Re: [Rdkit-discuss] Polymers, S-Groups, and molblock-parsing (oh my!)

[James D. <J.D...@ve...>]

Hi Greg:

James wrote:
>> So I guess the simple question is - should polymers, etc be handled by the
>> parser (maybe if not fully, just partially - eg by deleting the * atoms if
>> the S-Group data are found)?

Greg wrote:
> I'm reluctant to do this since I don't understand the semantics of
> Sgroups well enough to be able to tell if this modification only makes
> sense in this one case or if it's general. In the cases of polymers I
> would tend to say that the correct thing to do is to reject the
> molecule completely since the RDKit is incapable of correctly storing
> what the user intended with the mol block.

> I will try to find the time to grok the CTFile documentation for
> Sgroups, but I would be happy to get input on this from others.


I found some time to have a look into this a bit more myself, and would be inclined to agree that the best thing to do would be to reject polymers.  From my reading of the CTFILE spec, and the (extremely useful) Gushurst paper (J. Chem. Inf. Comput. Sci. 1991, 31, 447-454) I would suggest rejecting any molecule with "polymer" or "components, mixtures, and formulations" Sgroup data in the molblock; and ignoring or handling the "drawing and displaying shortcuts" Sgroup data (if there are no Sgroup data in the previous two categories).

I have copied below my understanding of the categories:

Sgroup types for "polymers":

SRU - structural repeating unit (for structure-based representation)
MON - monomer type (for source-based representation)
COP - copolymer
CRO - cross-link across two polymers
GRA - graft (eg terminally-attached) polymer2 on repeat unit of polymer1
MOD - for representing incomplete(?) modifications
MER - used when monomer repeat is 1 - ie alternating copolymers
ANY - (query) for posing more general polymer search queries


Sgroup types for "components, mixtures, and formulations":

COM - components (members of mixtures/formulations)
MIX - mixtures (order is not important)
FOR - formulations (order is important)


Sgroup types for "drawing and display shortcuts"

SUP - superatoms (can be contracted/expanded for representation purposes)
MUL - multiple groups (like a repeating superatom, but can only have 0 or 2 crossing bonds)
GEN - generic bracketing (does not affect structure)


Rejecting based on the first two categories should be straightforward(?), and equally applicable to V2000 and V3000.  Ignoring the SUP and MUL types will only (I think...) cause issues in 2D layout - so 'handling' could maybe be to force the expansion of these groups, then get rid of them and regenerate coordinates?

Kind regards

James


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