# Tutorial 6: Structure-Guided Generation — Outpainting (Fragment Extension)
# Usage: MolCraftDiff generate docs/cfg_examples/gen_outpaint
#
# Grow a molecule from a given fragment. The reference XYZ provides
# the fixed scaffold; the model appends new atoms according to the
# connector_dicts geometry constraints.

defaults:
  - tasks: diffusion
  - interference: gen_outpaint
  - _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: outpaint
  sampling_mode: "ddpm"
  num_generate: 100
  batch_size: 12
  max_mol_size: 100
  mol_size: [0, 0]
  target_values: []
  property_names: []
  seed: 86
  output_path: "${chkpt_directory}/output_outpaint"

  condition_configs:
    reference_structure_path: "data/my_fragment.xyz"  # <-- your fragment XYZ
    outpaint_cfgs:
      t_start: 0.75         # diffusion timestep to start outpainting
      t_critical: 0.0
      # connector_dicts: maps scaffold atom index → [number of new atoms to attach]
      connector_dicts:
        0: [2]              # <-- replace with your atom indices and valencies
        1: [2]
      spread: 1.25          # spatial spread of newly seeded atoms (Å)
      seed_dist: 1.25       # distance from connector atom for new atom seeding (Å)
      min_dist: 2.5         # minimum distance between new atoms (Å)