Hi Greg,
Thanks for the reply.
> > 1. In RDKit, has the 'cleaning / washing / salt-stripping' of
> > molecules already been formalised based on a set of rules, etc?
>
> Not that I'm aware of on the open-source side of things. All
> of the functionality required to do this is, I believe,
> present in the RDKit though.
Great - I certainly found all the functionality I was looking for, but just
wanted to make sure I wasn't missing any short-cuts!
> > 2. When identifying compounds that contain a non-allowed
> atom-type,
> > why do I find the SMARTS def [!H;!C;!N;!O;!F;!S;!Cl;!Br;!I] gives
> > unexpected results, but [!#1;!#6;!#7;!#8;!#9;!#16;!#17;!#35;!#53]
> > works as I would expect?
>
> This is a fairly common SMARTS "gotcha": in SMARTS the query "[C]"
> means "aliphatic C". This leads to the following behavior:
> [3]>>>
> Chem.MolFromSmiles('c1ccccc1').GetSubstructMatches(Chem.MolFro
> mSmarts('[!C]'))
> Out[3] ((0,), (1,), (2,), (3,), (4,), (5,)) If you want to be
> sure that your SMARTS will capture aliphatic or aromatic
> atoms, you need to provide the atomic numbers, as in your
> second query:
> [4]>>>
> Chem.MolFromSmiles('c1ccccc1').GetSubstructMatches(Chem.MolFro
> mSmarts('[!#6]'))
> Out[4] ()
Wow - I really was having some sort of mental block yesterday! (goes-off to
look for some sort of embarrassed + dunce smiley...)
Kind regards
James
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