Maximum Common Substructure Map

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This cube finds the maximum common substructure between input molecules and a query molecule.

The input molecules are read from the field specified by the Molecule Field parameter.

The query molecule is read from the first record on the init initialization port, from the field specified by the Query Field parameter.

The search algorithm can be customized by parameters listed in the Maximum Substructure Search Parameters section. The atoms and bonds of the first match are annotated in the molecule by utilizing the tag specified by the Match Tag parameter.

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

Note

For performance reason, hydrogen atoms are ignored during the search process.

See also

Related Cubes

Calculation Parameters

  • Atom Expression Options (atom_expr) type: string: Atom expression flag that controls how atoms are matched.
    Default: DefaultAtoms
    Choices: AutomorphAtoms, DefaultAtoms
  • Bond Expression Options (bond_expr) type: string: Bond expression flag that controls how bonds are matched.
    Default: DefaultBonds
    Choices: AutomorphBonds, DefaultBonds
  • 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
  • Match Tag (match_tag) type: string: The tag that is used to identify matched atoms and bonds.
  • 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
  • Minimum Atom Match (min_atoms) type: integer: The minimum number of atoms in a match that can be returned as a maximum common substructure.
    Default: 5 , Min: 3
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • MCS Search Type (search_type) type: string: The type of the maximum common substructure search algorithm.
    Default: Approximate
    Choices: Exhaustive, Approximate
  • 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

  • Molecule Field (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.

Maximum Substructure Search Parameters

The parameters of maximum substructure search.
  • MCS Search Type (None) type: string: The type of the maximum common substructure search algorithm.
    Default: Approximate
    Choices: Exhaustive, Approximate
  • Minimum Atom Match (None) type: integer: The minimum number of atoms in a match that can be returned as a maximum common substructure.
    Default: 5 , Min: 3
  • Atom Expression Options (None) type: string: Atom expression flag that controls how atoms are matched.
    Default: DefaultAtoms
    Choices: AutomorphAtoms, DefaultAtoms
  • Bond Expression Options (None) type: string: Bond expression flag that controls how bonds are matched.
    Default: DefaultBonds
    Choices: AutomorphBonds, DefaultBonds

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 Maximum Common 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