ICM Manual v.3.9
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2020, Molsoft LLC
May 17 2024

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Chemical Fingerprints

We construct fingerprint by enumerating linear and some non-linear fragments plus some information about rings. Atoms type mapping varies depending on the chain/fragment size. All this hashed into counted or non-counted vector. (counted are mostly used in prediction models)

Fingerprint properties:

  • Result vector size : (1536 for default chemical similarity/distance fingerprint)
  • Minimum/Maximum fragment size (chain length for linear fingerprints) : 1-6 default
  • Flexible atom typing which from the combination of the following features:
    • cd : element code
    • hyb: hybridization
    • a : aromaticity.
    • h : number of connected hydrogen
    • hp : number of connected hydrogen for polar atoms (0- others)
    • r : ring/chain attribute
    • b : number of heavy neighbors
    • rs : size of the smallest ring atom belongs to (0 - for non-ring atoms)
  • Flexible bond typing:
    • bt : bond order
    • ~r : ring/chain attribute
    • ~rt : rotatable attribute
  • enumeration method:
    • linear chains, rings and small branched fragments (this is the default for chemical distance/similarity)
    • ecfp (non-linear fragment enumeration)
    • 2D ph4
  • binary / counted

For the chemical distance/similarity and clustering the default fingerprint type type is 1. Length: 1536 Max linear chain length: 6 Atom typing depends on the chain length.

Custom fingerprints can be built using Descriptor function or in prediction models


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