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

[Peter Murray-R. <pm...@ca...>]

On Sat, Apr 9, 2011 at 11:05 PM, Dmitry Pavlov <dp...@gg...>wrote:

> Hello,
>
> I was wondering where I can get any examples on
> the following features of CML. Also, links to software
> (chemical editors/converters) that support these
> features would be very useful. I tried MarvinSketch --
> it does not seem to do any of these well.
>

Thanks very much. I can't answer for Marvin Sketch - it's a commercial
product and I don't have the code or docs. I have recently corresponded with
them about how they can emit compliant CML.

>
> 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?


> 2. Reaction centers (known from Rxnfile notation).
> I was not able to find them in the CML 2.4 spec...
>

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. It
could either be through a series of generic atoms (using elementType="R") or
through a cml:map element or both.

>
> 3. Polymers. I read about the headType and tailType,
> but it would be more understandable with an example.
> What is, for instance, the CML representation for
> polystyrene?
>

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

>
>
> Thanks very much. I would appreciate any pointers.
>
> This is great. CML is a flexible langauage and there ar different styles of
doing some things. We are now encapsulating these as "conventions" - see for
examples http://www.xml-cml.org where we have developed conventions for
dictionaries and molecules. This is now the type to do reactions.

I am delighted to see that you offer Open Source software and that - within
reason - would be happy to help with showing how this can be made valid
within one or more CML validation frameworks.

P.

> Best regards,
>
> Dmitry
>
>
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-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069