Make recently new cif_output arguments optional, do not break existing code

Colab notbook was broken by this change and potentially code of other users
as well. Keep backward compatibility by also allowing the old way.

openfold/np/relax/relax.py

@@ -57,7 +57,7 @@ class AmberRelaxation(object):
         self._use_gpu = use_gpu
 
     def process(
-        self, *, prot: protein.Protein, cif_output: bool
+        self, *, prot: protein.Protein, cif_output: bool = False
     ) -> Tuple[str, Dict[str, Any], np.ndarray]:
         """Runs Amber relax on a prediction, adds hydrogens, returns PDB string."""
         out = amber_minimize.run_pipeline(

openfold/utils/script_utils.py

@@ -228,7 +228,7 @@ def prep_output(out, batch, feature_dict, feature_processor, config_preset, mult
     return unrelaxed_protein
 
 
-def relax_protein(config, model_device, unrelaxed_protein, output_directory, output_name, cif_output):
+def relax_protein(config, model_device, unrelaxed_protein, output_directory, output_name, cif_output=False):
     amber_relaxer = relax.AmberRelaxation(
         use_gpu=(model_device != "cpu"),
         **config.relax,
@@ -257,4 +257,4 @@ def relax_protein(config, model_device, unrelaxed_protein, output_directory, out
     with open(relaxed_output_path, 'w') as fp:
         fp.write(struct_str)
 
-    logger.info(f"Relaxed output written to {relaxed_output_path}...")
+    logger.info(f"Relaxed output written to {relaxed_output_path}...")
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