AlloViz.Delta._make_struct_aln

Delta._make_struct_aln(pymol_aln)

Perform a PyMOL structural alignment.

Return a Bio.Align.MultipleSeqAlignment as a result of parsing the ClustalW-formatted structural alignment provided by PyMOL. The alignment is also used to create an _aln_mapper attribute in each Protein of the Delta object that maps the alignment positions to its residues, which can/will be used by the Protein’s private method _translate_ix.

Parameters:

pymol_aln{“super”, “align”, “cealign”}

PyMOL’s method to apply for the structural alignment of the two structures, usedto retrieve the corresponding residues between the two for subtraction of edge weights.

Returns:

Bio.Align.MultipleSeqAlignment

Notes

Check PyMol’s documentation for descriptions of the structural alignment methods and their fitness for identical or dissimilar structures.