inference:
  input_pdb: null
  num_designs: 10
  design_startnum: 0
  ckpt_override_path: null
  symmetry: null
  recenter: true
  radius: 10.0
  model_only_neighbors: false
  output_prefix: samples/design
  write_trajectory: true
  scaffold_guided: false
  model_runner: SelfConditioning
  cautious: true
  align_motif: true
  symmetric_self_cond: true
  final_step: 1
  deterministic: false
  trb_save_ckpt_path: null
  schedule_directory_path: null
  model_directory_path: null
contigmap:
  contigs: null
  inpaint_seq: null
  provide_seq: null
  length: null
model:
  n_extra_block: 4
  n_main_block: 32
  n_ref_block: 4
  d_msa: 256
  d_msa_full: 64
  d_pair: 128
  d_templ: 64
  n_head_msa: 8
  n_head_pair: 4
  n_head_templ: 4
  d_hidden: 32
  d_hidden_templ: 32
  p_drop: 0.15
  SE3_param_full:
    num_layers: 1
    num_channels: 32
    num_degrees: 2
    n_heads: 4
    div: 4
    l0_in_features: 8
    l0_out_features: 8
    l1_in_features: 3
    l1_out_features: 2
    num_edge_features: 32
  SE3_param_topk:
    num_layers: 1
    num_channels: 32
    num_degrees: 2
    n_heads: 4
    div: 4
    l0_in_features: 64
    l0_out_features: 64
    l1_in_features: 3
    l1_out_features: 2
    num_edge_features: 64
  freeze_track_motif: false
  use_motif_timestep: false
diffuser:
  T: 50
  b_0: 0.01
  b_T: 0.07
  schedule_type: linear
  so3_type: igso3
  crd_scale: 0.25
  partial_T: null
  so3_schedule_type: linear
  min_b: 1.5
  max_b: 2.5
  min_sigma: 0.02
  max_sigma: 1.5
denoiser:
  noise_scale_ca: 1
  final_noise_scale_ca: 1
  ca_noise_schedule_type: constant
  noise_scale_frame: 1
  final_noise_scale_frame: 1
  frame_noise_schedule_type: constant
ppi:
  hotspot_res: null
potentials:
  guiding_potentials: null
  guide_scale: 10
  guide_decay: constant
  olig_inter_all: null
  olig_intra_all: null
  olig_custom_contact: null
  substrate: null
contig_settings:
  ref_idx: null
  hal_idx: null
  idx_rf: null
  inpaint_seq_tensor: null
preprocess:
  sidechain_input: false
  motif_sidechain_input: true
  d_t1d: 22
  d_t2d: 44
  prob_self_cond: 0.0
  str_self_cond: false
  predict_previous: false
logging:
  inputs: false
scaffoldguided:
  scaffoldguided: false
  target_pdb: false
  target_path: null
  scaffold_list: null
  scaffold_dir: null
  sampled_insertion: 0
  sampled_N: 0
  sampled_C: 0
  ss_mask: 0
  systematic: false
  target_ss: null
  target_adj: null
  mask_loops: true
  contig_crop: null