Spruce Prep

Spruce-prepped OEDesignUnits is generated from input PDB/MTZ files on the input OERecord.

Main Parameters

Parameter Name Associated Port Port Type
Add interaction hints    
Add style    
Allow cap residue truncation    
Alternate location handling method    
Loop backbone clash threshold    
Build C-terminal caps    
Option to build disulfide bridges    
Build missing loops    
Build N-terminal caps    
Build partial sidechains    
Loop builder include crystal packing    
Assign charges and radii    
Collapse non-site alts    
Loop crop length    
Delete clashing solvent    
Duplicate removal    
Enumerate co-factor sites    
Generate Tautomers    
Hetgroup cluster distance    
Include SA term    
Include solvation    
Include Binding Site Grids    
Loop clash threshold    
Loop anchor atom distance buffer    
Make packing residues    
Maximum atoms in biological unit    
Maximum parts in biological unit    
Number of loops to minimize and evaluate    
Max atoms for a ligand    
Max residues for a ligand    
Max system atoms    
Minimum alignment score for BU extraction    
Min atoms for a ligand    
Optimize Experimental Protons    
Loop optimization shell    
Opt stage 1 step/residue multiplier    
Opt stage 2 step/residue multiplier    
Loop optimization tolerance    
Output BioDesignUnits    
Prefer author BIOMT records    
Protonate    
Restrict DUs to ref site removal    
Rotamer Coverage %    
Rotamer Library    
Size used to define binding site    
Enforce proline positions in loop templates    
Strict protonation mode    
Superpose design units    
Superposition method    
Target classication    
Number to transform    

