Shape and Color Overlap Depiction

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This cube generates two images, one depicting the shape overlap and the other depicting the color overlap between a fit molecule and a query (or reference) molecule.

The query molecule is read from the init initializer port, from the field specified by the Query Field parameter.

The fit molecules are read from the intake port, from the field specified by the Input Molecule Field parameter.

The shape overlap between the query and the fit molecule is visualized using the ‘property cloud’ style (see image below). In the generated image darker circles indicate better 3D shape overlap between the two molecules. The 2D molecule surface (dotted line) indicates the shape of the query molecule. When this 2D molecule surface is depicted on the image of the fit molecule, any clashes between the molecular graph and the dotted line imply a shape mismatch of the two molecules in 3D.

Color atom matches between the query and the fit molecule are represented by circles (or half circles if two color atoms occupy the same space in 3D). Each circle corresponds to a color atom in the query molecule. The color of the circle indicates the fitness of the color atom match in 3D. The lighter the color, the smaller the overlap between the reference and fit color atoms in 3D. Unfilled circles represent unmatched reference color atoms. If there is a good color atom match for a query color atom in 3D, then the circle representing the color atom is positioned on the matching fit color atom in 2D.

The generated SVG images are stored in the field specified by the Shape Overlap Depiction Field and Color Overlap Depiction Field parameters, and the record is sent to the success port.

Example of visualization of shape and color atom overlap

Example of visualizing color atom overlap
Hover the mouse over the "Query" button to reveal the corresponding
query molecule

Example of visualizing color atom overlap
Hover the mouse over the "Query" button to reveal the corresponding
query molecule and the "Legend" button to reveal the color atoms

Warning

No overlay is performed to maximize the shape and color overlap between molecules i.e. a molecule has to be pre-aligned to the query molecule beforehand.

Upstream Cubes

See also

Related Cubes

Calculation Parameters

  • 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
  • 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
  • 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

Field parameters

  • Color Overlap Depiction Field (color_overlap_field) type: Field Type: String: The name of the field that stores the color overlap depiction in SVG image format.
    Default: Color Overlap Depiction
  • None (in_mol_field) type: Field Type: Chem.Mol:
  • Query Field (init_mol_field) type: Field Type: Chem.Mol: The name of the field that stores the query molecule on the initialization record. If left blank the primary molecule field will be used.
  • Shape Overlap Depiction Field (shape_overlap_field) type: Field Type: String: The name of the field that stores the shape overlap depiction in SVG image format.
    Default: Shape Overlap Depiction

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 Shape and Color Overlap 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