Molecule Substructure Map

This cube finds substructure matches of input molecules against a molecule query, and annotates the matching atoms and bonds. Input molecules are read from the field specified by the Input Molecule Field parameter. The substructure is read from the first record on the init initialization port, from the field specified by the Query Field parameter.

Upon successful substructure search, the atoms and bonds of the first match are annotated in the target molecule with the tag specified by the Match Tag parameter. The annotated molecule is stored in the field specified by the Output Molecule Field parameter, and the record is sent to the success port. If no match is detected, the record is sent to the failure port.

Note

This cube has to modify the input molecule (performing necessary perceptions and adding/suppressing hydrogens prior to performing the substructure search). These changes will persist in the output molecule, when the record is sent to the success port.

See also

• Substructure Search section in OEChem TK manual

Related Cubes

• Parallel Molecule Substructure Map – parallel version of the cube

• SMARTS Substructure Map

Calculation Parameters

• Atom Expression Options (atom_expr) type: string: Atom expression flag that controls how atoms are matched.

  Default: DefaultAtoms

  Choices: AutomorphAtoms, DefaultAtoms, ExactAtoms
• Bond Expression Options (bond_expr) type: string: Bond expression flag that controls how bonds are matched.

  Default: DefaultBonds

  Choices: AutomorphBonds, DefaultBonds, ExactBonds
• 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
• Hydrogen Handling (hydrogen_handling) type: string: This parameter determines whether to suppress or add explicit hydrogens to the target molecules prior to performing the substructure search.

  
  

  Choices: AddExplicitHydrogens, SuppressHydrogens
• 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
• Match Tag (match_tag) type: string: The tag that is used to identify matched atoms and bonds.

  Default: selection
• 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:
• Query Field (init_mol_field) type: Field Type: Chem.Mol: The name of the field that stores the query molecule on the initialization record. If left blank the primary molecule field will be used.
• None (out_mol_field) type: Field Type: Chem.Mol:

Substructure Search Parameters

The parameters of substructure search.

• Hydrogen Handling (None) type: string: This parameter determines whether to suppress or add explicit hydrogens to the target molecules prior to performing the substructure search.

  
  

  Choices: AddExplicitHydrogens, SuppressHydrogens
• Match Tag (None) type: string: The tag that is used to identify matched atoms and bonds.

  Default: selection
• Atom Expression Options (None) type: string: Atom expression flag that controls how atoms are matched.

  Default: DefaultAtoms

  Choices: AutomorphAtoms, DefaultAtoms, ExactAtoms
• Bond Expression Options (None) type: string: Bond expression flag that controls how bonds are matched.

  Default: DefaultBonds

  Choices: AutomorphBonds, DefaultBonds, ExactBonds

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 Molecule Substructure Map

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