content: run_type = "scoring"
  output_csv = "scoring.csv"
  json_out_config = "_scoring.json"
  
  [parameters]
  
  smiles_file = "tests/chembl_random_100.smi"
  
  
  [scoring]
  
  type = "geometric_mean"
  parallel = false
  
  # filters
  [[scoring.component]]
  [scoring.component.UnwantedSubstructures]
  
  [[scoring.component.UnwantedSubstructures.endpoint]]
  name = "PAINS/CHEMBL_Glaxo"
  
  #params.catalogs = ['ALL']
  params.catalogs = ['PAINS', "CHEMBL_Glaxo"]
  
  
  [[scoring.component]]
  [scoring.component.UnwantedSubstructures]
  
  [[scoring.component.UnwantedSubstructures.endpoint]]
  name = "PAINS"
  
  params.catalogs = ['PAINS']
  
  
  [[scoring.component]]
  [scoring.component.UnwantedSubstructures]
  
  [[scoring.component.UnwantedSubstructures.endpoint]]
  name = "CHEMBL_Glaxo"
  
  params.catalogs = ["CHEMBL_Glaxo"]
  
  
  [[scoring.component]]
  [scoring.component.NIBRSubstructureFilters]
  
  [[scoring.component.NIBRSubstructureFilters.endpoint]]
  name = "NIBR"
  
  params.cutoff = 10
  
  
  # "normal" scoring components
  [[scoring.component]]
  [scoring.component.QED]
  
  [[scoring.component.QED.endpoint]]
  name = "QED"
  weight = 0.2
  
  
  [[scoring.component]]
  [scoring.component.LillyMedchemRules]
  
  [[scoring.component.LillyMedchemRules.endpoint]]
  name = "LillyMedchem"
  
  params.relaxed = false
  
  transform.type = "reverse_sigmoid"
  transform.high = 200
  transform.low = 0.0
  transform.k = 0.2
  
  
  [[scoring.component]]
  [scoring.component.TPSA]
  
  [[scoring.component.TPSA.endpoint]]
  name = "RDKit TPSA"
  
  transform.type = "double_sigmoid"
  transform.low = 50
  transform.high = 180
  transform.coef_div = 100
  transform.coef_si = 150
  transform.coef_se = 150
  
  
  [[scoring.component]]
  [scoring.component.LillyDescriptors]
  
  [[scoring.component.LillyDescriptors.endpoint]]
  name = "Novartis PSA"
  
  params.descriptors = "w_nvrtspsa"
  
  transform.type = "double_sigmoid"
  transform.low = 50
  transform.high = 180
  transform.coef_div = 100
  transform.coef_si = 150
  transform.coef_se = 150
  
  [[scoring.component.LillyDescriptors.endpoint]]
  name = "RO5 OHNH"
  
  params.descriptors = "w_ro5_ohnh"
  
  transform.type = "left_step"
  transform.high = 10
  
  
  [[scoring.component]]
  [scoring.component.LillyPAINS]
  
  [[scoring.component.LillyPAINS.endpoint]]
  name = "Alpha"
  
  params.assay = 'Alpha'
  
  transform.type = "sigmoid"
  transform.high = 100
  transform.low = 0.0
  transform.k = 0.2
  
  [[scoring.component.LillyPAINS.endpoint]]
  name = "FRET_HS"
  
  params.assay = "FRET_HS"
  
  transform.type = "sigmoid"
  transform.high = 100
  transform.low = 0.0
  transform.k = 0.2
  
  [[scoring.component.LillyPAINS.endpoint]]
  name = "QCEnrichment"
  
  params.assay = "QCEnrichment"
  
  transform.type = "sigmoid"
  transform.high = 100
  transform.low = 0.0
  transform.k = 0.2
  