Omega Macrocycle¶
- This cube generates conformers for input molecules, using
distance geometry. This is especially suitable for conformer generation of macrocycle molecules.
The generated conformers are added to the input record and emitted through the success port.
Calculation Parameters¶
CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 1 , Min: 1, Max: 128 Cube Metrics (cube_metrics) type: string: Set of metrics to be collectedChoices: cpu, disk, memory, network Dielectric constant (dielectric) type: decimal: Solvent dielectric constantDefault: 80.0 , Max: 100.0 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 Energy Window (ewindow) type: decimal: Energy window for conformer selection.Default: 20.0 , Max: 500.0 GPUs (gpu_count) type: integer: The number of GPUs to run this cube withDefault: 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 Iteration cycle size (iter_cycle) type: integer: Number of conformers generated per iteration cycleDefault: 100 , Max: 100000 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-evaluatedDefault: 600 , Min: 300 Maximum number of conformers (max_confs) type: integer: Maximum number of conformations to generateDefault: 400 , Min: 1, Max: 100000 Maximum number of iterations (max_iter) type: integer: Maximum number of iterations for convergenceDefault: 2000 , 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 secondsDefault: 60Choices: 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 CPUDefault: 32 Refinement tolerance (ref_tolerance) type: decimal: Optimizer tolerance for structure refinementDefault: 0.001 , Max: 1.0 Refine structure (refine) type: boolean: Refine structure after DG constructionDefault: True RMS Threshold (rms) type: decimal: RMS threshold for duplicate conformer removalDefault: 0.5 , Max: 100.0 Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to addressDefault: 64 Spot policy (spot_policy) type: string: Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required
Field parameters¶
Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log fieldDefault: Extended Log Field None (in_mol_field) type: Field Type: Chem.Mol: Log Field (log_field) type: Field Type: String: The field to store messages to floe reportDefault: Log Field Number of Conformers Field (num_confs_field) type: Field Type: Int: Field to store the number of conformersDefault: Number of Confs None (out_mol_field) type: Field Type: Chem.Mol:
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 addressDefault: 64
- Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPUDefault: 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-evaluatedDefault: 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 withDefault: 0 , Max: 16
- CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 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 instancesDefault: ProhibitedChoices: 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 secondsDefault: 60Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
- Cube Metrics (None) type: string: Set of metrics to be collectedChoices: cpu, disk, memory, network
Parallel Omega Macrocycle
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 itemDefault: 10 , Min: 1, Max: 100 Autoscale this Cube (autoscale) type: boolean: If True, let Orion manage the parallelism of this CubeDefault: True Maximum number of Cubes (max_parallel) type: integer: The maximum number of concurrently running copies of this CubeDefault: 1000 , Min: 1 Minimum number of Cubes (min_parallel) type: integer: The minimum number of concurrently running copies of this CubeDefault: 0