EON Overlay

This cube calculates EON electrostatic Tanimoto similarity between a query molecule and a database molecule. This is a calculation that performs both overlay and scoring and no pre-alignment of the input molecules is expected.

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

For each database molecule, electrostatic tanimoto is calculated for each conformer followed by calculation of the tanimoto combo (i.e., shape plus electrostatics). A single conformer with the highest Tanimoto Combo is emitted through the success port, as a new record.

By default electrostatics is modeled with charge density, however an option is supported of electrostatics modeling via potential.

Related Cubes

Calculation Parameters

  • Zap boundary spacing (boundary_spacing) type: decimal: Spacing between the molecule and the edge of the grid
    Default: 4.0 , Min: 1.0, Max: 10.0
  • 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
  • Zap grid spacing (grid_spacing) type: decimal: Grid spacing for the internal Zap calculations
    Default: 0.75 , Min: 0.5, Max: 1.5
  • Inner dielectric (inner_dielec) type: decimal: Protein dielectric constant for Zap calculations
    Default: 1.0 , Max: 80.0
  • 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
  • Number of top hits for potential (num_top_scores) type: integer: When potential mode is engaged, the shape and charge overlay will keep this many best hits for shape and potential scoring
    Default: 5
  • Outer dielectric (outer_dielec) type: decimal: Solvent dielectric constant for Zap calculations
    Default: 80.0 , Max: 80.0
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Potential (potential) type: boolean: Electrostatics scoring function using potential similarity
    Default: False
  • Salt concentration (salt_conc) type: decimal: Salt concentration in Zap calculation (only will be used when potential mode is engaged)
    Default: 0.04 , Min: 0.01, Max: 0.1
  • 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

  • Combo Tanimoto Field (combo_tani_field) type: Field Type: Float: Shape plus Electrostatic Tanimoto between the query and the fit molecule
    Default: Tanimoto Combo
  • Electrostatic Tanimoto Field (elect_tani_field) type: Field Type: Float: Electrostatic Tanimoto between the query and the fit molecule
    Default: Electrostatic Tanimoto
  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • None (in_mol_field) type: Field Type: Chem.Mol:
  • None (init_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
  • Shape Tanimoto Field (shape_tani_field) type: Field Type: Float: Shape Tanimoto between the query and the fit molecule
    Default: Shape Tanimoto

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 EON 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