Bemis Murcko Annotation

This cube annotates molecules with Bemis Murcko region oechem.Types.

Input molecules are read from the field specified by the Input Molecule Field parameter. The Bemis Murcko Region Type parameter controls what type of regions are annotated on the molecule with the tag specified by the Region Tag parameter.

If the Label Tag parameter is set, then atoms and bonds are also annotated with the region type. The additional parameters controlling the annotation are listed in the Annotation Parameters section.

The annotated molecule is stored in the field specified by the Output Molecule Field parameter, and the record is sent to the success port.

Downstream Cubes

• Subset Molecule

• Molecule Depiction with Atom Data

• Molecule Depiction with Bond Data

See also

• OEGetBemisMurcko in the OEMedChem TK manual

• Molecule Fragmentation section in OEMedChem TK manual

Related Cubes

• Parallel Bemis Murcko Annotation – parallel version of the cube

Calculation Parameters

• Clear Data (cleartag) type: boolean: This parameter determines whether to explicitly clear existing tagged data on the molecule.

  Default: True
• 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
• 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
• Label Tag (labeltag) type: string: The tag that is used to label Bemis Murcko regions for atoms/bonds

  Default: BM Region Label
• Tagged Objects (markobjs) type: string: This parameter determines whether to tag atoms or/and bonds.

  Default: all

  Choices: atoms, bonds, all
• Bemis Murcko Region Type (markregion) type: string: This parameter determines which ‘Bemis Murcko’ region to tag on the molecule.

  Default: all

  Choices: all, ring, linker, framework, sidechain
• 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
• Region Tag (regiontag) type: string: The tag that is used to mark atoms/bonds that are in any Bemis Murcko region.

  Default: BM Region
• Apply Data (settag) type: string: This parameter determines whether to apply boolean data to all objects, or only the selected objects.

  Default: selected

  Choices: selected, all
• 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:
• None (out_mol_field) type: Field Type: Chem.Mol:

Annotation Parameters

The parameters that determine how the information is annotated on the molecule.

• Region Tag (None) type: string: The tag that is used to mark atoms/bonds that are in any Bemis Murcko region.

  Default: BM Region
• Label Tag (None) type: string: The tag that is used to label Bemis Murcko regions for atoms/bonds

  Default: BM Region Label
• Tagged Objects (None) type: string: This parameter determines whether to tag atoms or/and bonds.

  Default: all

  Choices: atoms, bonds, all
• Bemis Murcko Region Type (None) type: string: This parameter determines which ‘Bemis Murcko’ region to tag on the molecule.

  Default: all

  Choices: all, ring, linker, framework, sidechain
• Clear Data (None) type: boolean: This parameter determines whether to explicitly clear existing tagged data on the molecule.

  Default: True
• Apply Data (None) type: string: This parameter determines whether to apply boolean data to all objects, or only the selected objects.

  Default: selected

  Choices: selected, all

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

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Parallel Bemis Murcko Annotation

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