Multistate pKaModel-based Ionization States Enumeration

This cube enumerates the reasonable pKa states of input molecules at neutral pH based on pKa assessed using the multistate pKa model.

The resulting molecules are added to the input record as a vector of molecules and emitted through the success port.

Calculation Parameters

CPUs (cpu_count) type: integer: The number of CPUs to run this cube with

Default: 1 , Min: 1, Max: 192

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: decimal: 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 Ionization States (max_count) type: integer: The maximum number of ionization states to enumerate.

Default: 256 , Min: 1, Max: 5000

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

Switch (switch) type: boolean: Output every possible ionization state as an individual molecule.

Default: True

To depict atomic pKaRange or not (todepictpkarange) type: boolean: Toggle to select whether to depict atomic pKaRange as assesed by Multistate pKamodel.

Default: False

Field parameters

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

Default: Extended Log Field

Failure Reason (failure_reason) type: Field Type: String: Failure Reason

Default: Failure Reason

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

Ionization States Vector (pka_states) type: Field Type: Chem.MolVec: Output record field with the vector of enumerated possible ionization states

Default: Ionization States Vector

Atomic pKaRange (svgdepictpkarange) type: Field Type: String: Atomic pKaRange as assesed by Multistate pKamodel.

Default: Atomic pKaRange

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: decimal: 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: 192
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 Multistate pKaModel-based Ionization States Enumeration

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

Starting number of Cubes (scaleup_start) type: integer: The initial number of concurrently running copies of this Cube

Default: 2 , Min: 1