Re: ORGLIST: Structures by E-mail.

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From: Rzepa, Henry (h.rzepa$##$ic.ac.uk)
Date: Wed Jun 16 1999 - 16:22:43 EDT


>About Structures in E-mails.
>There is a format called SMILES which allowes structures to be encoded/decoded
>for sending in E-mails. For instance:
>O=C(O[C@@H]2[C@@H]([C$##$H](C)C)CC[C$##$H](C)C2)[C$##$H]1[C$##$H](C(O)=O)C1
>when cut out and pasted in for instance CS ChemDraw as PasteSpecial-SMILES
>would decode the structure which in this case is the mono-(+)-menthylester of
>(1R,2R)-cyclopropane-1,2-dicarboxylic acid.


Actually, SMILES has one deficiency nicely illustrated by the above example.
The SMILES does not carry stereochemistry, and hence the above example is
NOT 1R,2R.

Also, of course, the user must manually recognise the SMILES, extract the relevant
characters (no more and no less), and paste them into a SMILES-aware program,
all error-prone steps.

A better (and in fact virus free method because there is no Macro support
in typical chemical data files, and even RasMol files have security checks)
 is chemical MIME attachments
about which we published an article in JCICS in November 1998;
J. Chem. Inf. Comp. Sci., 1998, 38, 976-982;
http://pubs.acs.org/subscribe/journals/jcisd8/jtoc.cgi?jcisd8/38/6

The best way of course is to mark up the email using XML since in theory the chemistry
is "lossless". However, as seen from occasional attempts by "clever" emailers
to markup emails in HTML, if you do not have a clever receiving program which
can recognise the markup and render the content readable, then such marked up emails
can be very irritating.
Still, I think in 2-3 years time, most chemistry will indeed be markep up in emails
and extracted by the receiving program.


Henry Rzepa. +44 171 594 5774 (Office) +44 171 594 5804 (Fax)
http://www.ch.ic.ac.uk/rzepa/
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