Omega Conformation

This cube generates conformers for input molecules, using

torsion driving.

The generated conformers are added to the input record and emitted through the success port.

Related Cubes

• Parallel Omega Conformation – parallel version of the cube

• Generate 3D

• Omega Conformation (dense mode)

• Omega Conformation (ROCS mode)

• Omega Conformation (pose mode)

Calculation Parameters

• Clear Fragments Library (clear_frag_lib) type: boolean: Flag indicating if internal fragments library should not be used

  Default: False
• 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
• Enumerate Nitrogen (enum_nitrogen) type: string: If conformers should be enumerated for invertible Nitrogen stereo

  Default: unspecified

  Choices: unspecified, all, off
• Enumerate Ring (enum_ring) type: boolean: If conformers should be enumerated for ring stereo

  Default: True
• Energy Window (ewindow) type: decimal: Energy window for conformer selection.

  Default: 10.0 , Min: 0.001, Max: 500.0
• Fix MCS (fix_mcs) type: boolean: If MCS should be used to fix part of molecule

  Default: False
• Fix Smarts (fix_smarts) type: string: (Optional) Set a string for SMARTS pattern matching to fix a portion of the fix molecule primarily or the input molecule secondarily. Molecules that do not match will be sent to the fail output. When the fix molecule is not provided, the input molecule has to be 3D and Stereo Behavior has to be Random.

  Default: “”
• GPUs (gpu_count) type: integer: The number of GPUs to run this cube with

  Default: 0 , Max: 16
• Ignore Stereo (ignore_stereo) type: boolean: If failure to respect stereo should be ignored

  Default: False
• Fragments library file (in_frag_file_field) type: file_in:
• 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 number of conformers (max_confs) type: integer: Maximum number of conformations to generate

  , Max: 100000
• Max Rotors (max_rotors) type: integer: Cutoff of rotatable bonds. The cube will skip molecules with rotors more than the cutoff.

  Default: 40 , Min: 1, Max: 9999
• 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
• Conformer generation mode (mode) type: string: Pre-set mode for generating conformers suitable for specific downstream application

  Default: Classic

  Choices: Classic, ROCS, Pose, FastROCS, Dense
• Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU

  Default: 32
• RMS Threshold (rms) type: decimal: RMS threshold for duplicate conformer removal

  Default: 0.5 , Max: 100.0
• Sample Hydrogen (sample_hydrogen) type: boolean: If hydrogen sampling should be done on conformers

  Default: False
• 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
• Strict Stereo (strict_stereo) type: boolean: Flag indicating if all chiral atoms and bonds must have specified stereo.

  Default: True
• Torsion Library Type (torlib_type) type: string: Specify the type of torsion library.

  Default: Original

  Choices: Original, Guba
• Apply warts (warts) type: boolean: Generate unique titles for conformers that reflect their position in the ensemble of conformations

  Default: False

Field parameters

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

  Default: Extended Log Field
• None (in_fix_mol_field) type: Field Type: Chem.Mol:
• 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
• None (out_mol_field) type: Field Type: Chem.Mol:
• Number of Conformers Field (out_num_confs_field) type: Field Type: Int: Field to store the number of conformers

  Default: Number of Confs

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 Omega Conformation

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