Prepare Molecule for 2D Depiction

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This cube generates 2D coordinates for an input molecule.

The molecule is read from the field specified by the Input Molecule Field parameter. If no Output Molecule Field Name parameter is set, the molecule with 2D coordinates will be stored in the same field.



Note

All molecule depiction cubes will generate 2D coordinates ‘on-the-fly’ if necessary prior to rendering. Using the Prepare Molecule for 2D Depiction cube is recommended if a specific orientation or layout is preferred.

Hint

This cube removes 3D conformation of the primary molecules by default. In order to preserve the original coordinates, please specify the Output Molecule Field Name parameter.

Downstream Cubes

Any depiction cube that visualizes 2D information for examples:

See also

Related Cubes

Calculation Parameters

  • Clear Coordinates (clear_coords) type: boolean: Clear and regenerate 2D coordinates of molecules. If the molecule has no 2D coordinates, then the 2D coordinates will be generated regardless of this setting.
    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
  • Depict Orientation (depict_orientation) type: string: The parameter that determines the preferred orientation of 2D coordinates
    Default: Horizontal
    Choices: Original, Square, Horizontal, Vertical
  • 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
  • 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
  • Output Molecule Field Name (out_mol_field_name) type: string: If set, molecules with 2D coordinates will be stored in the field with this name.
  • 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
  • Suppress Hydrogens (suppress_hydrogens) type: boolean: Suppress explicit (non-depiction) hydrogens in the molecule. Only hydrogens that are necessary to faithfully represent tetrahedral stereo-chemistry will be kept.
    Default: True

Field parameters

  • Input Molecule Field (in_mol_field) type: Field Type: Chem.Mol:

Prepare Depiction Parameters

The parameters to prepare 2D coordinates for depiction.
  • Output Molecule Field Name (None) type: string: If set, molecules with 2D coordinates will be stored in the field with this name.
  • Clear Coordinates (None) type: boolean: Clear and regenerate 2D coordinates of molecules. If the molecule has no 2D coordinates, then the 2D coordinates will be generated regardless of this setting.
    Default: False
  • Suppress Hydrogens (None) type: boolean: Suppress explicit (non-depiction) hydrogens in the molecule. Only hydrogens that are necessary to faithfully represent tetrahedral stereo-chemistry will be kept.
    Default: True
  • Depict Orientation (None) type: string: The parameter that determines the preferred orientation of 2D coordinates
    Default: Horizontal
    Choices: Original, Square, Horizontal, Vertical

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 Prepare Molecule for 2D 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