conkit.misc.distances module

Amino acid specific distance calculator

class DynamicDistances[source]

Bases: object

Dynamic distance calculator

The data stored in this class corresponds to Supplementary Table 3 in [1].

Examples

>>> DynamicDistances.cutoff('A', 'Y')
9.121
>>> DynamicDistances.percentile('A', 'Y')
0.443

References

[1]Kamisetty et al. (2013). Assessing the utility of coevolution based residue-residue contact predictions in a sequence and structure rich era. PNAS 110(39), 15674-9.
classmethod cutoff(x, y)[source]

Return the amino acid pair-specific cB-cB cutoff

Parameters:
  • x (str) – Single-letter amino acid
  • y (str) – Single-letter amino acid
classmethod percentile(x, y)[source]

Return 95-97 percentile data

Parameters:
  • x (str) – Single-letter amino acid
  • y (str) – Single-letter amino acid