Related Cubes

Calculation Parameters

  • Add interaction hints (boolean) : Option add interactions to the design units.
    Default: True
  • Add style (boolean) : Option add style to the design units.
    Default: True
  • Allow cap residue truncation (boolean) : Option to allow terminal residue to converted to cap, if cap will otherwise clash.
    Default: True
  • Alternate location handling method (string) : Option to pick method of handling alternate locations.
    Default: Default
    Choices: Primary, Enumerate, Default
  • Loop backbone clash threshold (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 (boolean) : Option to cap broken C-termini in protein chains.
    Default: True
  • Option to build disulfide bridges (boolean) : Allow the loop builder to build disulfide bridges during loop modeling (if possible).
    Default: True
  • Build missing loops (boolean) : Option to build missing loops (if information is available to do so)
    Default: True
  • Build N-terminal caps (boolean) : Option to cap broken N-termini in protein chains.
    Default: True
  • Build partial sidechains (boolean) : Option to build missing or partial protein sidechains.
    Default: True
  • Loop builder include crystal packing (boolean) : Include packing residues when building loops.
    Default: False
  • Assign charges and radii (boolean) : Option to assign partial charge and radii.
    Default: True
  • Add Cofactor code(s) (string) : Add uncommon, or custom, cofactor 3-letter codes.
  • Collapse non-site alts (boolean) : Option to deduplicate structures with different alts, if the alt locations are not near the binding site.
    Default: True
  • CPUs (integer) : The number of CPUs to run this cube with
    Default: 1 Min: 1 Max: 128
  • Loop crop length (integer) : Anchor residues on the protein to crop back for a better fit, results in longer loops being built.
    Default: 1
  • Cube Metrics (string) : Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Delete clashing solvent (boolean) : Option to allow build steps to remove clashing solvent.
    Default: True
  • 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
  • Duplicate removal (boolean) : Option to deduplicate identical structures resulting from symmetry operation.
    Default: True
  • Enumerate co-factor sites (boolean) : Option to generate individual design units based on the recognized co-factors.
    Default: False
  • Add Excipient code(s) (string) : Add uncommon, or custom, excipient 3-letter codes.
  • Generate Tautomers (boolean) : Option to generate and use tautomers in the hydrogen network optimization.
    Default: True
  • GPUs (integer) : The number of GPUs to run this cube with
    Default: 0 Max: 16
  • Hetgroup cluster distance (decimal) : Distance between heterogens used to determine optimization clusters for protonation.
    Default: 3.5
  • Include SA term (boolean) : Include solvent accessible surface area term when ranking the loops.
    Default: True
  • Include solvation (boolean) : Include simple solvation model when building loops.
    Default: True
  • Include Binding Site Grids (boolean) : Include electron density and difference density maps around the binding site
    Default: True
  • 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
  • Add Ligand Smiles (string) : Add ligand smiles and 3-letter codes, e.g. ‘c1ccccc1 BNZ’.
  • Ligand name(s) (string) : format 3-letter codes e.g. ‘LIG’, for peptides separate codes with dashes(e.g. ‘SER-VAL-TPO-ALA’.
  • Loop clash threshold (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 (decimal) : Fuzzy matches in the loop database has to have distance between anchor atoms correct, +/- buffer distance.
    Default: 1.0
  • A template loop database file (file_in) :
  • Make packing residues (boolean) : Generate packing residues from an asymmetric unit.
    Default: True
  • Maximum atoms in biological unit (integer) : Option to limit the size of BUs processed based on number of atoms.
    Default: 50000
  • Maximum parts in biological unit (integer) : Option to limit the size of BUs processed based on number of parts (chains).
    Default: 24
  • Number of loops to minimize and evaluate (integer) : Maximum number of loops to connect and minimize.
    Default: 5
  • Max atoms for a ligand (integer) : Maximum number of atoms in a molecule to be detected as a ligand.
    Default: 100
  • Max residues for a ligand (integer) : Maximum number of residues in a molecule to be detected as a ligand.
    Default: 5
  • Max system atoms (integer) : Maximum number of atoms in the system.
    Default: 50000
  • 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
  • Minimum alignment score for BU extraction (integer) : Option to specify minimum sequence alignment score for biounit extraction.
    Default: 200
  • Min atoms for a ligand (integer) : Minimum number of atoms in a molecule to be detected as a ligand.
    Default: 8
  • Optimize Experimental Protons (boolean) : Option to optimize hydrogens assigned in the experiment.
    Default: False
  • Loop optimization shell (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 (integer) : Number of steps per number of residues in the loop for the first stage optimizer.
    Default: 5
  • Opt stage 2 step/residue multiplier (integer) : Number of steps per number of residues in the loop for the second stage optimizer.
    Default: 10
  • Loop optimization tolerance (decimal) : Tolerance for the loop optimization, smaller numbers result in slower optimizations.
    Default: 0.001
  • Output BioDesignUnits (boolean) : Option to write intermediate work produce bio design units
    Default: False
  • Prefer author BIOMT records (boolean) : Option where the author BIOMT record is prefered over the software generated one.
    Default: True
  • Protonate (boolean) : Option to add and optimize protons in the system.
    Default: True
  • Restrict DUs to ref site removal (boolean) : Option to not generate design units with sites not matching the reference (if one is provided).
    Default: True
  • Rotamer Coverage % (decimal) : Coverage of the rotamers returned from the library in percent.
    Default: 100.0
  • Rotamer Library (string) : Rotamer library to use for side-chain building.
    Default: Richardson2016
    Choices: Dunbrack, Richardson, Richardson2016
  • Site residue entry (string) : Single site residue specification for APO structures. Format ‘name:num:insert:chain[:fragno:altloc]’, e.g. ‘ALA:325: :A’ (note the blank/whitespace insert code). The regex ‘.*’ notation can be used as a wildcard.
  • Size used to define binding site (decimal) : Distance used to determine the size of the site.
    Default: 5.0
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Enforce proline positions in loop templates (boolean) : Fuzzy matches in the loop database have to have proline in exact locations of sequence.
    Default: True
  • Strict protonation mode (boolean) : Option to fail prep if protons could not be added.
    Default: False
  • Superpose design units (boolean) : Option to superpose DUs (if multiple), first onto the reference structure (if provided).
    Default: True
  • Superposition method (string) : Superposition method.
    Default: SiteSequence
    Choices: GlobalSequence, SiteSequence, DDMatrix, SSE, SiteHopper
  • Target classication (string) : Option to pick whether target is protein or nucleic acid component.
    Default: Protein
    Choices: Protein, Nucleic
  • Number to transform (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
  • output verbosity (string) : verbose level
    Default: warning
    Choices: info, warning, error, debug, ddebug

Field parameters

  • None (Field Type: String) : Message log field.
    Default: Log Field

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

Parallel Spruce Prep

The parallel version adds these extra parameters.

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

Tip

filename: snowball/spruce/prep.py