compute_irmsd_fast

StructureSimilarity.compute_irmsd_fast(izone=None, method='svd', cutoff=10, check=True)[source]

Fast method to compute the i-rmsd.

i-RMSD is computed by selecting the backbone atoms of reference interface that is defined as any pair of heavy atoms from two chains within 10Å of each other. Align these backbone atoms as best as possible with their coutner part in the decoy and compute the RMSD. See reference:

DockQ: A Quality Measure for Protein-Protein Docking Models https://doi.org/10.1371/journal.pone.0161879

Parameters
  • izone (None, optional) – file name of the zone. if None the zones will be calculated automatically.

  • method (str, optional) – Method to align the fragments, ‘svd’ or ‘quaternion’.

  • cutoff (float, optional) – cutoff for the contact atoms

  • check (bool, optional) – Check if the sequences are aligned and fix it if not. Should be True.

Returns

float – i-RMSD value of the conformation