Overlap

This cube performs static overlap calculation between a query molecule and a database (fit) molecule.

The query molecule is read from the init port, and the database (fit) molecules are read from the intake port.

A series of calculated 3D similarity measures are added to the intake port record and emitted through the success port.

Related Cubes

Calculation Parameters

  • Color type (color_type) type: string: Type of function to be used for color score evaluation
    Default: Exact
    Choices: Exact, Grid, Analytic
  • 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
  • Shape type (shape_type) type: string: Type of function to be used for shape overlap evaluation
    Default: Grid
    Choices: Exact, Grid, Analytic
  • 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

  • Color Score field (color_score_field) type: Field Type: Float: Color Score between the query and the fit molecule
    Default: Color Score
  • Color Tanimoto field (color_tan_field) type: Field Type: Float: Color Tanimoto between the query and the fit molecule
    Default: Color Tanimoto
  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • Fit Self Color field (fit_color_field) type: Field Type: Float: Self Color score of the fit molecule
    Default: Fit Self Color
  • Fit Color Tversky field (fit_color_tvr_field) type: Field Type: Float: Color Tversky calculated at beta of 0.95
    Default: Fit Color Tversky
  • Fit Tversky Combo field (fit_combo_tvr_field) type: Field Type: Float: Sum of shape and color Tversky calculated at beta of 0.95
    Default: Fit Tversky Combo
  • Fit Self Overlap field (fit_shape_field) type: Field Type: Float: Self overlap of the fit molecule
    Default: Fit Self Overlap
  • Fit Shape Tversky field (fit_shape_tvr_field) type: Field Type: Float: Shape Tversky calculated at beta of 0.95
    Default: Fit Shape Tversky
  • Database Molecule Field (in_mol_field) type: Field Type: Chem.Mol: Database molecule for overlay calculation
  • Query Molecule Field (init_mol_field) type: Field Type: Chem.Mol: Query molecule for overlay calculation
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • Overlap field (overlap_field) type: Field Type: Float: Shape Overlap between the query and the fit molecule
    Default: Overlap
  • Ref Self Color field (ref_color_field) type: Field Type: Float: Self Color score of the query molecule
    Default: Ref Self Color
  • Ref Color Tversky field (ref_color_tvr_field) type: Field Type: Float: Color Tversky calculated at alpha of 0.95
    Default: Ref Color Tversky
  • Ref Tversky Combo field (ref_combo_tvr_field) type: Field Type: Float: Sum of shape and color Tversky calculated at alpha of 0.95
    Default: Ref Tversky Combo
  • Ref Self Overlap field (ref_shape_field) type: Field Type: Float: Self overlap of the query molecule
    Default: Ref Self Overlap
  • Ref Shape Tversky field (ref_shape_tvr_field) type: Field Type: Float: Shape Tversky calculated at alpha of 0.95
    Default: Ref Shape Tversky
  • Shape Tanimoto field (shape_tan_field) type: Field Type: Float: Shape Tanimoto between the query and the fit molecule
    Default: Shape Tanimoto
  • Tanimoto Combo field (tan_combo_field) type: Field Type: Float: Sum of shape and color Tanimoto between query and fit molecule
    Default: Tanimoto Combo

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 Overlap

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