./scripts/get_tolerance_labels.pl -in my_chain.list -c -p data/human_TSL.dump -out my_out_dir/ -i -x data/human_best_grouping_scheme.dat
./scripts/get_tolerance_labels.pl -in my_chain.list -c -p data/human_TSL.dump -out my_out_dir/ -i -x data/human_best_grouping_scheme.dat
If you have a list of PDB files rather than PDB codes, change the -c option to -d
./scripts/get_tolerance_labels.pl -in my_file.list -d -p data/human_TSL.dump -out my_out_dir/ -i -x data/human_best_grouping_scheme.dat
Input format example for list of PDB chains:
1a2y C
2qza A B
Input format example list of PDB files:
path/to/1a2y.pdb C
path/to/2qza.pdb A B
There are three steps involved.
First run IntPred like so
path/to/IntPred/bin/runIntPred.pl -f pdb -p out_patch_dir/ -o intpred.preds -c test.intpred.in
Where test.intpred.in is formatted for IntPred (run runIntPred.pl with -h option for more details).
Change -f option to file if test.intpred.in lists file paths rather than pdb codes.
Then run
path/to/IntPred/bin/transformPatch2ResiduePred.pl -c intpred.preds out_patch_dir/ class1.confusion_table_all_residues.instances
Where class1.confusion_table_all_residues.instances is the output from get_tolerance_labels.pl
Finally, use filter_intpred_labels.pl to filter IntPred predictions.
./scripts/filter_intpred_labels.pl residue.preds class1.confusion_table_all_residues.instances
where residue.preds is the output from transformPatch2ResiduePred.pl
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