Flipper

This cube either performs a stereo enumeration or passes through: intake port molecules to the success port, based on the desired stereo behavior flag.

Related Cubes

Parallel Flipper – 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

Enhanced Stereo Info (enhanced_stereo) type: boolean: Consider enhanced stereo information during enumeration.

Default: True

Enumerate Nitrogen (enum_nitrogen) type: boolean: Flag indicating if non-planar nitrogens should be enumerated as possible stereo centers.

Default: False

Apply flipper warts (flipper_warts) type: boolean: Add wart to title of each stereoisomer.

Default: True

Force flip (force_flip) type: boolean: Flag indicating if all stereo centers should be enumerated. By default, only unspecified stereo centers are enumerated.

Default: False

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

Maximum stereo centers (max_centers) type: integer: The maximum number of stereo centers to enumerate. The maximum number of molecules generated is 2 to the power of N, where N is the number of stereo centers

Default: 12 , Min: 1, Max: 50

Max Rotors (max_rotors) type: integer: Cutoff of rotatable bonds. The cube will skip molecules with rotors more than the cutoff.

Default: 40 , Min: 1, Max: 9999

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

Stereo Behavior (stereo_flag) type: string: Specify if stereo centers should be enumerated or randomly chosen, for molecules with unspecified stereo-chemistry.

Default: Enumeration

Choices: Enumeration, Random

Field parameters

Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field

Default: Extended Log Field

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

Log Field (log_field) type: Field Type: String: The field to store messages to floe report

Default: Log Field

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

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 Flipper

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