peppr.bisy_rmsd#
- peppr.bisy_rmsd(reference: AtomArray, pose: AtomArray, inclusion_radius: float = 4.0, outlier_distance: float = 3.0, max_iterations: int = 5, min_anchors: int = 3) float[source]#
Compute the Binding-Site Superposed, Symmetry-Corrected Pose RMSD (BiSyRMSD) for the given PLI complex as defined in [1].
- Parameters:
- reference, poseAtomArray
The reference and pose of the PLI complex.
- 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. The default value is taken from [1].
- 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. The default value is taken from [1]. To disable outlier removal, set this value to
inf.- max_iterationsint, optional
The maximum number of iterations for the superimposition. The default value is taken from [1].
- 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. The default value is taken from [1].
- Returns:
- float
The BiSyRMSD.
References