Best Overlay Transform

This cube performs overlay optimization between a shape query and a database (fit) molecule, and returns the transforms required for optimal overlap.

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

A series of calculated 3D similarity measures, along with the best overlaid query fit molecule conformers, are added to the intake port record and emitted through the success port. This cube does not transform the output fit molecule to the best overlaid position.

Related Cubes

Calculation Parameters

  • Color Force Field (color_ff) type: string: Color force field to be used
    Default: ImplicitMillsDean
    Choices: ImplicitMillsDean, ExplicitMillsDean, ImplicitMillsDeanNoRings, ExplicitMillsDeanNoRings
  • 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
  • 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
  • Output All Results (output_all_res) type: boolean: Output all possible overlay results
    Default: True
  • 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
  • Sorter type (sorter_type) type: string: Type of predicate for sorting scores
    Default: HighestTanimotoCombo
    Choices: HighestTanimotoCombo, HighestFitTverskyCombo, HighestRefTverskyCombo
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • start type (start_type) type: string: Type of starts to be used
    Default: Inertial
    Choices: Inertial, Rocs, AsIs, AtAtom, Subrocs, Random

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
  • None (in_mol_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_mol_field) type: Field Type: Chem.Mol:
  • 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
  • Rotation field (rot_field) type: Field Type: FloatVec: Rotation to be applied on the fit molecule
    Default: Rotation
  • Shape Tanimoto field (shape_tan_field) type: Field Type: Float: Shape Tanimoto between the query and the fit molecule
    Default: Shape Tanimoto
  • Scores to sort field (sort_field) type: Field Type: Float: Scores to sort on for hit list generation
    Default: Scores to sort
  • Tanimoto Combo field (tan_combo_field) type: Field Type: Float: Sum of shape and color Tanimoto between query and fit molecule
    Default: Tanimoto Combo
  • Translation field (trans_field) type: Field Type: FloatVec: Translation to be applied on the fit molecule
    Default: Translation

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 Best Overlay Transform

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