RBFEC Mapper Cube

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.

Data record Stream - Streamed-in of a set of similar ligands

OPTIONAL: Text file text file with the user defined edges based on the ligand titles

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

Main Parameters

Parameter Name

Associated Port

Port Type

Mapper Output File

Calculation Parameters

  • CPUs (integer) : The number of CPUs to run this cube with
    Default: 1 Min: 1 Max: 128
  • Cube Metrics (string) : Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Mapper Output File (dataset_out) : Mapper Output text file
  • 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 with
    Default: 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
  • Ligand Edge Map file (file_in) : Ligand Edge Map file
  • 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 seconds
    Default: 60 Min: 1 Max: 300
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required

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 with
    Default: 0 Max: 16
  • CPUs (integer) : The number of CPUs to run this cube with
    Default: 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 instances
    Default: Prohibited
    Choices: 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 seconds
    Default: 60 Min: 1 Max: 300
  • Cube Metrics (string) : Set of metrics to be collected

    Choices: cpu, disk, memory, network

Tip

filename: fec/rbfe/cubes.py