Ligand Identifier Reader Cube¶
A cube that reads the identifiers of ligands from a text file. Each line corresponds to one drug
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
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
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
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
Identification Number for the Molecule (Optional) (mol_id) type: string: This can be any identification number (e.g., CHEMBL ID) associated with the molecule.Leave the parameter empty to not change it.
Molecule Name (Optional) (mol_name) type: string: The name for the molecule. Leave the parameter empty to not change it.
Reference Permeability Coefficient (Logarithmic, Optional) (ref_perm) type: string: This can be a value determined by an experiment or determined by other methods as a referencefor comparison. The reference value should have a unit of cm/s and then converted to the log scale. An error can be included in a pair of parentheses, if available. Example input: -6.0 (0.1). Leave the parameter empty to not change it.
Reference Permeability Coefficient Source (Optional) (ref_src) type: string: Source of the reference permeability coefficient, which can be the type of the experiment orthe name of the method that used to determine permeability. Leave the parameter empty to not change it.
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
Log Verbosity (verbosity) type: string: verbose levelDefault: debugChoices: info, warning, error, debug, ddebug
Field parameters¶
Dry Molecule Field (dry_molecule_field) type: Field Type: Chem.Mol: Field containing the unsolvated molecule.Default: Dry Molecule
Experiment Type Field (experiment_type_field) type: Field Type: String: Field containing the type of the permeability experiment.Default: Experiment Type
Log Experimental Permeability Field (experimental_permeability_field) type: Field Type: FloatVec: Field containing the experimentally measured permeability and their variance (or standard deviation) in log-scale.Default: Log Experimental Permeability
Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log fieldDefault: Extended Log Field
Log Field (log_field) type: Field Type: String: The field to store messages to floe reportDefault: Log Field
Molecule with Membrane Field (membrane_molecule_field) type: Field Type: Chem.Mol: Field containing the solvated molecule and the membrane.Default: Molecule with Membrane
Molecule ID Field (mol_id_field) type: Field Type: String: Field containing the identification number of the molecule.Default: Molecule ID
Molecule Name Field (mol_name_field) type: Field Type: String: Field containing the name of the molecule.Default: Molecule Name
Primary Molecule Field (primary_molecule_field) type: Field Type: Chem.Mol: Field containing the primary molecule.
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
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