Structural violation losses of AlphaFold

Supplement section 1.9.11, equations (44)-(47) of Jumper et al. (2021), p. 40. Three flat-bottom penalties that charge nothing while the geometry stays within tolerance and grow linearly beyond it: bond lengths against literature values, bond angles through the cosine of the angle, and a one-sided clash term that penalises only distances that are too short.

Usage

Alfviol(
  blen = NULL,
  blen_lit = NULL,
  blen_sigma = NULL,
  cosang = NULL,
  cosang_lit = NULL,
  cosang_sigma = NULL,
  dnb = NULL,
  dnb_lit = NULL,
  factor = 12,
  clash_tol = 1.5
)

Arguments

blen, blen_lit, blen_sigma

Predicted bond lengths, literature values and standard deviations (equation 44).

cosang, cosang_lit, cosang_sigma

Cosines of predicted and literature bond angles and their standard deviations (equation 45).

dnb, dnb_lit

Non-bonded distances and clashing distances (eq. 46).

factor

Multiplier on the literature standard deviation, 12 in the spec.

clash_tol

Clash tolerance in angstrom, 1.5 in the spec.

Value

A list with bondlength, bondangle, clash, their sum estimate (equation 47) and method.

Details

Equations (44) and (45) average over bonds and angles while (46) sums over non-bonded pairs; that asymmetry is in the published text and is reproduced rather than tidied away.

References

Jumper et al (2021) Nature 596:583-589, Suppl. eq. (44)-(47)

Examples

Alfviol()
#> $bondlength
#> [1] 0
#> 
#> $bondangle
#> [1] 0
#> 
#> $clash
#> [1] 0
#> 
#> $estimate
#> [1] 0
#> 
#> $method
#> [1] "AlphaFold structural violation loss"
#>