Posit Mod

Generates relaxed high probability poses for ligands that are analogs of the ligand in the receptor. This cube is suitable for pose generation when working with multiple receptors.

Related Cubes

Calculation Parameters

  • Allowed clash type (allow_clash_type) type: string: Types of clashes acceptable between protein and ligand in the pose.
    Default: HYDROGEN
    Choices: ANY, HYDROGEN, NONE
  • Best Receptor Only (best_receptor_only) type: boolean: Only use the best receptor, instead of exploring all the receptors, while generating multiple poses.
    Default: True
  • 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
  • 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
  • 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
  • Max Rotors (max_rotors) type: integer: Cutoff of rotatable bonds. The cube will skip molecules with rotors more than the cutoff.
    Default: 40 , Min: 1, Max: 9999
  • 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
  • None (min_prob) type: decimal: The minimum probability that a ligand crystal will be within 2A of the predicted pose. This probability assumes the ligand binds, which may not be the case.
    Default: 0.33 , Max: 1.0
  • Number of poses (num_poses) type: integer: Number of poses to generate per ligand
    Default: 1 , Min: 1, Max: 200
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Poser cache size (poser_count) type: integer: Number of receptor/poser pairs held in memory at once. Each poser takes ~0.75G of memory.
    Default: 1
  • Posit Method (posit_method) type: string: Posit method to use
    Default: All
    Choices: FRED, Hybrid, ShapeFit, All
  • Relaxation Mode (relax_mode) type: string: Mode to determine if a post pose prediction relaxation should be performed
    Default: NONE
    Choices: ALL, CLASHED, NONE
  • 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

  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • None (in_mol_field) type: Field Type: Chem.Mol:
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • Output Bound ligand field (out_bound_field) type: Field Type: Chem.Mol: Bound ligand corresponding to the receptor used
    Default: Bound Ligand
  • None (out_du_field) type: Field Type: Chem.DesignUnit:Record:
    Default: designunit
  • None (out_mol_field) type: Field Type: Chem.Mol:
  • Posit Method Field (posit_method_field) type: Field Type: String: Posit method used for prediction
    Default: Posit Method
  • Posit Probability Field (prob_field) type: Field Type: Float: Posit estimated pose probability
    Default: Posit Probability
  • None (receptor_field) type: Field Type: Chem.DesignUnit:Record:
    Default: designunit

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

Parallel Posit Mod

The parallel version adds these extra parameters.

  • Number of messages to distribute at a time (item_count) type: integer: The maximum number of messages to bundle together for a parallel cube.
    Default: 1 , Min: 1, Max: 65535
  • Maximum Failures (max_failures) type: integer: The maximum number of times to attempt processing a work item
    Default: 10 , Min: 1, Max: 100
  • Autoscale this Cube (autoscale) type: boolean: If True, let Orion manage the parallelism of this Cube
    Default: True
  • Maximum number of Cubes (max_parallel) type: integer: The maximum number of concurrently running copies of this Cube
    Default: 1000 , Min: 1
  • Minimum number of Cubes (min_parallel) type: integer: The minimum number of concurrently running copies of this Cube
    Default: 0