Add LigandMPNN Nextflow pipeline for protein sequence design

run_examples.sh

@@ -0,0 +1,244 @@
+#!/bin/bash
+
+#1
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/default"
+#2
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --temperature 0.05 \
+        --out_folder "./outputs/temperature"
+
+#3
+python run.py \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/random_seed"
+
+#4
+python run.py \
+        --seed 111 \
+        --verbose 0 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/verbose"
+
+#5
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/save_stats" \
+        --save_stats 1
+
+#6
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/fix_residues" \
+        --fixed_residues "C1 C2 C3 C4 C5 C6 C7 C8 C9 C10" \
+        --bias_AA "A:10.0"
+
+#7
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/redesign_residues" \
+        --redesigned_residues "C1 C2 C3 C4 C5 C6 C7 C8 C9 C10" \
+        --bias_AA "A:10.0"
+
+#8
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/batch_size" \
+        --batch_size 3 \
+        --number_of_batches 5
+
+#9
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --bias_AA "W:3.0,P:3.0,C:3.0,A:-3.0" \
+        --out_folder "./outputs/global_bias"
+
+#10
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --bias_AA_per_residue "./inputs/bias_AA_per_residue.json" \
+        --out_folder "./outputs/per_residue_bias"
+
+#11
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --omit_AA "CDFGHILMNPQRSTVWY" \
+        --out_folder "./outputs/global_omit"
+
+#12
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --omit_AA_per_residue "./inputs/omit_AA_per_residue.json" \
+        --out_folder "./outputs/per_residue_omit"
+
+#13
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/symmetry" \
+        --symmetry_residues "C1,C2,C3|C4,C5|C6,C7" \
+        --symmetry_weights "0.33,0.33,0.33|0.5,0.5|0.5,0.5"
+
+#14
+python run.py \
+        --model_type "ligand_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/4GYT.pdb" \
+        --out_folder "./outputs/homooligomer" \
+        --homo_oligomer 1 \
+        --number_of_batches 2
+
+#15
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/file_ending" \
+        --file_ending "_xyz"
+
+#16
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/zero_indexed" \
+        --zero_indexed 1 \
+        --number_of_batches 2
+
+#17
+python run.py \
+        --model_type "ligand_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/4GYT.pdb" \
+        --out_folder "./outputs/chains_to_design" \
+        --chains_to_design "A,B"
+
+#18
+python run.py \
+        --model_type "ligand_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/4GYT.pdb" \
+        --out_folder "./outputs/parse_these_chains_only" \
+        --parse_these_chains_only "A,B"
+
+#19
+python run.py \
+        --model_type "ligand_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/ligandmpnn_default"
+
+#20
+python run.py \
+        --checkpoint_ligand_mpnn "./model_params/ligandmpnn_v_32_005_25.pt" \
+        --model_type "ligand_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/ligandmpnn_v_32_005_25"
+
+#21
+python run.py \
+        --model_type "ligand_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/ligandmpnn_no_context" \
+        --ligand_mpnn_use_atom_context 0
+
+#22
+python run.py \
+        --model_type "ligand_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/ligandmpnn_use_side_chain_atoms" \
+        --ligand_mpnn_use_side_chain_context 1 \
+        --fixed_residues "C1 C2 C3 C4 C5 C6 C7 C8 C9 C10"
+
+#23
+python run.py \
+        --model_type "soluble_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/soluble_mpnn_default"
+
+#24
+python run.py \
+        --model_type "global_label_membrane_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/global_label_membrane_mpnn_0" \
+        --global_transmembrane_label 0
+
+#25
+python run.py \
+        --model_type "per_residue_label_membrane_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/per_residue_label_membrane_mpnn_default" \
+        --transmembrane_buried "C1 C2 C3 C11" \
+        --transmembrane_interface "C4 C5 C6 C22"
+
+#26
+python run.py \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/fasta_seq_separation" \
+        --fasta_seq_separation ":"
+
+#27
+python run.py \
+        --pdb_path_multi "./inputs/pdb_ids.json" \
+        --out_folder "./outputs/pdb_path_multi" \
+        --seed 111
+
+#28
+python run.py \
+        --pdb_path_multi "./inputs/pdb_ids.json" \
+        --fixed_residues_multi "./inputs/fix_residues_multi.json" \
+        --out_folder "./outputs/fixed_residues_multi" \
+        --seed 111
+
+#29
+python run.py \
+        --pdb_path_multi "./inputs/pdb_ids.json" \
+        --redesigned_residues_multi "./inputs/redesigned_residues_multi.json" \
+        --out_folder "./outputs/redesigned_residues_multi" \
+        --seed 111
+
+#30
+python run.py \
+        --pdb_path_multi "./inputs/pdb_ids.json" \
+        --omit_AA_per_residue_multi "./inputs/omit_AA_per_residue_multi.json" \
+        --out_folder "./outputs/omit_AA_per_residue_multi" \
+        --seed 111
+
+#31
+python run.py \
+        --pdb_path_multi "./inputs/pdb_ids.json" \
+        --bias_AA_per_residue_multi "./inputs/bias_AA_per_residue_multi.json" \
+        --out_folder "./outputs/bias_AA_per_residue_multi" \
+        --seed 111
+
+#32
+python run.py \
+        --model_type "ligand_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --ligand_mpnn_cutoff_for_score "6.0" \
+        --out_folder "./outputs/ligand_mpnn_cutoff_for_score"
+
+#33
+python run.py \
+        --seed 111 \
+        --pdb_path "./inputs/2GFB.pdb" \
+        --out_folder "./outputs/insertion_code" \
+        --redesigned_residues "B82 B82A B82B B82C" \
+        --parse_these_chains_only "B"