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BuriedUnsatHbonds2

Calculate the number of buried unsatisfied H-bonds across a given interface. (Specifically, the difference in the number of buried unsatisfied hydrogen bonds in the bound state versus the bound state. This uses a different algorithm than the BuriedUnsatHbonds filter. What the differences were not properly documented, unfortunately.)

Autogenerated Tag Syntax Documentation:


A filter for computing the number of buried unsatisfied hydrogen bond donors and/or acceptors, and discarding poses with too many. This is the same thing that the BuriedUnsatHbonds filter does, but this filter does it a somewhat different way. What the difference is has been lost to the mists of time.

<BuriedUnsatHbonds2 name="(&string;)" jump_number="(1 &non_negative_integer;)"
        cutoff="(20 &non_negative_integer;)" generous_hbonds="(true &bool;)"
        sasa_burial_cutoff="(0.01 &real;)" AHD_cutoff="(120 &real;)"
        dist_cutoff="(3.0 &real;)" hxl_dist_cutoff="(3.5 &real;)"
        sulph_dist_cutoff="(3.3 &real;)" metal_dist_cutoff="(2.7 &real;)"
        scorefxn="(&string;)"
        task_operations="(&task_operation_comma_separated_list;)"
        packer_palette="(&named_packer_palette;)" confidence="(1.0 &real;)" />
  • jump_number: Jump, numbered sequentially from 1, that defines the interface
  • cutoff: Upper threshold beyond which the filter fails
  • generous_hbonds: Use a generous definition of H-bonds
  • sasa_burial_cutoff: SASA threshold to define residue burial
  • AHD_cutoff: Cutoff for AHD angle, in degrees, to define a hydrogen bond
  • dist_cutoff: Cutoff for distance, in Angstroms, to define a hydrogen bond
  • hxl_dist_cutoff: Cutoff for distance, in Angstroms, to define a hydrogen bond to a hydroxyl
  • sulph_dist_cutoff: Cutoff for distance, in Angstroms, to define a hydrogen bond to a sulfur
  • metal_dist_cutoff: Cutoff for distance, in Angstroms, to define a hydrogen bond to a metal
  • scorefxn: Name of score function to use
  • task_operations: A comma-separated list of TaskOperations to use.
  • packer_palette: A previously-defined PackerPalette to use, which specifies the set of residue types with which to design (to be pruned with TaskOperations).
  • confidence: Probability that the pose will be filtered out if it does not pass this Filter

See Also