RDKit's Chem.MolFromPDBBlock ignores atoms if AltLoc is not ' ' or 'A' or '1'

[rwxayheee]

Currently, atom lines are ignored 😭 if AltLoc is not ' ' (space), 'A' or '1'?
https://github.com/rdkit/rdkit/blob/a44cbe86994583da3a828bed3df97804ef48fb59/Code/GraphMol/FileParsers/PDBParser.cpp#L62-L64

A check somewhere near this might be helpful:

Meeko/meeko/linked_rdkit_chorizo.py

Lines 1418 to 1430 in 904f6a2

	for line in pdb_string.splitlines(True):
	if line.startswith("TER") and reskey is not None:
	_add_if_new(blocks_by_residue, reskey, pdb_block, interrupted_residues)
	blocks_by_residue[reskey] = pdb_block
	pdb_block = ""
	reskey = None
	buffered_reskey = None
	if line.startswith("ATOM") or line.startswith("HETATM"):
	# Generating dictionary key
	resname = line[17:20].strip()
	resid = int(line[22:26].strip())
	chainid = line[21].strip()
	icode = line[26:27].strip()

We can print the atom PDB line if unexpected AltLoc is encountered, and a warning message that this atom will not go through Chem.MolFromPDBBlock

It seems like prody's parsePDB also defaults to ' ' or 'A'

[rwxayheee]

closing as fixed by #186