compute_irmsd_pdb2sql

StructureSimilarity.compute_irmsd_pdb2sql(cutoff=10, method='svd', izone=None, exportpath=None)[source]

Slow 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 first.

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

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

  • exportpath (str, optional) – file name where the aligned pdbs are exported.

Returns:

float – i-RMSD value of the conformation

See also

compute_irmsd_fast()