# Tutorial 6: Structure-Guided Generation — Inpainting (Scaffold Decoration)
# Usage: MolCraftDiff generate docs/cfg_examples/gen_inpaint
#
# Provide a reference XYZ structure and specify which atoms (0-indexed)
# to mask. The model regenerates the masked region while preserving
# the rest of the molecule.

defaults:
  - tasks: diffusion
  - interference: gen_inpaint
  - _self_

chkpt_directory: "training_outputs/benchmark/EDM_geom/"  # <-- path to your trained model
atom_vocab: [H, B, C, N, O, F, Al, Si, P, S, Cl, As, Se, Br, I, Hg, Bi]
diffusion_steps: 900

interference:
  _target_: MolecularDiffusion.runmodes.generate.GenerativeFactory
  task_type: inpaint
  sampling_mode: "ddpm"
  num_generate: 100
  batch_size: 1             # inpainting typically requires batch_size: 1
  max_mol_size: 100
  mol_size: [0, 0]
  target_values: []
  property_names: []
  seed: 86
  output_path: "${chkpt_directory}/output_inpaint"

  condition_configs:
    reference_structure_path: "data/my_molecule.xyz"  # <-- your reference XYZ
    inpaint_cfgs:
      denoising_strength: 0.5    # higher → more creative freedom for masked region
      # 0-indexed atom indices to mask and regenerate:
      mask_node_index: [5, 6, 7, 8, 9]   # <-- replace with your target indices
      noise_initial_mask: True