Topological Polar Surface Area Depiction

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

This cube creates a depiction showing atomic contributions to topological polar surface area (TPSA).

A “white to dark blue” linear color gradient is used to visualize TPSA atom contributions on the 2D molecule surface, where the darker colors and longer spikes indicate larger contributions.

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

The tag that identifies the pre-generated contributions attached to each atom is specified by the TPSA Atom Tag parameter. The Topological Polar Surface Area Calculation cube can be used upstream to generate these atom contributions.

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

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

Example of depicting TPSA atom contributions

../../../../../_images/DepictTopologicalPolarSurfaceAreaCube.svg

Upstream Cubes

Related Cubes

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
  • TPSA Atom Tag (atom_tag) type: string: The tag is used to store TPSA atom contributions.
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 192
  • 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: decimal: 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
  • Interactive Legend (interactive_legend) type: boolean: The parameter that defines whether an interactive legend is added to the generated image.
    Default: True
  • 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 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
  • 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.
  • 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

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 when hovering over or clicking on atoms/bond in an interactive image.
    Default: NoOp
    Choices: Hover, Toggle, NoOp
  • Interactive Legend (None) type: boolean: The parameter that defines whether an interactive legend is added to the generated image.
    Default: True

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: decimal: 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: 192
  • 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 Topological Polar Surface Area Depiction

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
  • Starting number of Cubes (scaleup_start) type: integer: The initial number of concurrently running copies of this Cube
    Default: 2 , Min: 1