Autogenerated Tag Syntax Documentation:


XRW TODO

<CartesianSampler name="(&string;)" scorefxn="(&string;)"
        fascorefxn="(&string;)" mcscorefxn="(&string;)" debug="(&bool;)"
        fullatom="(&bool;)" bbmove="(&bool;)" temp="(&real;)" rms="(&real;)"
        nminsteps="(&non_negative_integer;)" overlap="(&non_negative_integer;)"
        ncycles="(&non_negative_integer;)" fragbias="(&string;)"
        recover_low="(true &bool;)" force_ss="(D &char;)"
        strategy="(&strategy_type;)"
        rsd_wdw_to_refine="(&non_negative_integer;)" score_threshold="(&real;)"
        cumulate_prob="(&bool;)" automode_scorecut="(&real;)"
        wdw_to_freeze="(&integer;)" freeze_endpoints="(&bool;)"
        residues="(&resnum_list_with_ranges;)" loops_in="(&string;)"
        residues_to_include="(&resnum_list_with_ranges;)"
        residues_to_exclude="(&resnum_list_with_ranges;)"
        reference_model="(&string;)" reference_cst_wt="(&real;)"
        reference_cst_maxdist="(&real;)" nfrags="(25 &non_negative_integer;)"
        fraglens="(&positive_integer_cslist;)" >
    <Fragments fragfile="(&string;)" nfrags="(&non_negative_integer;)" />
</CartesianSampler>
  • scorefxn: (centroid) scorefunction
  • fascorefxn: (fullatom) scorefunction
  • mcscorefxn: Monte Carlo (?) scorefunction
  • debug: XRW TODO
  • fullatom: XRW TODO
  • bbmove: Allow/disalllow bb minimization during min.
  • temp: XRW TODO
  • rms: Maximum RMS deviation of fragment insertion
  • nminsteps: XRW TODO
  • overlap: XRW TODO
  • ncycles: XRW TODO
  • fragbias: XRW TODO
  • recover_low: XRW TODO
  • force_ss: XRW TODO
  • strategy: fragment bias strategies. This string is a comma-separated list; allowed values include 'user', 'uniform', 'auto', 'density', 'density_nbr', 'geometry', 'rama', 'bfactors', 'chainbreak'
  • rsd_wdw_to_refine: residue window to refine
  • score_threshold: Sets the FragmentBiasAssigner score_threshold
  • cumulate_prob: XRW TODO
  • automode_scorecut: XRW TODO
  • wdw_to_freeze: XRW TODO
  • freeze_endpoints: XRW TODO
  • residues: The residues to set as equal probability (1.0) ONLY IF strategy is 'user'
  • loops_in: XRW TODO. Looks for a Loops object in the DataMap with this name. 'residues' and 'loops_in' are mutually exclusive.
  • residues_to_include: Sets the residues to probability of 1.0 AFTER fragment bias strategy is applied
  • residues_to_exclude: Sets the residues to probability of 1.0 AFTER fragment bias strategy and residues_to_include is applied
  • reference_model: XRW TODO; if 'input' uses the Pose from apply(); otherwise loads this pdb file
  • reference_cst_wt: XRW TODO
  • reference_cst_maxdist: XRW TODO
  • nfrags: XRW TODO; unclear if this should be used with the Fragments subelement
  • fraglens: XRW TODO; comma separated list of positive integers, unclear if this should be used with the Fragments subelement

Subtag Fragments: Instructions for fragments files.

  • fragfile: (REQUIRED) file to read fragments from
  • nfrags: read this many fragments from the top of 'fragfile'