Merge pull request #21 from brennanaba/save-multi-conformation-to-dir

Fixed unnamed arg issue in save of multi conformations
brennanaba · Jun 26, 2023 · 3e04f1f · 3e04f1f
2 parents 960412d + bdc2fd0
commit 3e04f1f
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git 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
@@ -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
@@ -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)