56 lines
1.9 KiB
Bash
56 lines
1.9 KiB
Bash
#1 design a new sequence and pack side chains (return 1 side chain packing sample - fast)
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python run.py \
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--model_type "ligand_mpnn" \
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--seed 111 \
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--pdb_path "./inputs/1BC8.pdb" \
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--out_folder "./outputs/sc_default_fast" \
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--pack_side_chains 1 \
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--number_of_packs_per_design 0 \
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--pack_with_ligand_context 1
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#2 design a new sequence and pack side chains (return 4 side chain packing samples)
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python run.py \
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--model_type "ligand_mpnn" \
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--seed 111 \
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--pdb_path "./inputs/1BC8.pdb" \
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--out_folder "./outputs/sc_default" \
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--pack_side_chains 1 \
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--number_of_packs_per_design 4 \
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--pack_with_ligand_context 1
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#3 fix specific residues for design and packing
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python run.py \
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--model_type "ligand_mpnn" \
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--seed 111 \
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--pdb_path "./inputs/1BC8.pdb" \
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--out_folder "./outputs/sc_fixed_residues" \
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--pack_side_chains 1 \
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--number_of_packs_per_design 4 \
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--pack_with_ligand_context 1 \
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--fixed_residues "C6 C7 C8 C9 C10 C11 C12 C13 C14 C15" \
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--repack_everything 0
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#4 fix specific residues for sequence design but repack everything
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python run.py \
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--model_type "ligand_mpnn" \
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--seed 111 \
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--pdb_path "./inputs/1BC8.pdb" \
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--out_folder "./outputs/sc_fixed_residues_full_repack" \
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--pack_side_chains 1 \
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--number_of_packs_per_design 4 \
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--pack_with_ligand_context 1 \
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--fixed_residues "C6 C7 C8 C9 C10 C11 C12 C13 C14 C15" \
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--repack_everything 1
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#5 design a new sequence using LigandMPNN but pack side chains without considering ligand/DNA etc atoms
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python run.py \
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--model_type "ligand_mpnn" \
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--seed 111 \
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--pdb_path "./inputs/1BC8.pdb" \
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--out_folder "./outputs/sc_no_context" \
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--pack_side_chains 1 \
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--number_of_packs_per_design 4 \
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--pack_with_ligand_context 0
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