Molecular Complexity Calculation¶

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This cube calculates the total molecular complexity descriptor for molecules.

Input molecules are read from the field specified by the Input Molecule Field parameter. The generated descriptor is stored in the field specified by the Total Molecular Complexity Field parameter, and the record is sent to the success port. If the calculation fails, the record is sent to the failure port.

If the Export Complexity Terms parameter is set, then additional complexity descriptors are also calculated. See fields listed in the Field parameters section.

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

Export Complexity Terms (details) type: boolean: This parameter determines whether to output all the terms that are used to generate the total molecular complexity value

Default: False

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¶

Connectivity Complexity Field (conncomplex) type: Field Type: Float: The name of the molecular connectivity complexity field

Default: Connectivity Complexity

Elemental Complexity Field (elemcomplex) type: Field Type: Float: The name of the molecular elemental complexity field

Default: Elemental Complexity

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

Total Molecular Complexity Field (molcomplex) type: Field Type: Float: The name of the total molecule complexity field

Default: Total Molecular Complexity

Normal Molecular Complexity Filed (normalmol) type: Field Type: Float: The name of the normal molecular complexity field

Default: Normal Molecular Complexity

Normal Stereo Complexity Field (normalste) type: Field Type: Float: The name of the normal stereo complexity field

Default: Normal Stereo Complexity

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 Molecular Complexity Calculation

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