Molecule Highlighting¶
This cube generates a 2D depiction, highlighting tagged atoms and bonds using various styles.
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 is determined by the Highlight Style and Highlight Color parameters. The molecule depiction can be customized using the parameters listed in the Image Parameters and Molecule Depiction Parameters sections.
The generated SVG image is stored in the field specified by 2D Depiction Field and the record is sent to the success port.
Example of molecule highlighting using the ‘lasso’ style¶
Upstream Cubes
See also
OEHighlightStyle in OEDepict TK manual
Highlighting section in OEDepict TK manual
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: KekuleChoices: Kekule, Circle, Dash Atom Color Style (atom_color_style) type: string: The atom color style of molecule depiction.Default: WhiteMonochromeChoices: WhiteCPK, BlackCPK, WhiteMonochrome, BlackMonochrome CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 1 , Min: 1, Max: 128 Cube Metrics (cube_metrics) type: string: Set of metrics to be collectedChoices: 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 withDefault: 0 , Max: 16 Highlight Color (highlight_color) type: string: The color used to highlight atoms or/and bondsDefault: RedChoices: Black, Blue, BlueTint, DarkRed, Green, GreenTint, Grey, PinkTint, Red, Yellow, White Highlight Style (highlight_style) type: string: The style used to highlight atoms or/and bondsDefault: StickChoices: Color, Stick, BallAndStick, Cogwheel, Lasso 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-evaluatedDefault: 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 secondsDefault: 60Choices: 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 CPUDefault: 32 Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to addressDefault: 64 Spot policy (spot_policy) type: string: Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required Title Location (title_location) type: string: The position of the title in molecule depiction.Default: HiddenChoices: 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 Style (None) type: string: The style used to highlight atoms or/and bondsDefault: StickChoices: Color, Stick, BallAndStick, Cogwheel, Lasso
- Highlight Color (None) type: string: The color used to highlight atoms or/and bondsDefault: RedChoices: Black, Blue, BlueTint, DarkRed, Green, GreenTint, Grey, PinkTint, Red, Yellow, White
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: HiddenChoices: Top, Bottom, Hidden
- Aromaticity Style (None) type: string: The aromaticity style of molecule depiction.Default: KekuleChoices: Kekule, Circle, Dash
- Atom Color Style (None) type: string: The atom color style of molecule depiction.Default: WhiteMonochromeChoices: 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 addressDefault: 64
- Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPUDefault: 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-evaluatedDefault: 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 withDefault: 0 , Max: 16
- CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 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 instancesDefault: ProhibitedChoices: 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 secondsDefault: 60Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
- Cube Metrics (None) type: string: Set of metrics to be collectedChoices: cpu, disk, memory, network
Parallel Molecule Highlighting
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 itemDefault: 10 , Min: 1, Max: 100 Autoscale this Cube (autoscale) type: boolean: If True, let Orion manage the parallelism of this CubeDefault: True Maximum number of Cubes (max_parallel) type: integer: The maximum number of concurrently running copies of this CubeDefault: 1000 , Min: 1 Minimum number of Cubes (min_parallel) type: integer: The minimum number of concurrently running copies of this CubeDefault: 0