# APED Pipeline Configuration
# For reproducibility of results

# Dataset Parameters
dataset:
  name: "APED-Thermophile-Module"
  version: "1.0.0"
  
# Data Sources
sources:
  alphafold_db: "https://alphafold.ebi.ac.uk"
  uniprot: "https://www.uniprot.org"

# Organism Taxonomy IDs (UniProt)
organisms:
  - name: "Thermus thermophilus"
    taxonomy_id: 274
  - name: "Thermococcus kodakarensis"
    taxonomy_id: 69014
  - name: "Sulfolobus solfataricus"
    taxonomy_id: 2287
  - name: "Pyrococcus furiosus"
    taxonomy_id: 2261

# Feature Extraction Parameters
features:
  structural:
    - mean_plddt
    - helix_fraction
    - sheet_fraction
    - coil_fraction
  sequence:
    - sequence_length
    - molecular_weight
    - isoelectric_point
    - instability_index
    - aromaticity
    - hydrophobicity
    - charge

# RFdiffusion Parameters
rfdiffusion:
  colab_notebook: "https://colab.research.google.com/github/sokrypton/ColabDesign/blob/main/rf/examples/diffusion.ipynb"
  parameters:
    contigs: "A1-50/50-100"
    iterations: 50
    num_designs: 5
    symmetry: "none"
    use_beta_model: false

# ProteinMPNN Parameters
proteinmpnn:
  sequences_per_backbone: 8
  sampling_temperature: 0.1

# Validation Thresholds
validation:
  min_plddt: 90.0
  max_rmsd: 1.0
  min_ptm: 0.7

# Output
output:
  huggingface_repo: "electricsheepafrica/APED-African-Protein-Engineering-Dataset"
  formats:
    - parquet
    - fasta
    - csv