compute_lrmsd_pdb2sql

StructureSimilarity.compute_lrmsd_pdb2sql(exportpath=None, method='svd', **kwargs)[source]

Slow 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. 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:

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

  • method (str, optional) – Method to align the fragments,

  • 'quaternion'. ('svd' or) –

Kwargs: selection keywords used in the pdb2sql.get() method :

‘rowID’, ‘serial’, ‘name’, ‘altLoc’, ‘resName’, ‘resSeq’, ‘iCode’, ‘x’, ‘y’, ‘z’, ‘occ’, ‘temp’, ‘element’, ‘model’

Returns:

float – L-RMSD value of the conformation

See also

compute_lrmsd_fast()