Molecule Similarity Depiction¶

../../../../../_images/DepictionInitCubeIcon.svg

This cube depicts 2D molecule similarity to a reference molecule, based on 2D fingerprints.

The reference molecule is read from the init initialization port, from the field specified by the init_mol_field parameter.

The input molecules are read from the intake port, from the field specified by the in_mol_field parameter.

The type of the fingerprint on which the visualization is based on is determined by the Fingerprint Type parameter.

This cube uses “pink to yellow to dark green” linear color gradient to visualize molecular similarity. When there is 2D similarity detected between the two molecules, the color green is used to highlight the bonds and the color gets darker with increasing similarity. The color pink is used to highlight parts of the molecules that are not sharing any common fragments i.e. it represents dissimilarity.

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

Example of depiction of 2D molecular similarity

Related Cubes

Parallel Molecule Similarity Depiction – parallel version of the cube

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

Fingerprint Type (fingerprint_type) type: string: The fingerprint type generated for similarity calculation.

Default: Tree

Choices: Circular, Lingo, MACCS, Path, Tree

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¶

2D Similarity Depiction Field (depiction_field) type: Field Type: String: The name of the field that stores the 2D depiction in SVG image format.

Default: “”

None (in_mol_field) type: Field Type: Chem.Mol:

None (init_mol_field) type: Field Type: Chem.Mol: The name of the field on the initialization record that stores the query molecule. If left blank, the primary molecule field will be used.

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 Molecule Similarity 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