Generate User-Defined Fingerprints

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Role-based/Medicinal Chemist

  • Task-based/Cheminformatics/Fingerprint Generation

  • Solution-based/Virtual-screening/DB Search/2D Similarity and SubSearch

Description

Generate a user-customizable fingerprint type. The generated fingerprints can be customized with the following parameters: Fingerprint Type parameter determines the type of fingerprint (circular - ECFP-like, path, tree), Fingerprint Size parameter determines the size of the generated fingerprint (in bits), Minimum Fragment Size and Maximum Fragment Size parameters determine the minimum and maximum size of the fragments that are exhaustively enumerated during the fingerprint generation, and Fingerprint Atom Typing and Fingerprint Bond Typing parameters determine which atom and bond properties are encoded into the fingerprints.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Input Dataset (in): Dataset to generate fingerprints

  • Required

  • Type: data_source

Outputs

Output User-Defined Fingerprints (out): Name of output fingerprint dataset

  • Required

  • Type: dataset_out

  • Default: fingerprints

Fingerprint Type

Fingerprint Field (fp_field): Tag name for the field that stores fingerprints.

  • Required

  • Type: field_parameter

  • Default: Fingerprint

Fingerprint Type (fp_type): The fingerprint type generated for similarity calculation.

  • Required

  • Type: string

  • Default: Tree

  • Choices: [‘Circular’, ‘Path’, ‘Tree’]

Fingerprint Size (fp_size): The size of the fingerprint (in bits) generated for similarity calculation. It is recommended to generate fingerprints with the size of multiple of 256.

  • Required

  • Type: integer

  • Default: 4096

Fingerprint Atom Typing (fp_atom_type): The atom properties encoded into the fingerprints.

  • Required

  • Type: string

  • Default: [‘Atomic number’]

  • Choices: [‘Atomic number’, ‘Aromaticity’, ‘Chiral’, ‘Formal charge’, ‘Heavy degree’, ‘Hybridization’, ‘In ring’, ‘Hydrogen count’, ‘Halogen equivalent’, ‘Aromatic equivalent’, ‘HBond acceptor equivalent’, ‘HBond donor equivalent’]

Fingerprint Bond Typing (fp_bond_type): The bond properties encoded into the fingerprints.

  • Required

  • Type: string

  • Default: [‘Bond order’]

  • Choices: [‘Bond order’, ‘Chiral’, ‘In ring’]

Minimum Fragment Size (fp_min_frag_size): The smallest fragments that are enumerated during the fingerprint generation. In case of path and tree fingerprint type, this means minimum number of bonds in a fragment. In case of circular fingerprint type, this numbers means bond distance from central atoms.

  • Required

  • Type: integer

  • Default: 0

Maximum Fragment Size (fp_max_frag_size): The largest fragments that are enumerated during the fingerprint generation. In case of path and tree fingerprint types, this means maximum number of bonds in a fragment. In case of circular fingerprint type, this numbers means bond distance from central atoms.

  • Required

  • Type: integer

  • Default: 4