Fingerprint Set Similarity Calculation¶
Parameter Details¶
Calculation Parameters¶
CPUs (integer) : The number of CPUs to run this cube withDefault: 1 Min: 1 Max: 128
Cube Metrics (string) : Set of metrics to be collectedChoices: cpu, disk, memory, network
Temporary Disk Space (MiB) (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 (integer) : The number of GPUs to run this cube withDefault: 0 Max: 16
Instance Tags (string) : Only run on machines with matching tags (comma separated)Default: “”
Instance Type (string) : The type of instance that this cube needs to be run on
Memory (MiB) (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 (decimal) : How often to sample metrics, in secondsDefault: 60 Min: 1 Max: 300
Maximum Similarity Score Cutoff (decimal) : The cutoff score for similarity calculation.
Similarity Measure (string) : The similarity measure used to 2D similarity calculation.Default: TanimotoChoices: Cosine, Dice, Euclid, Manhattan, Tanimoto, Tversky
Minimum Similarity Score Cutoff (decimal) : The cutoff score for similarity calculation.
Spot policy (string) : Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required
Field parameters¶
Histogram Counts (Field Type: FloatVec) : The field to store histogram counts of similarity calculation.Default: Histogram Counts
Histogram Bin Centers (Field Type: FloatVec) : The field to store histogram bin centers of similarity calculation.and molecules.Default: Histogram Bin Centers
Fingerprint Field (Field Type: Chem.FingerPrint) : Tag name for the field that stores fingerprints.
Fingerprint Set (Field Type: RecordVec) : Fingerprint record sets
Histogram Bin Centers (Field Type: FloatVec) : The field to store histogram bin centers of similarity calculation.and molecules.Default: Histogram Bin Centers
Histogram Counts (Field Type: FloatVec) : The field to store histogram counts of similarity calculation.Default: Histogram Counts
Similarity Score Field (Field Type: Float) : Name for the field that stores fingerprint similarity scores.
UUID (Field Type: String) : The field to store unique identifiers for fingerprints and molecules.
2D Similarity Parameters¶
The parameters of the 2D fingerprint similarity calculation.
Similarity Measure (string) : The similarity measure used to 2D similarity calculation.Default: TanimotoChoices: Cosine, Dice, Euclid, Manhattan, Tanimoto, Tversky
Minimum Similarity Score Cutoff (decimal) : The cutoff score for similarity calculation.
Maximum Similarity Score Cutoff (decimal) : The cutoff score for similarity calculation.
Hardware Parameters¶
Machine hardware requirements
Memory (MiB) (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
Temporary Disk Space (MiB) (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 (integer) : The number of GPUs to run this cube withDefault: 0 Max: 16
CPUs (integer) : The number of CPUs to run this cube withDefault: 1 Min: 1 Max: 128
Instance Type (string) : The type of instance that this cube needs to be run on
Spot policy (string) : Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required
Instance Tags (string) : Only run on machines with matching tags (comma separated)Default: “”
Metrics Parameters¶
Cube Metric Parameters
Metric Period (decimal) : How often to sample metrics, in secondsDefault: 60 Min: 1 Max: 300
Cube Metrics (string) : Set of metrics to be collectedChoices: cpu, disk, memory, network
Parallel Fingerprint Set Similarity Calculation
The parallel version adds these extra parameters.
Number of messages to distribute at a time (integer) : The maximum number of messages to bundle together for a parallel cube.Default: 1 Min: 1 Max: 65535
Maximum Failures (integer) : The maximum number of times to attempt processing a work itemDefault: 10 Min: 1 Max: 100
Autoscale this Cube (boolean) : If True, let Orion manage the parallelism of this CubeDefault: True
Maximum number of Cubes (integer) : The maximum number of concurrently running copies of this CubeDefault: 1000 Min: 1
Minimum number of Cubes (integer) : The minimum number of concurrently running copies of this CubeDefault: 0
Tip
filename: cheminfo/graphsim/sim2d_set_calc.py