Fragment Overlay

This cube performs Overlay optimization between a query fragment against the fragments from records in intake port. Records containing similarity scores are emitted through the success port, upon completion.

Related Cubes

Calculation Parameters

  • Attachment Cutoff (attach_cut) type: decimal: Minimum acceptable attachment point tanimoto
    Default: 0.78 , Max: 1.0
  • Attachment Scale (attach_scale) type: decimal: Scale factor weighting the importance of attachment points
    Default: 1.5 , Min: 1.0, Max: 10.0
  • Use Bond Order (bond_order) type: boolean: Require same attachment bond order
    Default: True
  • Bump Radius (bump_radius) type: decimal: Protein-ligand bump radius
    Default: 2.25 , Min: 1.0, Max: 5.0
  • Charge type (charge_type) type: string: Charge type to be used for Overlay
    Default: fileChrg
    Choices: mmff94, fileChrg
  • Check Geometry (check_geom) type: boolean: Require minimal geometric difference at attachment points
    Default: True
  • 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
  • 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
  • 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
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Property (property) type: boolean: Filter fragments by property
    Default: False
  • Ring Requirement (ring_only) type: integer: Ring requirement between attachment points in fragment.-2: Ring of any size; -1: Exclude rings; 0: Ring agnostic,1-12: Ring of specified size
    Default: -2 , Min: -2, Max: 12
  • Score type (score_type) type: string: Score type to be used for Overlay
    Default: rocs
    Choices: rocs, ET, LinkOnly
  • Shape Cutoff (shape_cut) type: decimal: Minimum acceptable shape tanimoto
    Default: 0.6 , Max: 1.0
  • 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

  • Attachment score field (attach_field) type: Field Type: Float: Attachment tanimoto score
    Default: attach
  • Color tanimoto field (color_field) type: Field Type: Float: Color tanimoto score
    Default: color
  • Combo tanimoto field (combo_field) type: Field Type: Float: Combined shape and color tanimoto score
    Default: combo
  • Attachment score field (et_attach_field) type: Field Type: Float: Attachment tanimoto score
    Default: etattach
  • PB tanimoto field (et_color_field) type: Field Type: Float: PB tanimoto score
    Default: etpb
  • Combo tanimoto field (et_combo_field) type: Field Type: Float: Combined shape and color tanimoto score
    Default: etcombo
  • Shape tanimoto field (et_shape_field) type: Field Type: Float: Shape tanimoto score
    Default: etshape
  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • None (in_frag_field) type: Field Type: Chem.Mol:
  • None (in_query_field) type: Field Type: Chem.Mol:
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • None (out_frag_field) type: Field Type: Chem.Mol:
  • LinkOnly score field (score_field) type: Field Type: Float: LinkOnly score
    Default: score
  • Shape tanimoto field (shape_field) type: Field Type: Float: Shape tanimoto score
    Default: shape
  • Scores to sort field (sort_field) type: Field Type: Float: Scores to sort on for hit list generation
    Default: Scores to sort

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

Parallel Fragment Overlay

The parallel version adds these extra parameters.

  • Number of messages to distribute at a time (item_count) type: integer: The maximum number of messages to bundle together for a parallel cube.
    Default: 1 , Min: 1, Max: 65535
  • Maximum Failures (max_failures) type: integer: The maximum number of times to attempt processing a work item
    Default: 10 , Min: 1, Max: 100
  • Autoscale this Cube (autoscale) type: boolean: If True, let Orion manage the parallelism of this Cube
    Default: True
  • Maximum number of Cubes (max_parallel) type: integer: The maximum number of concurrently running copies of this Cube
    Default: 1000 , Min: 1
  • Minimum number of Cubes (min_parallel) type: integer: The minimum number of concurrently running copies of this Cube
    Default: 0