Atom Property Depiction (Molecule Surface Style)

This cube depicts atom properties using the molecule surface style.

Calculation Parameters

  • Add Signature (add_signature) type: boolean: This parameter controls whether a signature is drawn at the bottom right corner of the image.
    Default: True
  • Aromaticity Style (aromatic_style) type: string: The aromaticity style of molecule depiction.
    Default: Kekule
    Choices: Kekule, Circle, Dash
  • Atom Tag (atom_tag) type: string: The tag that used to attach properties to atoms being visualized.
  • 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
  • Draw Border (draw_border) type: boolean: This parameter controls whether a border is drawn around the generated image.
    Default: False
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Image Height (image_height) type: integer: The height of the generated image.
    Default: 200 , Min: 100, Max: 1000
  • Image Width (image_width) type: integer: The width of the generated image.
    Default: 300 , Min: 100, Max: 1000
  • 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
  • Maximum Atom Property Value (max_value) type: decimal: The maximum value of atom property.
  • 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
  • Minimum Atom Property Value (min_value) type: decimal: The minimum value of atom property.
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Property Render Style (property_render_style) type: string: This parameter determines whether the atom/bond property will be displayed when hovering over or clicking on atoms/bond in an interactive image.
    Default: NoOp
    Choices: Hover, Toggle, NoOp
  • None (record_cache_size) type: integer:
    Default: 1000
  • 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

  • 2D Depiction Field (depiction_field) type: Field Type: String: The name of the field that stores the 2D depiction in SVG image format.
    Default: “”
  • None (in_mol_field) type: Field Type: Chem.Mol:

Image Parameters

The parameters of the generated image.
  • Image Width (None) type: integer: The width of the generated image.
    Default: 300 , Min: 100, Max: 1000
  • Image Height (None) type: integer: The height of the generated image.
    Default: 200 , Min: 100, Max: 1000
  • Draw Border (None) type: boolean: This parameter controls whether a border is drawn around the generated image.
    Default: False
  • Add Signature (None) type: boolean: This parameter controls whether a signature is drawn at the bottom right corner of the image.
    Default: True

Molecule Depiction Parameters

The parameters of 2D molecule depiction.
  • Aromaticity Style (None) type: string: The aromaticity style of molecule depiction.
    Default: Kekule
    Choices: Kekule, Circle, Dash

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