From bdc2fd0789a97ce8194fc2a7d19c71d9b859f8db Mon Sep 17 00:00:00 2001 From: Nele Quast Date: Mon, 26 Jun 2023 18:07:00 +0100 Subject: [PATCH] fixed unnamed arg issue in save of multi conformations --- ImmuneBuilder/ABodyBuilder2.py | 4 ++-- ImmuneBuilder/NanoBodyBuilder2.py | 4 ++-- ImmuneBuilder/TCRBuilder2.py | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/ImmuneBuilder/ABodyBuilder2.py b/ImmuneBuilder/ABodyBuilder2.py index 3006647..f9fa8ea 100644 --- a/ImmuneBuilder/ABodyBuilder2.py +++ b/ImmuneBuilder/ABodyBuilder2.py @@ -176,11 +176,11 @@ def command_line_interface(): print("Antibody modelled succesfully, starting refinement.", flush=True) if args.to_directory: - antibody.save_all(args.output,check_for_strained_bonds) + antibody.save_all(args.output,check_for_strained_bonds=check_for_strained_bonds) if args.verbose: print("Refinement finished. Saving all outputs to directory", flush=True) else: - antibody.save(args.output,check_for_strained_bonds) + antibody.save(args.output,check_for_strained_bonds=check_for_strained_bonds) if args.verbose: outfile = "ABodyBuilder2_output.pdb" if args.output is None else args.output print(f"Refinement finished. Saving final structure to {outfile}", flush=True) diff --git a/ImmuneBuilder/NanoBodyBuilder2.py b/ImmuneBuilder/NanoBodyBuilder2.py index f5cae13..14a4c03 100644 --- a/ImmuneBuilder/NanoBodyBuilder2.py +++ b/ImmuneBuilder/NanoBodyBuilder2.py @@ -180,11 +180,11 @@ def command_line_interface(): print("Nanobody modelled succesfully, starting refinement.", flush=True) if args.to_directory: - antibody.save_all(args.output,check_for_strained_bonds) + antibody.save_all(args.output,check_for_strained_bonds=check_for_strained_bonds) if args.verbose: print("Refinement finished. Saving all outputs to directory", flush=True) else: - antibody.save(args.output,check_for_strained_bonds) + antibody.save(args.output,check_for_strained_bonds=check_for_strained_bonds) if args.verbose: outfile = "NanoBodyBuilder2_output.pdb" if args.output is None else args.output print(f"Refinement finished. Saving final structure to {outfile}", flush=True) diff --git a/ImmuneBuilder/TCRBuilder2.py b/ImmuneBuilder/TCRBuilder2.py index 620ff11..35169c4 100644 --- a/ImmuneBuilder/TCRBuilder2.py +++ b/ImmuneBuilder/TCRBuilder2.py @@ -177,11 +177,11 @@ def command_line_interface(): print("TCR modelled succesfully, starting refinement.", flush=True) if args.to_directory: - tcr.save_all(args.output,check_for_strained_bonds) + tcr.save_all(args.output,check_for_strained_bonds=check_for_strained_bonds) if args.verbose: print("Refinement finished. Saving all outputs to directory", flush=True) else: - tcr.save(args.output,check_for_strained_bonds) + tcr.save(args.output,check_for_strained_bonds=check_for_strained_bonds) if args.verbose: outfile = "TCRBuilder2_output.pdb" if args.output is None else args.output print(f"Refinement finished. Saving final structure to {outfile}", flush=True)