Re: [cml/ccml-discuss] AAM numbers, reaction centers, polymers

[Dmitry P. <dp...@gg...>]

Dear Peter,

>     1. AAM numbers in a separate section referenced by
>     "atomMap". This means the cases where USE_IDS is
>     not sufficient.
>
> Please explain in more detail - are these Marvin concepts?

No, Marvin does not seem to support AAM in CML at all.
I read about atomMap and USE_IDS in the CML 2.4 schema
on the xml-cml.org site. xml-cml.org is currently down,
so here is a link to another site where this is described:

http://www.wipo.int/standards/XMLSchema/HTML/ST96TechnicalSpecification/V0-2/Patent/PatentSchemaTechnicalSpecification_atomMap.html

> Reaction centers can be done in CML. There are different approaches to
> reactions and I'd be interested in knowing what you wish to support.

We would like to support special flags on bonds involved
(or not) in the reaction. This concept came to Indigo from
the Rxnfile format. I am copy-pasting the constants which
describe the types of the reacting centers from Indigo
code:

    RC_NOT_CENTER     = -1,
    RC_UNMARKED       =  0,
    RC_CENTER         =  1,
    RC_UNCHANGED      =  2,
    RC_MADE_OR_BROKEN =  4,
    RC_ORDER_CHANGED  =  8,

Combinations (like "made or broken or order changes") are also
possible. You can read the original Rxnfile document here:
http://www.symyx.com/downloads/public/ctfile/ctfile.pdf
(search for RXCTR)

> polystyrene is described in
> http://pubs.acs.org/doi/abs/10.1021/ci8002123 - I will hope to post this
> Openly soon.

That would be great, thanks!

Best regards,

Dmitry