Tautomer Enumeration

This cube enumerates the reasonable tautomers of input molecules.

The resulting molecules are added as a vector of molecules in the input record and emitted through the success port.

Note

This cube removes formal charge of the molecule.

See also

Main Parameters

Parameter Name Associated Port Port Type
Individual Molecules Switch    

Related Cubes

Calculation Parameters

  • Apply Warts (boolean) : Returns setting for warts application of {title}_1, {title}_2, etc, on tautomers.
    Default: False
  • 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
  • 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
  • Maximum Tautomer States (integer) : The maximum number of Tautomer states returned.
    Default: 1000 Min: 1 Max: 50000
  • Maximum Tautomer States Generated (integer) : How many tautomer states should be generated before ranking. If 0, then as many tautomer states as possible are generated
    Default: 1000 Max: 50000
  • Max Rotors (integer) : Cutoff of rotatable bonds. The cube will skip molecules with rotors more than the cutoff.
    Default: 20 Min: 1 Max: 9999
  • 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
  • pKa Normalization (boolean) : This parameter determines whether to apply pKa normalization. If True the ionization state of each tautomer will be assigned to a predominate state at pH~7.4.
    Default: True
  • Reasonable Tautomers Only (boolean) : Flag to obtain only the reasonable looking unique tautomers. The program will output the most aromatic tautomer of the first 64 attempted.
    Default: False
  • Save Stereo (boolean) : Flag to not allow for any atom or bond with stereochemistry set in tautomerization. Without this setting it is possible for stereochemistry to removed during tautomerization.
    Default: False
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Individual Molecules Switch (boolean) : Output tautomers as individual molecules on the primary output molecule
    Default: True

Field parameters

  • None (Field Type: StringVec) : Message extended log field
    Default: Extended Log Field
  • None (Field Type: Chem.Mol) :
  • None (Field Type: String) : Message log field
    Default: Log Field
  • None (Field Type: Chem.Mol) :
  • Output Tautomers field (Field Type: Chem.MolVec) : Output record field with the vector of enumerated tautomers
    Default: Output Tautomers

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 Tautomer Enumeration

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: snowball/quacpac/tautomer_enum.py