Brood Hit list¶
This cube builds a hit list from the input BROOD matches. The generated hit list records are emitted through the success port.
Calculation Parameters¶
Attachment Scale (attach_scale) type: decimal: Scale factor weighting the importance of attachment pointsDefault: 1.5 , Min: 1.0, Max: 10.0 Bump Radius (bump_radius) type: decimal: Protein-ligand bump radiusDefault: 2.25 , Min: 1.0, Max: 5.0 Check Bond (check_bond) type: boolean: Check for chemically stable attachment bondsDefault: True 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 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 Generate idea (idea) type: boolean: Generate cluster information for hitlistsDefault: True 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-evaluatedDefault: 600 , Min: 300 Maximum Hits (max_hits) type: integer: Maximum number of desired hitsDefault: 1000 , Min: 1, Max: 50000 Maximum Local Strain (max_strain) type: decimal: Maximum local strain allowed in analogsDefault: 6.5 , Min: 1.0, Max: 100.0 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 Neutral PH (neutral_ph) type: boolean: Apply neutral pH model to newly constructed analogsDefault: True Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPUDefault: 32 Score type (score_type) type: string: Score type to be used for OverlayDefault: rocsChoices: rocs, ET, LinkOnly 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 tautomers (tautomers) type: boolean: Apply reasonable tautomer model to newly constructed analogsDefault: False
Field parameters¶
Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log fieldDefault: Extended Log Field None (in_query_field) type: Field Type: Chem.Mol: Input Scores (in_scores_field) type: Field Type: RecordVec: Input Scores fieldDefault: Scores Log Field (log_field) type: Field Type: String: The field to store messages to floe reportDefault: Log Field p(F>10%) Out Field (out_abbott_field) type: Field Type: Float: Field to store pfgt10 percent infoDefault: p(F>10%) AroRingCt Out Field (out_arom_ring_field) type: Field Type: Int: Field to store aroringct infoDefault: AroRingCt Attach Out Field (out_attach_field) type: Field Type: Float: Field to store attach infoDefault: attach ClusterID Out Field (out_cluster_idx_field) type: Field Type: Int: Field to store clusterid infoDefault: ClusterID Color Out Field (out_color_field) type: Field Type: Float: Field to store color infoDefault: color Combo Out Field (out_combo_field) type: Field Type: Float: Field to store combo infoDefault: combo Complexity Out Field (out_complexity_field) type: Field Type: Float: Field to store complexity infoDefault: Complexity Fragment Out Field (out_fragment_field) type: Field Type: String: Field to store fragment infoDefault: Fragment Freq Out Field (out_freq_field) type: Field Type: Int: Field to store freq infoDefault: freq fsp3C Out Field (out_fsp3c_field) type: Field Type: Float: Field to store fsp3c infoDefault: fsp3C HvyAtoms Out Field (out_heavy_field) type: Field Type: Int: Field to store hvyatoms infoDefault: HvyAtoms LipinskiAcc Out Field (out_lipinski_acc_field) type: Field Type: Int: Field to store lipinskiacc infoDefault: LipinskiAcc LipinskiDon Out Field (out_lipinski_don_field) type: Field Type: Int: Field to store lipinskidon infoDefault: LipinskiDon LipinskiFail Out Field (out_lipinski_fail_field) type: Field Type: Int: Field to store lipinskifail infoDefault: LipinskiFail LocalStrain Out Field (out_local_strain_field) type: Field Type: Float: Field to store localstrain infoDefault: Local Strain None (out_mol_field) type: Field Type: Chem.Mol: p(active) Out Field (out_pactive_field) type: Field Type: Float: Field to store pactive infoDefault: p(active) PB Out Field (out_pb_field) type: Field Type: Float: Field to store PB electrostatics infoDefault: PB RingCt Out Field (out_ring_field) type: Field Type: Int: Field to store ringct infoDefault: RingCt Ring Ratio Out Field (out_ring_ratio_field) type: Field Type: Float: Field to store ringratio infoDefault: RingRatio Rotors Out Field (out_rotors_field) type: Field Type: Int: Field to store rotors infoDefault: Rotors Shape Out Field (out_shape_field) type: Field Type: Float: Field to store shape infoDefault: shape tPSA Out Field (out_tpsa_field) type: Field Type: Float: Field to store tpsa infoDefault: tPSA XLogP Out Field (out_xlogp_field) type: Field Type: Float: Field to store xlogp infoDefault: XLogP
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