Molecule Highlighting (Stick Style)

This cube generates a 2D depiction with highlighted atoms and bonds, using the ‘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.

Example of molecule highlighting using the ‘stick’ style

Upstream Cubes

• SMARTS Substructure Map

• Molecule Substructure Map

See also

• OEHighlightByStick in OEDepict TK manual

• Highlighting section in OEDepict TK manual

Related Cubes

• Parallel Molecule Highlighting (Stick Style) – parallel version of the cube

• Molecule Multi Highlighting (Stick Style)

• Molecule Highlighting

• Molecule Highlighting (Color Style)

• Molecule Highlighting (Ball And Stick Style)

• Molecule Highlighting (Lasso Style)

• Molecule Highlighting (Cogwheel 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 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
• 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
• Atom External Highlight Ratio (external_highlight) type: decimal: The ratio of the external highlight of the atoms i.e. atom highlights are extended to bonds not being highlighted.

  Default: 0.0 , Max: 0.5
• 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
• Atom External Highlight Ratio (None) type: decimal: The ratio of the external highlight of the atoms i.e. atom highlights are extended to bonds not being highlighted.

  Default: 0.0 , Max: 0.5

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

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Parallel Molecule Highlighting (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