Molecule Highlighting (Ball And Stick Style)

../../../../../_images/DepictionCubeIcon.svg

This cube generates a 2D depiction with highlighted atoms and bonds, using the ‘ball and stick’ highlighting style.

The input molecule is read from the field specified by the Input Molecule Field parameter.

The tag that identifies the atoms and bond being highlighted is specified by the Highlight Tag parameter. The style of the highlighting can be customized by parameters listed in the Highlight Parameters section. The molecule depiction can be customized using the parameters listed in the Image Parameters and the Molecule Depiction Parameters sections.

The generated SVG image is stored in the field specified by the 2D Depiction Field paramter, and the record is sent to the success port.

../../../../../_images/HighlightByBallAndStickCube.svg

Example of molecule highlighting using the ‘ball and stick’ style

See also

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 Color Style (atom_color_style) type: string: The atom color style of molecule depiction.
    Default: WhiteMonochrome
    Choices: WhiteCPK, BlackCPK, WhiteMonochrome, BlackMonochrome
  • Atom Monochrome Label (atom_label_monochrome) type: boolean: The parameter that determines whether or not to change the label color of the highlighted atom(s).
    Default: False
  • Ball Radius Scale (ball_radius_scale) type: decimal: The multiplier that can be used to increase or decrease the ball radius of the highlighted atom(s).
    Default: 3.0 , Min: 0.5, Max: 5.0
  • 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
  • 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
  • Highlight Color (highlight_color) type: string: The color used to highlight atoms or/and bonds
    Default: Red
    Choices: Black, Blue, BlueTint, DarkRed, Green, GreenTint, Grey, PinkTint, Red, Yellow, White
  • Highlight Tag (highlight_tag) type: string: The tag that is used to mark atoms and bonds being highlighted.
    Default: selection
  • 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
  • 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
  • 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
  • Stick Width Scale (stick_width_scale) type: decimal: The multiplier that can be used to increase or decrease the stick width of the highlighted bond(s).
    Default: 3.0 , Min: 1.0, Max: 8.0
  • Title Location (title_location) type: string: The position of the title in molecule depiction.
    Default: Hidden
    Choices: Top, Bottom, Hidden

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: “”
  • Input Molecule Field (mol_field) type: Field Type: Chem.Mol:

Highlight Parameters

The parameters of highlighting.
  • Highlight Tag (None) type: string: The tag that is used to mark atoms and bonds being highlighted.
    Default: selection
  • Highlight Color (None) type: string: The color used to highlight atoms or/and bonds
    Default: Red
    Choices: Black, Blue, BlueTint, DarkRed, Green, GreenTint, Grey, PinkTint, Red, Yellow, White
  • Atom Monochrome Label (None) type: boolean: The parameter that determines whether or not to change the label color of the highlighted atom(s).
    Default: False
  • Stick Width Scale (None) type: decimal: The multiplier that can be used to increase or decrease the stick width of the highlighted bond(s).
    Default: 3.0 , Min: 1.0, Max: 8.0
  • Ball Radius Scale (None) type: decimal: The multiplier that can be used to increase or decrease the ball radius of the highlighted atom(s).
    Default: 3.0 , Min: 0.5, Max: 5.0

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.
  • Title Location (None) type: string: The position of the title in molecule depiction.
    Default: Hidden
    Choices: Top, Bottom, Hidden
  • Aromaticity Style (None) type: string: The aromaticity style of molecule depiction.
    Default: Kekule
    Choices: Kekule, Circle, Dash
  • Atom Color Style (None) type: string: The atom color style of molecule depiction.
    Default: WhiteMonochrome
    Choices: WhiteCPK, BlackCPK, WhiteMonochrome, BlackMonochrome

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 Molecule Highlighting (Ball And Stick Style)

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