Exhaustive Docking (Single Receptor)

Docks multi-conformer molecules to a receptor using either FRED or HYBRID.

Ligands are read from the intake port, and the receptor is read from the init port.

HYBRID is an exhaustive docking algorithm that uses a bound ligand to guide docking into a protein structure. FRED is an exhaustive docking algorithm that uses only the protein structure.

Details

Docking modes:

  • AUTO - Use HYBRID if receptor has a bound ligand otherwise use FRED.
  • FRED - Forces use of FRED.
  • HYBRID - Forces use of HYBRID (will fail if receptor does not have a bound ligand).

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
  • None (string) : Force FRED or HYBRID mode, or AUTO select based on receptor
    Default: AUTO
    Choices: AUTO, FRED, HYBRID
  • 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
  • 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
  • None (integer) : Maximum number of top-scoring docked conformers to retain per molecule
    Default: 1 Min: 1 Max: 1000
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required

Field parameters

  • None (Field Type: StringVec) : Message extended log field
    Default: Extended Log Field
  • None (Field Type: Chem.Mol) :
  • None (Field Type: Chem.Mol) :
  • None (Field Type: String) : Message log field
    Default: Log Field
  • None (Field Type: Chem.Mol) :
  • Chemgauss4 Score field (Field Type: Float) : Score field for the docked molecule
    Default: Chemgauss4 Score

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 Exhaustive Docking (Single Receptor)

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/docking/docking_single_receptor.py