Spruce rotamers cube

A Cube that returns rotamers of a residue based on a residue identifier.

Main Parameters

Parameter Name Associated Port Port Type
Minimum clash contact fraction    
Minimum hydrogen bond contact fraction    
Remove clashing rotamers    
Residue Chain ID    
Residue Insertion Code    
Residue Name    
Residue Number    
Rotamer Coverage %    
Rotamer Library    

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
  • 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
  • Minimum clash contact fraction (decimal) : Minimum clash contact fraction to determine if something is clashing.
    Default: 0.8
  • Minimum hydrogen bond contact fraction (decimal) : Minimum hydrogen bond clash contact fraction to determine if something is clashing.
    Default: 0.5
  • Remove clashing rotamers (boolean) : Remove rotamers that clash with the remaining atoms.
    Default: True
  • Residue Altloc (string) : Alternate location identifier of residue to get rotamers for.
  • Residue Chain ID (string) : Chain ID of residue to get rotamers for.
  • Residue FragNo (integer) : Fragment number of residue to get rotamers for.
  • Residue Insertion Code (string) : Insertion code of residue to get rotamers for.
    Default: :blue:` `
  • Residue Name (string) : Name of residue to get rotamers for.
  • Residue Number (integer) : Number of residue to get rotamers for.
  • Rotamer Coverage % (decimal) : Coverage of the rotamers returned from the library in percent.
    Default: 100.0
  • Rotamer Library (string) : Rotamer library to use for side-chain building.
    Default: Richardson2016
    Choices: Dunbrack, Richardson, Richardson2016
  • 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: String) : Message log field
    Default: Log Field

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 Spruce rotamers cube

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/spruce/rotamers.py