cleanup configs

models/rf3/configs/model/components/rf3_net_with_confidence_head.yaml

@@ -36,11 +36,10 @@ confidence_head:
       d_hidden: 32
     attention_pair_bias:
       n_head: 16 
-      kq_norm: true
   n_bins_pae: 64
   n_bins_pde: 64
   n_bins_plddt: 50
   n_bins_exp_resolved: 2
   use_Cb_distances: False
   use_af3_style_binning_and_final_layer_norms: True
-  symmetrize_Cb_logits: True
+  symmetrize_Cb_logits: True

models/rfd3/configs/datasets/design_base.yaml

@@ -62,9 +62,6 @@ global_transform_args:
   min_ss_island_len: 1
   max_ss_island_len: 10
 
-  # Nucleic acid features
-  add_na_pair_features: false
-
   train_conditions:
     unconditional:
       frequency: 5.0
@@ -98,8 +95,3 @@ global_transform_args:
     # PPI
     add_ppi_hotspots: 0.75
     full_binder_crop: 0.75
-
-    # Nucleic SS:
-    p_is_nucleic_ss_example: 0.0
-    p_nucleic_ss_show_partial_feats: 0.0
-    

models/rfd3/configs/datasets/train/pdb/base.yaml

@@ -9,6 +9,6 @@ weights:
   beta: 0.5
   alphas:
     a_prot: 3.0 # 3 for AF-3
-    a_nuc: 3.0 # 3 for AF-3
+    a_nuc: 0.0 # 3 for AF-3
     a_ligand: 1.0 # 1 for AF-3
     a_loi: 5.0 # 5 for AF-3

models/rfd3/configs/datasets/val/pseudoknot.yaml

@@ -6,5 +6,4 @@ defaults:
 dataset:
   name: pseudoknot
   eval_every_n: 1
-  #data: ${paths.data.design_benchmark_data_dir}/pseudoknot_debug.json
   data: ${paths.data.design_benchmark_data_dir}/pseudoknot.json

models/rfd3/configs/experiment/rfd3na_fine_tune.yaml

@@ -10,8 +10,7 @@ defaults:
 
 name: rfd3na-fine-tune-ss0.5
 tags: [print-model]
-#ckpt_path: /projects/ml/aa_design/models/rfd3_latest_foundry.ckpt
-ckpt_path: /net/scratch/raktim/training/logs/train/rfd3na-fine-tune-ss0.5/2026-02-23_23-57_JOB_4717793/ckpt/epoch-0820.ckpt
+ckpt_path: null
 
 model:
   net:
@@ -78,6 +77,15 @@ datasets:
     # These are the ratios used in the preprint but we set all pdb sampling by default since not everyone might download the distillation data.
     pdb:
       probability: 0.6
+      sub_datasets:
+        pn_unit:
+          weights:
+            alphas:
+              a_nuc: 3.0
+        interface:
+          weights:
+            alphas:
+              a_nuc: 3.0
     rna_monomer_distillation:
       probability: 0.3
     monomer_distillation:

models/rfd3/configs/inference_engine/rfdiffusion3.yaml

@@ -25,9 +25,9 @@ inference_sampler:
   kind: "default" # "default" or "symmetry" to choose the sampler
   # Classifier-free guidance args:
   cfg_features:  # set to 0 in the reference CFG step
-    #- active_donor
-    #- active_acceptor
-    #- ref_atomwise_rasa
+    - active_donor
+    - active_acceptor
+    - ref_atomwise_rasa
     - bp_partners
 
   use_classifier_free_guidance: False