content: # REINVENT4 TOML input example for scoring
  #
  
  run_type = "scoring"
  json_out_config = "_scoring.json"  # write this TOML to JSON
  
  [parameters]
  
  smiles_file = "compounds.smi"  # SMILES file with 1 molecule per line
  output_csv = "scoring.csv"  # name of output CSV to write, optional
  
  
  [scoring]
  
  type = "geometric_mean"  # or arithmetic_mean
  parallel = false  # do not run scoring components in parallel
  
  [[scoring.component]]
  # Custom alerts if a filter of unwanted groups
  [scoring.component.custom_alerts]
  
  [[scoring.component.custom_alerts.endpoint]]
  name = "Alerts"  # user chosen name for output
  # no weight because as a filter it will be applied globally
  
  params.smarts = [
      "[*;r8]",
      "[*;r9]",
      "[*;r10]",
      "[*;r11]",
      "[*;r12]",
      "[*;r13]",
      "[*;r14]",
      "[*;r15]",
      "[*;r16]",
      "[*;r17]",
      "[#8][#8]",
      "[#6;+]",
      "[#16][#16]",
      "[#7;!n][S;!$(S(=O)=O)]",
      "[#7;!n][#7;!n]",
      "C#C",
      "C(=[O,S])[O,S]",
      "[#7;!n][C;!$(C(=[O,N])[N,O])][#16;!s]",
      "[#7;!n][C;!$(C(=[O,N])[N,O])][#7;!n]",
      "[#7;!n][C;!$(C(=[O,N])[N,O])][#8;!o]",
      "[#8;!o][C;!$(C(=[O,N])[N,O])][#16;!s]",
      "[#8;!o][C;!$(C(=[O,N])[N,O])][#8;!o]",
      "[#16;!s][C;!$(C(=[O,N])[N,O])][#16;!s]"
  ]
  
  [[scoring.component]]
  [scoring.component.QED]
  
  [[scoring.component.QED.endpoint]]
  name = "QED"
  weight = 0.25  # weight to fine-tune the importance of this component
  
  [[scoring.component]]
  [scoring.component.MolecularWeight]
  
  [[scoring.component.MolecularWeight.endpoint]]
  name = "MW"
  weight = 0.25
  
  # transforms can be used for any component if desired
  transform.type = "double_sigmoid"
  transform.high = 500.0
  transform.low = 200.0
  transform.coef_div = 500.0
  transform.coef_si = 20.0
  transform.coef_se = 20.0
  
  [[scoring.component]]
  [scoring.component.TanimotoDistance]
  
  [[scoring.component.TanimotoDistance.endpoint]]
  name = "Tanimoto similarity ECF6"
  weight = 0.1
  
  # component specific parameters
  params.smiles = [
      "n1(nc(c(c1C)-c2n[nH]c(c2)[C@@]3([C@@H](CN(CC3)Cc4nc5c(c(n4)C)cccc5)O)OC)C)C"
  ]
  params.radius = 3
  params.use_counts = true
  params.use_features = true
  
  
  # Multiple end-points for many scoring components: each is a separate component
  # with its own weight
  [[scoring.component]]
  [scoring.component.pmi]
  name = "PMI 3D-likeness"
  
  [[scoring.component.pmi.endpoint]]
  weight = 0.79
  params.property = 'npr1'  # component specific parameters
  
  [[scoring.component.pmi.endpoint]]
  weight = 0.21
  params.property = 'npr2'  # component specific parameters
  
  