peppr.BiSyRMSD#

class peppr.BiSyRMSD(threshold: float, inclusion_radius: float = 4.0, outlier_distance: float = 3.0, max_iterations: int = 5, min_anchors: int = 3)[source]#

Compute the Binding-Site Superposed, Symmetry-Corrected Pose RMSD (BiSyRMSD) for the given PLI complex.

The method and default parameters are described in [1].

Parameters:
thresholdfloat

The RMSD threshold to use for the good predictions.

inclusion_radiusfloat, optional

All residues where at least one heavy atom is within this radius of a heavy ligand atom, are considered part of the binding site.

outlier_distancefloat, optional

The binding sites of the reference and pose are superimposed iteratively. In each iteration, atoms with a distance of more than this value are considered outliers and are removed in the next iteration. To disable outlier removal, set this value to inf.

max_iterationsint, optional

The maximum number of iterations for the superimposition.

min_anchorsint, optional

The minimum number of anchors to use for the superimposition. If less than this number of anchors are present, the superimposition is performed on all interface backbone atoms.

References

__init__(threshold: float, inclusion_radius: float = 4.0, outlier_distance: float = 3.0, max_iterations: int = 5, min_anchors: int = 3) → None#

Methods

__init__(threshold[, inclusion_radius, ...])

evaluate(reference, pose)

Apply this metric on the given predicted pose with respect to the given reference.

smaller_is_better()

Whether as smaller value of this metric is considered a better prediction.

Attributes

name

thresholds