Freeform Conf Prepare Ensemble

This cube generates an appropriate conformer ensemble and prepares it for Freeform Conf calculation.

The generated molecule conformer ensemble is added to the intake port record and emitted through the success port. Additionally, prepped free and restrained molecules for strain energy calculation are added to the record, if input molecule is 3D

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
  • Force field (string) : Force field model to be used. Built-in types are: MMFF94S, Smirnoff99Frost, PARSLEY_OPENFF100, PARSLEY_OPENFF111, PARSLEY_OPENFF120. The name of a .offxml file that defines a SMIRNOFF force field can also be used as input.
    Default: MMFF94S
  • GPUs (integer) : The number of GPUs to run this cube with
    Default: 0 Max: 16
  • Include input conformer (boolean) : Flag to include the input conformers in ensemble
    Default: False
  • 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
  • Prep for strain analysis (boolean) : Flag to acknowledge if restriction energy would be calculated downstream
    Default: False
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Use input ensemble (boolean) : Flag to use input ensemble conformers
    Default: False

Field parameters

  • None (Field Type: StringVec) : Message extended log field
    Default: Extended Log Field
  • None (Field Type: Chem.Mol) : Output Free ligand for strain analysis
    Default: Free mol
  • None (Field Type: Chem.Mol) :
  • None (Field Type: Chem.Mol) : As is Input ligand for strain analysis
    Default: Input mol
  • None (Field Type: String) : Message log field
    Default: Log Field
  • None (Field Type: Chem.Mol) :
  • None (Field Type: Chem.Mol) : Output Restrained ligand for strain analysis
    Default: Restrained mol

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 Freeform Conf Prepare Ensemble

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/freeform/freeform_adv.py