Spruce DU to Mol

A cube that converts the design unit on the input record(s) to a primary molecule and additional molecules per user specification.

Related Cubes

Calculation Parameters

  • Components to be part of the molecule (components_1) type: string: Components to make part of the molecule. If set to ‘undefined’, will not be included in output.
    Default: [‘protein’, ‘nucleic’, ‘cofactors’, ‘solvent’, ‘other_ligands’, ‘other_cofactors’]
    Choices: protein, nucleic, ligand, solvent, metals, counter_ions, lipids, packing_residues, sugars, undefined, cofactors, excipients, polymers, post_translational, other_proteins, other_nucleics, other_ligands, other_cofactors
  • Components to be part of the molecule (components_2) type: string: Components to make part of the molecule. If set to ‘undefined’, will not be included in output.
    Default: [‘undefined’]
    Choices: protein, nucleic, ligand, solvent, metals, counter_ions, lipids, packing_residues, sugars, undefined, cofactors, excipients, polymers, post_translational, other_proteins, other_nucleics, other_ligands, other_cofactors
  • Components to be part of the molecule (components_3) type: string: Components to make part of the molecule. If set to ‘undefined’, will not be included in output.
    Default: [‘undefined’]
    Choices: protein, nucleic, ligand, solvent, metals, counter_ions, lipids, packing_residues, sugars, undefined, cofactors, excipients, polymers, post_translational, other_proteins, other_nucleics, other_ligands, other_cofactors
  • 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 Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • 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
  • Components to be part of the molecule (primary_components) type: string: Components to make part of the molecule. If set to ‘undefined’, will not be included in output.
    Default: [‘ligand’]
    Choices: protein, nucleic, ligand, solvent, metals, counter_ions, lipids, packing_residues, sugars, undefined, cofactors, excipients, polymers, post_translational, other_proteins, other_nucleics, other_ligands, other_cofactors
  • Convert R-groups to Hydrogen atoms (r2h) type: boolean: Convert R-groups on ligand and biomolecules to hydrogens from broken covalent bonds. An example could be on glycosylation sites where sugars are excluded from the component selection, another common use case would be for covalent ligands.
    Default: True
  • 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

  • None (None) type: Field Type: Chem.Mol:
    Default: Protein
  • None (None) type: Field Type: Chem.Mol:
    Default: Optional 1
  • None (None) type: Field Type: Chem.Mol:
    Default: Optional 2
  • Molecule Field (primary_mol_field_param) type: Field Type: Chem.Mol: Field to put the primary molecule onto.
    Default: Ligand
  • 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
  • None (mol_field_param_1) type: Field Type: Chem.Mol:
    Default: Protein
  • None (mol_field_param_2) type: Field Type: Chem.Mol:
    Default: Optional 1
  • None (mol_field_param_3) type: Field Type: Chem.Mol:
    Default: Optional 2
  • Molecule Field (primary_mol_field_param) type: Field Type: Chem.Mol: Field to put the primary molecule onto.
    Default: Ligand

Molecule selection group 1

  • Components to be part of the molecule (None) type: string: Components to make part of the molecule. If set to ‘undefined’, will not be included in output.
    Default: [‘protein’, ‘nucleic’, ‘cofactors’, ‘solvent’, ‘other_ligands’, ‘other_cofactors’]
    Choices: protein, nucleic, ligand, solvent, metals, counter_ions, lipids, packing_residues, sugars, undefined, cofactors, excipients, polymers, post_translational, other_proteins, other_nucleics, other_ligands, other_cofactors

Molecule selection group 2

  • Components to be part of the molecule (None) type: string: Components to make part of the molecule. If set to ‘undefined’, will not be included in output.
    Default: [‘undefined’]
    Choices: protein, nucleic, ligand, solvent, metals, counter_ions, lipids, packing_residues, sugars, undefined, cofactors, excipients, polymers, post_translational, other_proteins, other_nucleics, other_ligands, other_cofactors

Molecule selection group 3

  • Components to be part of the molecule (None) type: string: Components to make part of the molecule. If set to ‘undefined’, will not be included in output.
    Default: [‘undefined’]
    Choices: protein, nucleic, ligand, solvent, metals, counter_ions, lipids, packing_residues, sugars, undefined, cofactors, excipients, polymers, post_translational, other_proteins, other_nucleics, other_ligands, other_cofactors

Primary molecule selection group

  • Components to be part of the molecule (None) type: string: Components to make part of the molecule. If set to ‘undefined’, will not be included in output.
    Default: [‘ligand’]
    Choices: protein, nucleic, ligand, solvent, metals, counter_ions, lipids, packing_residues, sugars, undefined, cofactors, excipients, polymers, post_translational, other_proteins, other_nucleics, other_ligands, other_cofactors

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
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • 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 Spruce DU to Mol

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