OEMapper¶
The mapper cube produces edges made of ligand pairs to run relative binding affinity calculations. In general given N ligands N(N-1)/2 edges can be used to run RBFE calculations. The mapper selects a reasonable subset of these edges with the goal to keep the computational demand low. The edges are selected based on set of heuristics like ligand mcs similarities, equal charges and OpenEye rocs score. The mapper output can be used with the NES floe to run RBFE calculations. In order to have successful RBFE results the ligands should be similar and do not attempt large mutations. The Mapper cube can accept a edge text input a text file as well. In this case the produced map is defined in the provide text file and no attempt to use internal heuristics is done. The text file has the following syntax:
ligAname >> ligBname
where “ligAname” and “ligBname” are the ligand name titles for the ligands to be transformed.
- Input
Data record Stream - Streamed-in of a set of similar ligands with 3D coordinates and correct Chemistry
OPTIONAL: Text file text file with the user defined edges based on the ligand titles
- Output
Data Record Stream - Streamed-out of records containing the edge ligand pairs
Mapper floe report - The Mapper floe report used in the Orion UI to visualize the generated edge map
Calculation Parameters¶
change_charge_weight (change_charge_weight) type: decimal: The change charge weight in [0,1] used to facilitate or penalize thecreation of edges between ligands of different charges. | Default: 0.5
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
Mapper Output File (data_out) type: dataset_out: Mapper Output text file
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
Ligand Edge Map file (map_file) type: file_in: Ligand Edge Map file
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
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¶
Log Field (log_field) type: Field Type: String: The field to store messages to floe reportDefault: Log Field
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
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