Atropisomerism

This cube determines whether molecules have atropisomerism or not.

Molecules are read from the field specified by the Input Molecule Field parameter, and the atropisomerism is stored in the field specified by the Atropisomerism Field paramter. The record is then sent to the success port.

Related Cubes

Parallel Atropisomerism – 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

Force Field (ff_type) type: string: Built-in force field model to be used.

Default: sage

Choices: mmff94s, parsley, sage

GPUs (gpu_count) type: integer: The number of GPUs to run this cube with

Default: 0 , Max: 16

Delta (in_delta) type: decimal: Determines the number of points in that is (360.0/delta+1) in the [0.0,360.0] degree range for the torsion scan.

Default: 30.0 , Min: 0.1, Max: 60.0

Solvent model (in_solvent_type) type: string: Solvent model to be used for ligand

Default: Gas-phase

Choices: Gas-phase, Sheffield, PB, SheffieldPB

Torsion Energy Field (in_torsion_energy) type: decimal: Torsion energy (kcal/mol) used to decide if atropisomerism exits in a molecule. If the molecule has one or more torsion energy greater than this value, atropisomerism exits.

Default: 12.0 , Min: 1.0, Max: 1000.0

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

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

Field parameters

Atropisomerism Field (atropisomerism_field) type: Field Type: Bool: The tag name of the atropisomerism field.

Default: Atropisomerism

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

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 Atropisomerism

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