Report (raise warning or error for) lone hydrogens from bad input PDB

[rwxayheee]

When input PDB has lone hydrogens (from a strained structure), atom.GetNeighbors() becomes an empty tuple and an error will occur from here:

Meeko/meeko/polymer.py

Lines 2519 to 2524 in c938ebd

	if element == "H":
	nei_idx = atom.GetNeighbors()[0].GetIdx()
	if nei_idx in mapping_inv:
	result[element]["excess"].append(mapping_inv[nei_idx])
	else:
	result[element]["excess"].append(-1)

To raise an error:

                if element == "H": 
                    if atom.GetNeighbors(): 
                        nei_idx = atom.GetNeighbors()[0].GetIdx()
                        if nei_idx in mapping_inv: 
                            result[element]["excess"].append(mapping_inv[nei_idx])
                        else:
                            result[element]["excess"].append(-1)
                    else: # lone hydrogen
                        raise ValueError(f"Lone hydrogen {atom.GetMonomerInfo().GetName()} found from input structure")

If we allow the lone hydrogens to pass, the bad residue with lone hydrogens will be deleted silently (no template match results printed) from the result structure.

But alternatively, lone hydrogens can be detected at an earlier point than template matching.

[diogomart]

Wow, this was a sneaky one!