rstoolbox.components.FragmentFrame.add_quality_measure¶

FragmentFrame.add_quality_measure(filename, pdbfile=None)¶

Add RMSD quality measure to the fragment data.

The RMSD quality measurement is performed by the r_fraq_qual application from Rosetta. It can be called as:

r_fraq_qual.linuxgccrelease -in:file:native <pdb> -f <fragfile> -out:qual <output>

Parameters:	filename (str) – Name containing the quality measure. If filename is None, it assumes that RMSD quality has not been calculated yet, so it’ll run the r_fraq_qual application as long as the FragmentFrame has a source_file. Standart output will be the name of the source file with the extension “.qual”. If a file with this naming schema exists, it will be automatically picked. To be able to run Rosetta it will need a pdbfile. pdbfile (str) – In case the quality has to be calculated. Provide the PDB over which to calculate it. Default is None.
Returns:	FragmentFrame
Raises:	IOError: if filename does not exist. IOError: if pdbfile is provided and does not exist. IOError: if the Rosetta executable is not found. AttributeError: if filename is None and there is no attached source_file to the object. ValueError: if no rmsd data is assigned. Might indicate that wrong data is trying to be assigned.

Note

Depends on rosetta.path and rosetta.compilation, if the quality file is not provided.

Attention

Some configurations of this function require a local installation of Rosetta.