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Author: Jared Adolf-Bryfogle (

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Author: Jared Adolf-Bryfogle ( A SimpleMetric that calculates the total number of atom-atom clashes from a residue in a residue selector to all other residues defined in a second residue selector using the LJ radius of each atom Can use a soft radius, which reduces it by 33% (by default - see dampening_percent option. DETAILS: Does NOT calculate INTRA-RESIDUE clashes!

<PerResidueClashMetric name="(&string;)" custom_type="(&string;)"
        output_as_pdb_nums="(false &bool;)" residue_selector="(&string;)"
        use_hydrogens="(false &bool;)" soft_clash="(true &bool;)"
        dampening_percent="(.33 &real;)" residue_selector2="(&string;)" />
  • custom_type: Allows multiple configured SimpleMetrics of a single type to be called in a single RunSimpleMetrics and SimpleMetricFeatures. The custom_type name will be added to the data tag in the scorefile or features database.
  • output_as_pdb_nums: If outputting to scorefile use PDB numbering+chain instead of Rosetta (1 - N numbering)
  • residue_selector: If a residue selector is present, we only calculate and output metrics for the subset of residues selected.
  • use_hydrogens: Use Hydrogens OR calculate only heavy atom clashes
  • soft_clash: IF TRUE, soften the clashing by a percent (dampening_percent). When we calculate atom-atom distances using LJ distances, clash if distance less_than (atomI_LJ + atomJ_LJ)*(1 - dampening_percent)
  • dampening_percent: If we use soft_clash, dampen by this percent. Number is between 0 and .99. IE- When we calculate atom-atom distances using LJ distances, clash if distance less_then (atomI_LJ + atomJ_LJ)*(1 - dampening_percent)
  • residue_selector2: The residue selector to use for calculating clashes TO for each residue of the primary selector. Default is to calculate clashes of each residue to ALL OTHER residues (including those in the primary selector)

See Also