Reverting changes to flag name, so you still use scaffoldguided.scaffoldguided=True instead of scaffoldguided_enabled

Author: woodsh17

config/inference/base.yaml

@@ -126,7 +126,7 @@ logging:
   inputs: False
 
 scaffoldguided:
-  scaffoldguided_enable: False
+  scaffoldguided: False
   target_pdb: False
   target_path: null
   scaffold_list: null

examples/design_ppi_scaffolded.sh

@@ -7,4 +7,4 @@
 # We then provide a path to a directory of different scaffolds (we've provided some for you to use, from Cao et al., 2022)
 # We generate 10 designs, and reduce the noise added during inference to 0 (which improves the quality of designs)
 
-../scripts/run_inference.py scaffoldguided.target_path=input_pdbs/insulin_target.pdb inference.output_prefix=example_outputs/design_ppi_scaffolded scaffoldguided.scaffoldguided_enable=True 'ppi.hotspot_res=[A59,A83,A91]' scaffoldguided.target_pdb=True scaffoldguided.target_ss=target_folds/insulin_target_ss.pt scaffoldguided.target_adj=target_folds/insulin_target_adj.pt scaffoldguided.scaffold_dir=./ppi_scaffolds/ inference.num_designs=10 denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0
+../scripts/run_inference.py scaffoldguided.target_path=input_pdbs/insulin_target.pdb inference.output_prefix=example_outputs/design_ppi_scaffolded scaffoldguided.scaffoldguided=True 'ppi.hotspot_res=[A59,A83,A91]' scaffoldguided.target_pdb=True scaffoldguided.target_ss=target_folds/insulin_target_ss.pt scaffoldguided.target_adj=target_folds/insulin_target_adj.pt scaffoldguided.scaffold_dir=./ppi_scaffolds/ inference.num_designs=10 denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0

rfdiffusion/inference/model_runners.py

@@ -78,14 +78,14 @@ def initialize(self, conf: DictConfig) -> None:
                 if conf.contigmap.provide_seq is not None:
                     # this is only used for partial diffusion
                     assert conf.diffuser.partial_T is not None, "The provide_seq input is specifically for partial diffusion"
-                if conf.scaffoldguided.scaffoldguided_enable:
+                if conf.scaffoldguided.scaffoldguided:
                     self.ckpt_path = f'{model_directory}/InpaintSeq_Fold_ckpt.pt'
                 else:
                     self.ckpt_path = f'{model_directory}/InpaintSeq_ckpt.pt'
-            elif conf.ppi.hotspot_res is not None and conf.scaffoldguided.scaffoldguided_enable is False:
+            elif conf.ppi.hotspot_res is not None and conf.scaffoldguided.scaffoldguided is False:
                 # use complex trained model
                 self.ckpt_path = f'{model_directory}/Complex_base_ckpt.pt'
-            elif conf.scaffoldguided.scaffoldguided_enable is True:
+            elif conf.scaffoldguided.scaffoldguided is True:
                 # use complex and secondary structure-guided model
                 self.ckpt_path = f'{model_directory}/Complex_Fold_base_ckpt.pt'
             else:

rfdiffusion/inference/utils.py

@@ -502,7 +502,7 @@ def get_next_pose(
 
 
 def sampler_selector(conf: DictConfig):
-    if conf.scaffoldguided.scaffoldguided_enable:
+    if conf.scaffoldguided.scaffoldguided:
         sampler = model_runners.ScaffoldedSampler(conf)
     else:
         if conf.inference.model_runner == "default":