Atom-typing the Hetgroup Dictionary

So I posted this to CDK-devel, but probably this is the better place...

I've been trying to make a map between the atom IDs used in the HET dictionary (which is in CIF format) and atom types of some sort. To see what this looks like, here is a tail of the file:

ZZZ.O6A:O.sp2
ZZZ.H7C1:H
ZZZ.H7C2:H
ZZZ.H8:H
ZZZ.H2N1:H
ZZZ.H2N2:H
ZZZ.H3:H
ZZZ.H5:H
ZZZ.H6:H
ZZZ.H6A:H

'Zzzz', you may be thinking, but although many atom ids are quite obvious (like H8 is a hydrogen), some are probably not. One annoying aspect of this process was that the CIF file format is not especially friendly, and particularly, the file has 'loop_'s that don't terminate in octothorpes ('#'), as I thought they would.

Probably the parser (an IteratingCIFReader) could be much better written - in fact, it will probably only parse this one CIF! So my initial estimates of 13,000 typing failures is now down to only 3,508. What are the atoms that fail? There are some that are bound to like TBR, which is decidedly a non-organic molecule.

Quite a few, however, are aromatic chlorines:

Null type for 00A CL4A [CL]([C]([C]=[C]))
Null type for 014 CL [CL]([C]([C]=[C]))
Null type for 01A CL4A [CL]([C]([C]=[C]))
Null type for 01W N [N]([C]([C][C][H])[H][H][H])
Null type for 024 BR19 [BR]([C]([C]=[C]))
Null type for 032 CL13 [CL]([C](=[C][C]))
Null type for 039 CL [CL]([C](=[C][C]))
Null type for 055 CL1 [CL]([C](=[C][C]))
Null type for 062 CL1 [CL]([C]([C]=[C]))
Null type for 064 CL13 [CL]([C]([C]=[C]))
Null type for 064 CL15 [CL]([C](=[C][C]))
Null type for 064 CL25 [CL]([C](=[C][C]))
Null type for 088 CL32 [CL]([C](=[C][C]))
Null type for 088 CL37 [CL]([C]([C]=[C]))

The last part is the height-2 signature, just to give a quick idea of the environment of the atom. Aha! Some quick "cut | sort | uniq -c | sort -n" gives me:

24 [BR]([C]([C][H][H]))
29 [CL]([C](=[C][N]))
29 [CL]([C](=[C][S]))
38 [N]([C]([C][C][H])[H][H][H])
42 [N]([C]([C][H][H])[H][H][H])
48 [CL]([C]([C][H][H]))
75 [N]([C]([C][H][H])[C]([H][H][H])[C]([H][H][H])[C]([H][H][H]))
337 [BR]([C]([C]=[C]))
1176 [CL]([C]([C]=[C]))

gives the 'top-10' worst offenders. That nitrogen one is N(CH3)4 - perhaps charge is a problem here?

Comments

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