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#!/bin/bash |
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source activate mlfold |
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folder_with_pdbs="../PDB_complexes/pdbs/" |
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output_dir="../PDB_complexes/example_2_outputs" |
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if [ ! -d $output_dir ] |
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then |
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mkdir -p $output_dir |
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fi |
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path_for_parsed_chains=$output_dir"/parsed_pdbs.jsonl" |
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path_for_assigned_chains=$output_dir"/assigned_pdbs.jsonl" |
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chains_to_design="A B" |
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python ../helper_scripts/parse_multiple_chains.py --input_path=$folder_with_pdbs --output_path=$path_for_parsed_chains |
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python ../helper_scripts/assign_fixed_chains.py --input_path=$path_for_parsed_chains --output_path=$path_for_assigned_chains --chain_list "$chains_to_design" |
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python ../protein_mpnn_run.py \ |
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--jsonl_path $path_for_parsed_chains \ |
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--chain_id_jsonl $path_for_assigned_chains \ |
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--out_folder $output_dir \ |
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--num_seq_per_target 2 \ |
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--sampling_temp "0.1" \ |
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--batch_size 1 |
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