Make Design Unit from Target

An OEDesignUnit is generated from input target on input records. The complex can optionally be prepared.

Main Parameters

Parameter Name

Add interaction hints

Loop backbone clash threshold

Build C-terminal caps

Option to build disulfide bridges

Build missing loops

Build N-terminal caps

Build partial sidechains

Build missing tails

Loop builder include crystal packing

Assign charges and radii

Loop crop length

Extended Log Field

Fix backbone atom issues

Include SA term

Include solvation

Log Field

Loop clash threshold

Loop anchor atom distance buffer

Number of loops to minimize and evaluate

Optimize Existing Protons

Loop optimization shell

Opt stage 1 step/residue multiplier

Opt stage 2 step/residue multiplier

Loop optimization tolerance

Protonate

Enforce proline positions in loop templates

Strict protonation mode

Number to transform

Related Cubes

Calculation Parameters

  • Add interaction hints (add_interactions) type: boolean: Option add interactions to the design units.
    Default: False
  • Loop backbone clash threshold (bb_clash_threshold) type: decimal: Loops from the database where more than the threshold fraction of the backbone atoms clash, are rejected.
    Default: 0.25
  • Build C-terminal caps (build_cterm_caps) type: boolean: Option to cap broken C-termini in protein chains.
    Default: False
  • Option to build disulfide bridges (build_disulfidebridges) type: boolean: Allow the loop builder to build disulfide bridges during loop modeling (if possible).
    Default: True
  • Build missing loops (build_loops) type: boolean: Option to build missing loops (if information is available to do so)
    Default: False
  • Build N-terminal caps (build_nterm_caps) type: boolean: Option to cap broken N-termini in protein chains.
    Default: False
  • Build partial sidechains (build_sidechains) type: boolean: Option to build missing or partial protein sidechains.
    Default: False
  • Build missing tails (build_tails) type: boolean: Option to build missing tails (if information is available to do so)
    Default: False
  • Loop builder include crystal packing (build_with_crystalpacking) type: boolean: Include packing residues when building loops.
    Default: False
  • Assign charges and radii (charge_radii) type: boolean: Option to assign partial charge and radii. Charges cannot be assignedif there are missing hydrogen atoms. In thise case protonate will need to be enabled.
    Default: False
  • Add Cofactor code(s) (cofactor_codes) type: string: Add uncommon, or custom, cofactor 3-letter codes.
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Loop crop length (crop_length) type: integer: Anchor residues on the protein to crop back for a better fit, results in longer loops being built.
    Default: 1
  • 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
  • Add Excipient code(s) (excipient_codes) type: string: Add uncommon, or custom, excipient 3-letter codes.
  • Fix backbone atom issues (fix_backbone) type: boolean: Option to fix backbone atom issues in protein chains.
    Default: False
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Include SA term (incl_SA_term) type: boolean: Include solvent accessible surface area term when ranking the loops.
    Default: True
  • Include solvation (incl_solvation) type: boolean: Include simple solvation model when building loops.
    Default: True
  • 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
  • Loop clash threshold (loop_clash_threshold) type: decimal: Loops from the database where more than the threshold fraction of the loops atoms in addition to the bacbkone clashing ones clash, are rejected.
    Default: 0.2
  • Loop anchor atom distance buffer (loop_distance_buffer) type: decimal: Fuzzy matches in the loop database has to have distance between anchor atoms correct, +/- buffer distance.
    Default: 1.0
  • Number of loops to minimize and evaluate (max_eval_loops) type: integer: Maximum number of loops to connect and minimize.
    Default: 5
  • 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
  • Optimize Existing Protons (opt_expt_protons) type: boolean: Option to re-optimize hydrogens already assigned.
    Default: False
  • Loop optimization shell (opt_shell) type: decimal: Include atoms within this distance in the loop optimization, larger distance results in slower optimizations.
    Default: 15.0
  • Opt stage 1 step/residue multiplier (opt_stage1_iter_multiplier) type: integer: Number of steps per number of residues in the loop for the first stage optimizer.
    Default: 5
  • Opt stage 2 step/residue multiplier (opt_stage2_iter_multiplier) type: integer: Number of steps per number of residues in the loop for the second stage optimizer.
    Default: 10
  • Loop optimization tolerance (opt_tolerance) type: decimal: Tolerance for the loop optimization, smaller numbers result in slower optimizations.
    Default: 0.001
  • Protonate (protonate) type: boolean: Option to add and optimize protons in the system.
    Default: False
  • 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
  • Enforce proline positions in loop templates (strict_proline_match) type: boolean: Fuzzy matches in the loop database have to have proline in exact locations of sequence.
    Default: True
  • Strict protonation mode (strict_protonate) type: boolean: Option to fail prep if protons could not be added.
    Default: True
  • Number to transform (transform_threshold) type: integer: Number of loops to allow through the sidechain clash checker. No matter this number, will process all with an identical sequence to target.
    Default: 25

Field parameters

  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • Target field (target_field) type: Field Type: Chem.Mol: Molecule field to read target from

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
  • 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 Make Design Unit from Target and Ligand

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