'base_pairs()' does not work for structures with non-standard atom-order

[padix-key]

The function structure.base_pairs() gives incorrect results, in my experience missing base pairs, if the input nucleic acid structure has an order for their atoms within each residue that is different from the RCSB standard.

The reason is that a standard base is superimposed on each nucleotide:

biotite/src/biotite/structure/basepairs.py

Lines 851 to 855 in d5e7207

	# Match the selected std_base to the base.
	fitted, transformation = superimpose(
	nucleotide[np.isin(nucleotide.atom_name, std_base.atom_name)],
	std_base[np.isin(std_base.atom_name, nucleotide.atom_name)]
	)

Even though missing atoms are checked before the superimposition, the correct order is not.
This means that atoms can be superimposed onto each other, that are not equivalent.

[padix-key]

This issue was falsely automatically closed