compute_lrmsd_fast

StructureSimilarity.compute_lrmsd_fast(lzone=None, method='svd', check=True, name=['C', 'CA', 'N', 'O'])[source]

Fast routine to compute the L-RMSD.

L-RMSD is computed by aligning the longest chain of the decoy to the one of the reference and computing the RMSD of the shortest chain between decoy and reference. By default, both fitting and

rms calculation use only backbone atoms. See reference:

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

Parameters
  • lzone (None, optional) – name of the file containing the zone definition. If None the file will be calculated first.

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

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

  • name (list, optional) – atom name to include in the zone. Defaults to [‘C’, ‘CA’, ‘N’, ‘O’]

Returns

float – L-RMSD value of the conformation