Molecule Depiction with Bond Indices

This cube generates a 2D depiction with bond indices displayed.

The input molecule is read from the field specified by the Input Molecule Field parameter. The generated SVG image is stored in the field specified by 2D Depiction Field and the record is sent to the success port.

The molecule depiction can be customized using the parameters listed in the Image Parameters, Molecule Depiction Parameters and Property Depiction Parameters sections.

Example of depicting bond indices using 'toggle' style
(bonds with attached data are marked with black circles)

Upstream Cubes

• Prepare Molecule for 2D Depiction

See also

• Molecule Depiction section in OEDepict TK manual

Related Cubes

• Parallel Molecule Depiction with Bond Indices – parallel version of the cube

• Molecule Depiction

• Molecule Depiction with Bond oechem.Types

• Molecule Depiction with Bond Data

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: WhiteCPK

  Choices: WhiteCPK, BlackCPK, WhiteMonochrome, BlackMonochrome
• 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
• 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
• Property Mark (property_mark) type: boolean: This parameter determines whether to mark atom/bonds if their property are displayed in in the interactive styles (‘Hover’ or ‘Toggle’).

  Default: False
• Property Render Style (property_render_style) type: string: This parameter determines whether the atom/bond property will be displayed permanently in a static image or displayed when hovering over or clicking on an atom or a bond in an interactive image.

  Default: Permanent

  Choices: Permanent, Hover, Toggle
• 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
• 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:

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
• Atom Color Style (None) type: string: The atom color style of molecule depiction.

  Default: WhiteCPK

  Choices: WhiteCPK, BlackCPK, WhiteMonochrome, BlackMonochrome
• Title Location (None) type: string: The position of the title in molecule depiction.

  Default: Hidden

  Choices: Top, Bottom, Hidden

Property Depiction Parameters

The parameters of atom/bond property depiction.

• Property Render Style (None) type: string: This parameter determines whether the atom/bond property will be displayed permanently in a static image or displayed when hovering over or clicking on an atom or a bond in an interactive image.

  Default: Permanent

  Choices: Permanent, Hover, Toggle
• Property Mark (None) type: boolean: This parameter determines whether to mark atom/bonds if their property are displayed in in the interactive styles (‘Hover’ or ‘Toggle’).

  Default: False

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 Depiction with Bond Indices

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