Input PDB Codes for Spruce

Spruce input datasets are generated from input PDB codes

Related Cubes

Calculation Parameters

  • Inputs delimiter (codes_delim) type: string: Delimiter to separate multiple PDB codes or UniprotKB IDs.
    Default: ,
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 192
  • 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
  • Download EM maps (em_maps) type: boolean: Download EM maps for storage and visualization with the design unit.
    Default: True
  • Get all PDB codes (get_all_codes) type: boolean: Option to get all public PDB codes from the RCSB
    Default: False
  • GPUs (gpu_count) type: decimal: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • PDB code(s) to download (input_codes) type: string: Separate multiple codes with a (default) comma delimiter, e.g. ‘1ABC, DEF2, G3HI’. or ‘pdb00001abc, pdb0000def2, pdb0000g3hi’.
  • 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
  • Max File Size (Gb) (max_file_size) type: integer: Max allowable structure file size (Gb) when attempting to download structure files for each PDB code. If this value is increased you may need to increase cube memory.
    Default: 3
  • 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
  • PDB CSV Header Name (pdb_column_name) type: string:
    Default: PDB
  • 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
  • UniprotKB Target IDs (target_ids) type: string: The UniprotKB IDs of the desired target.
  • Download timeout (timeout) type: integer: Timeout when attempting to download files for each PDB code.
    Default: 600
  • Uniprot ID CSV Header Name (ukbid_column_name) type: string:
    Default: SP_PRIMARY

Field parameters

  • PDB Code Field (code_field) type: Field Type: String: The field to store or that stores a PDB code.
    Default: pdb_code
  • Cryo EM Map Contour (em_map_contour_field) type: Field Type: Float: The field to store or that stores a cryoEM Map contour value.
    Default: em_map_contour
  • CryoEM Map File Field (em_map_file_field) type: Field Type: Blob: The field to store or that stores a cryoEM Map file.
    Default: em_map_file
  • Experimental Method Field (exp_method_field) type: Field Type: String: Field to store the structure experimental method parsed from PDB/mmCIF metadata.
    Default: experimental_method
  • MacroMolecule File Extension Field (format_ext_field) type: Field Type: String: The field to store or that stores MacroMolecule file extensions.
    Default: pdb_ext
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • MacroMolecule Structure Field (mol_field) type: Field Type: Chem.Mol: The field to store or that stores a MacroMolecule structure.
    Default: structure
  • PDB File Field (pdb_file_field) type: Field Type: Blob: The field to store or that stores a PDB file.
    Default: pdb_file
  • PDB Code Revision Field (rev_field) type: Field Type: Int: The field to store or that stores a PDB code revision ordinal number.
    Default: pdb_rev
  • Structure Factor 2FoFc File Field (sfcif_2fofoc_file_field) type: Field Type: Blob: The field to store or that stores a 2Fo-Fc Structure Factor (sfCIF) file.
    Default: sfcif_2fofc_file
  • Structure Factor FoFc File Field (sfcif_fofoc_file_field) type: Field Type: Blob: The field to store or that stores a Fo-Fc Structure Factor (sfCIF) file.
    Default: sfcif_fofc_file

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: decimal: 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: 192
  • 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 Input PDB Codes for Spruce

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
  • Starting number of Cubes (scaleup_start) type: integer: The initial number of concurrently running copies of this Cube
    Default: 2 , Min: 1