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 the creation of edges between ligands of different charges.
    Default: 0.5
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Cube Metrics (cube_metrics) type: string: Set of metrics to be collected

    Choices: 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 with
    Default: 0 , Max: 16
  • Star map hub ligand names (hub) type: string: Names of the center ligands of the star map. For the binary star maps, multiple ligand names separated by commas will be parsed. If none is specified, for the star map, a ligand with the highest similarity to other ligands (the largest sum of edge scores) will be chosen as a hub, and for the binary star map, it will choose the two ligands with the top two highest similarities to other ligands.
  • 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
  • Map type (map_type) type: string: ‘Default map’ generates OELOMAP, and if ‘Star map’ or ‘Binary star map’ is selected, a user is expected to provide the name(s) of the hub (reference) ligand(s), or the hub(s) will be automatically selected based on the similarities to other ligands.
    Default: Default map
    Choices: Default map, Star map, Binary star map
  • 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 seconds
    Default: 60
    Choices: 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 CPU
    Default: 32
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required

Field parameters

  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: 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 address
    Default: 64
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 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 with
    Default: 0 , Max: 16
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 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 instances
    Default: Prohibited
    Choices: 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 seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Cube Metrics (None) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network