Fingerprint Generation (User-Defined)

modules/cheminfo-floes/docs/source/images/CalculationCubeIcon.svg

This cube generates custom 2D fingerprints for input molecules.

The molecules are read from the field specified by the Input Molecule Field parameter. The generated fingerprints can be customized with the following parameters:

  • Fingerprint Type parameter determines the type of fingerprint

  • 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

  • Fingerprint Atom Typing and Fingerprint Bond Typing parameters determine which atom and bond properties are encoded into the fingerprints

The generated fingerprint is stored in the field specified by the Fingerprint Field parameter, and the record is sent to the success port.


Downstream Cubes

See also

Main Parameters

Parameter Name

Associated Port

Port Type

Fingerprint Field

Related Cubes

Calculation Parameters

  • CPUs (integer) : The number of CPUs to run this cube with
    Default: 1 Min: 1 Max: 128
  • Cube Metrics (string) : Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Temporary Disk Space (MiB) (decimal) : The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 Min: 128.0 Max: 8589934592
  • Fingerprint Atom Typing (string) : The atom properties encoded into the fingerprints.
    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 (string) : The bond properties encoded into the fingerprints.
    Default: [‘Bond order’]
    Choices: Bond order, Chiral, In ring
  • Maximum Fragment Size (integer) : 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.
    Default: 4 Min: 1 Max: 8
  • Minimum Fragment Size (integer) : 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.
    Default: 0 Max: 5
  • Fingerprint Size (integer) : The size of the fingerprint (in bits) generated for similarity calculation. It is recommended to generate fingerprints with the size of multiple of 256.
    Default: 4096 Min: 256 Max: 16384
  • Fingerprint Type (string) : The fingerprint type generated for similarity calculation.
    Default: Tree
    Choices: Circular, Path, Tree
  • GPUs (integer) : The number of GPUs to run this cube with
    Default: 0 Max: 16
  • Instance Tags (string) : Only run on machines with matching tags (comma separated)
    Default: “”
  • Instance Type (string) : The type of instance that this cube needs to be run on
  • Memory (MiB) (decimal) : The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 Min: 256.0 Max: 8589934592
  • Metric Period (decimal) : How often to sample metrics, in seconds
    Default: 60 Min: 1 Max: 300
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required

Field parameters

  • Fingerprint Field (Field Type: Chem.FingerPrint) : Tag name for the field that stores fingerprints.
  • None (Field Type: Chem.Mol) :

2D Similarity Parameters

The parameters of the 2D fingerprint similarity calculation.

  • Fingerprint Type (string) : The fingerprint type generated for similarity calculation.
    Default: Tree
    Choices: Circular, Path, Tree
  • Fingerprint Size (integer) : The size of the fingerprint (in bits) generated for similarity calculation. It is recommended to generate fingerprints with the size of multiple of 256.
    Default: 4096 Min: 256 Max: 16384
  • Fingerprint Atom Typing (string) : The atom properties encoded into the fingerprints.
    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 (string) : The bond properties encoded into the fingerprints.
    Default: [‘Bond order’]
    Choices: Bond order, Chiral, In ring
  • Minimum Fragment Size (integer) : 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.
    Default: 0 Max: 5
  • Maximum Fragment Size (integer) : 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.
    Default: 4 Min: 1 Max: 8

Hardware Parameters

Machine hardware requirements

  • Memory (MiB) (decimal) : The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 Min: 256.0 Max: 8589934592
  • Temporary Disk Space (MiB) (decimal) : The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 Min: 128.0 Max: 8589934592
  • GPUs (integer) : The number of GPUs to run this cube with
    Default: 0 Max: 16
  • CPUs (integer) : The number of CPUs to run this cube with
    Default: 1 Min: 1 Max: 128
  • Instance Type (string) : The type of instance that this cube needs to be run on
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (string) : Only run on machines with matching tags (comma separated)
    Default: “”

Metrics Parameters

Cube Metric Parameters

  • Metric Period (decimal) : How often to sample metrics, in seconds
    Default: 60 Min: 1 Max: 300
  • Cube Metrics (string) : Set of metrics to be collected

    Choices: cpu, disk, memory, network

Parallel Fingerprint Generation (User-Defined)

The parallel version adds these extra parameters.

  • Number of messages to distribute at a time (integer) : The maximum number of messages to bundle together for a parallel cube.
    Default: 1 Min: 1 Max: 65535
  • Maximum Failures (integer) : The maximum number of times to attempt processing a work item
    Default: 10 Min: 1 Max: 100
  • Autoscale this Cube (boolean) : If True, let Orion manage the parallelism of this Cube
    Default: True
  • Maximum number of Cubes (integer) : The maximum number of concurrently running copies of this Cube
    Default: 1000 Min: 1
  • Minimum number of Cubes (integer) : The minimum number of concurrently running copies of this Cube
    Default: 0

Tip

filename: cheminfo/graphsim/sim2d_userdef_fp.py