dEVA/configs/substrate_example.yml at main · ProteinDesignLab/dEVA · GitHub

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# config
general:
  cuda: true
  seed: 2
  outputs: /scratch/users/gelnesr/dEVA/substrate_example_B1 # path for outputs
  save_outputs: true

input:
  pdb: inputs/B1.pdb #"inputs/2VVB.pdb" # the pdb

evolution:
  n_generations: 10
  n_individuals: 5
  n_mutations: 1

seq_model: ligandmpnn   # choices: ligandmpnn or proteinmpnn

models:

  pocket_shape:
    ligand_pdb: ./inputs/B1_ligand.pdb
    target_occ: 105.0
    r_clash: 2.4
    w_clash: 1.0
    w_seal: 0.0          # see below
    verbose: false

  metal3d:
    model_path: ./models/metal3d/weights/metal3d_cat.pth #./models/metal3d/weights/metal_0.5A_v3_d0.2_16Abox.pth
    max_metal_p: 0.2
    threshold: 5

  ligandmpnn:
    model_path: ./models/ligandmpnn/model_params/ligandmpnn_v_32_020_25.pt
    packer_path: ./models/ligandmpnn/model_params/ligandmpnn_sc_v_32_002_16.pt
    var_residues: "" # residues to mutate
    fixed_residues: "A15 A190 A194"                      # e.g. "A12 A13 A14 B2 B25"
    bias_AA:  "H:0.5,E:-0.5,D:-0.5"         # e.g. "A:-1.024,P:2.34,C:-12.34"
    bias_AA_per_residue: ""                 # e.g. "A12:A:-1.024,P:2.34"
    omit_AA: "C"
    omit_AA_per_residue: ""
    symmetry_residues: ""                   # e.g. "A12,A13,A14|C2,C3|A5,B6"
    symmetry_weights: ""
    homo_oligomer: 0
    repack_everything: 0
    sc_num_denoising_steps: 8
    sc_num_samples: 1
    ligand_mpnn_cutoff_for_score: 20.0
    use_atom_context: 1
    temperature: 0.5
    zero_indexed: 0
    autoregressive_score: 0
    single_aa_score: 1
    chains_to_design: ""
    parse_these_chains_only: ""
    parse_atoms_with_zero_occupancy: 0
    verbose: false

  proteinmpnn:
    model_path: ./models/ligandmpnn/model_params/proteinmpnn_v_48_010.pt
    ligand_mpnn_cutoff_for_score: 20.0
    temperature: 0.5
    zero_indexed: 0
    autoregressive_score: 0
    single_aa_score: 1
    fixed_residues: ""       # e.g. "A12 A13 A14 B2 B25"
    bias_AA: ""              # e.g. "A:-1.024,P:2.34,C:-12.34"
    bias_AA_per_residue: ""  # e.g. "A12:A:-1.024,P:2.34"
    omit_AA: "C"
    omit_AA_per_residue: ""
    symmetry_residues: ""    # e.g. "A12,A13,A14|C2,C3|A5,B6"
    symmetry_weights: ""
    homo_oligomer: 0
    chains_to_design: ""
    parse_these_chains_only: ""
    parse_atoms_with_zero_occupancy: 0
    verbose: false