fix: allow ccd residues with missing coords

[davegrays]

There are a number of ligands/residues in the CCD with missing coordinates that cannot be retrieved now with structure.info.residue due to a ValueError that is raised twice and not excepted the second time. Relative to v0, this is new behavior.

This allows these residues to be returned from the second attempt with nans where missing.

[codspeed-hq]

CodSpeed Performance Report

Merging #730 will not alter performance

_{Comparing davegrays:fix/allow-all-ccd-residues (2a7fcbd) with main (e76eb24)}

Summary

✅ 47 untouched benchmarks

[padix-key]

Hi, from my perspective having a molecule without atom coordinates has barely a benefit. Consequently, getting an exception, that can be easily captured, is more clearer than checking for NaN coordinates in my opinion. However, I would be curious what your use case is.

[davegrays]

@padix-key Makes sense. My use case is that I'm identifying missing atoms in the experimental structure by constructing molecular templates from the CCD (essentially just the list of atom names per residue). So for that I use the CCD's AtomArray and I'm ignoring the coords anyway.

I get your concern tho... what would you think about an optional arg for this in get_components() that can propagate to structure.info.residue?