adjust call to pdb_selaltloc

[mgiulini]

currently our pdb deals with alternate locations on the pdb with a call to select_by_occupancy

arctic3d/src/arctic3d/modules/pdb.py

Lines 171 to 176 in 6b83c5d

	log.debug("Selecting residues with highest occupancy")
	out_pdb_fname = Path(f"{inp_pdb_f.stem}-occ.pdb")
	with open(inp_pdb_f, "r") as pdb_fh:
	with open(out_pdb_fname, "w") as f:
	for line in select_by_occupancy(pdb_fh):
	f.write(line)

Unfortunately, this call always results in the residues with alternate locations being completely removed. I would rather select the residue with the highest occupancy. This was not a big problem when the call was performed after retrieving the file from pdb_renum, but removing that dependency (PR #118) can give rise to potential problems.

[mgiulini]

unable to reproduce the issue, alternate locations seem to be correctly selected. I am closing this.

[mgiulini]

Re-opening this, as I was able to reproduce the issue: when all the entries of a residue show alternate locations, then the residue is completely removed from the pdb. I guess this should be handled at the pdbtools level

[mgiulini]

haddocking/pdb-tools#153