Molecular Formula Calculation

This cube generates molecular formulas for input molecules.

It reads molecules from the field specified in the Input Molecule Field parameter. and the molecular formulas are stored in the field specified by the Molecular Formula Field parameter. The record is then sent to the success port.

See also

• OEMolecularFormula in OEChem TK manual

Related Cubes

• Parallel Molecular Formula Calculation – 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: 192
• Cube Metrics (cube_metrics) type: string: Set of metrics to be collected

  
  

  Choices: cpu, disk, memory, network
• Dot Disconnect Formula (ddfmla) type: boolean: This parameter determines whether to generate the dot disconnect version of the molecular formula.

  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: 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
• Hydrogen Isotope Formula (isotope) type: boolean: This parameter determines whether to consider isotopic hydrogens when generating the molecular formula.

  Default: False
• 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

• None (in_mol_field) type: Field Type: Chem.Mol:
• Molecular Formula Field (molfmla) type: Field Type: String: The name of the molecular formula field.

  Default: Mol Formula

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

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

  Default: 2 , Min: 1