcif/mmcif_files/  EC dataset Started at around 4pm on 3/28/22.<jupyter_code>%%bash
python3 run_pretrained_openfold.py  --fasta_path data/deepfri_ec/train/fastas_below_150/ --template_mmcif_dir ../../ga122/alphafold/pdb_mmcif/mmcif_files/ --use_precomputed_alignments data/deepfri_ec/train/alignments/ --output_dir data/deepfri_ec/train/outputs/ --model_device "cuda:1" --model_name "model_1" --param_path ../../ga122/alphafold/params/params_model_1.npz
 
%%bash
python3 run_pretrained_openfold.py
python3 run_pretrained_openfold.py  --fasta_path data/deepfri_ec/val/fastas_below_150/ --template_mmcif_dir ../../ga122/alphafold/pdb_mmcif/mmcif_files/ --use_precomputed_alignments data/deepfri_ec/val/alignments/ --output_dir data/deepfri_ec/val/outputs/ --model_device "cuda:1" --model_name "model_1" --param_path ../../ga122/alphafold/params/params_model_1.npz
    
%%bash
python3 run_pretrained_openfold.py
python3 run_pretrained_openfold.py  --fasta_path data/deepfri_ec/test/fastas_below_150/ --template_mmcif_dir ../../ga122/alphafold/pdb_mmcif/mmcif_files/ --use_precomputed_alignments data/deepfri_ec/test/alignments/ --output_dir data/deepfri_ec/test/outputs/ --model_device "cuda:1" --model_name "model_1" --param_path ../../ga122/alphafold/params/params_model_1.npz<jupyter_output><empty_output>
{'fraction_non_alphanumeric': 0.13064628214037527, 'fraction_numerical': 0.04447533009034051, 'mean_word_length': 5.02510460251046, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '1', 'dir': 'jupyter-structured-clean-dedup', 'id': '365160', 'license': 'Apache-2.0', 'n_tokens_mistral': 596, 'n_tokens_neox': 542, 'n_words': 74, 'path': 'run_openfold.ipynb', 'repo_name': 'crochereau/openfold', 'size': '1439'}