Model Builder: 3D Regression (Features Port)

This cube builds a 3D-QSAR model, using ROCS scores as descriptors. The cube assumes that pose conformers of the input molecules have been provided and only static ROCS scores are calculated to generate descriptors.

Calculation Parameters

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

    Choices: cpu, disk, memory, network
  • Descriptor type (desc_types) type: string: Descriptor types for CUSTOM-GPR Model.
    Default: [‘custom’]
    Choices: fp_tanimoto, rocs_tanimoto, rocs_overlap, eon_overlap, eon_tanimoto, plif_tanimoto, custom
  • Temporary Disk Space (MiB) (disk_space) type: 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 (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • Max Rotors (max_rotors) type: integer: Cutoff of rotatable bonds. The cube will skip molecules with rotors more than the cutoff.
    Default: 40 , Min: 1, Max: 9999
  • Memory (MiB) (memory_mb) type: 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 (metric_period) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • None (min_prob) type: decimal: The minimum acceptable posit probability for including a ligand into model.
    Default: 0.5 , Max: 1.0
  • Types of model to build (model_type) type: string:
    Default: [‘ROCS-GPR’, ‘EON-GPR’, ‘CUSTOM-GPR’, ‘ROCS-KPLS’, ‘EON-KPLS’]
    Choices: ROCS-GPR, EON-GPR, CUSTOM-GPR, ROCS-KPLS, EON-KPLS
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Pose prediction method (pose_method) type: string: Method for 3D pose conformer generation.
    Default: none
    Choices: none, posit, hybrid, rocs, eon, flexi-rocs, auto
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required

Field parameters

  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • KPLS number of features (in_features_field) type: Field Type: Int: Field containing KPLS number of features.
    Default: Features
  • None (in_mol_field) type: Field Type: Chem.Mol:
  • Input Potency field (in_potency_field) type: Field Type: Float: Training set input potency data.
    Default: potency
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • None (receptor_field) type: Field Type: Chem.DesignUnit:Record:
    Default: designunit

Hardware Parameters

Machine hardware requirements
  • Memory (MiB) (memory_mb) type: 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
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • Temporary Disk Space (MiB) (disk_space) type: 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 (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”

Metrics Parameters

Cube Metric Parameters
  • Metric Period (None) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Cube Metrics (None) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network