Egon Willighagen <[EMAIL PROTECTED]> wrote: > > Can you post this to the user list? And possibly include a PNG with the paper > representation of the MDL file?
Yes I did, re-sending now with PNGs.
Nina
>
> Egon
>
> On Wednesday 14 December 2005 10:21, Nina Jeliazkova wrote:
> > Egon Willighagen <[EMAIL PROTECTED]> wrote:
> > > On Tuesday 13 December 2005 10:59, Nina Jeliazkova wrote:
> > > > I would like to ask if there is a way to store in CML a nonspecific
> > > > structure (i.e. - any structure which contains a repeating group where
> > > > repeat count is not fixed).
> > > > If it is not possible in CML, is there CDK support (beside Polymer
> > > > class)?
> > >
> > > I am not aware of use of the CDK in representation of organic polymers.
> > >
> > > If you list your requirements, then we can think of some way to
represent
> > > things.
> > >
> > > Egon
> >
> > I guess first requirement will be to parse SDF file SGroup block
(currently
> > it is ignored by MDLReader)
> > M STY 1 1 SRU
> > M SCN 1 1 HT
> > M SAL 1 3 1 2 3
> > M SDI 1 4 3.3640 -0.8608 3.3640 0.3938
> > M SDI 1 4 5.6399 0.3938 5.6399 -0.8608
> >
> > not to say it is easy, it may require some new data structures
> >
> > Two examples below:
> > NAME: Poly(oxy-1,2-ethanediyl), alpha-2-propenyl-omega-hydroxy- RN:
> > 27274-31-3
> >
> > Marvin 05210520152D
> >
> > 7 6 0 0 0 0 999 V2000
> > 3.7840 -0.4365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 4.4997 -0.0262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 5.2199 -0.4408 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> > 2.8151 -0.0218 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> > 6.1452 -0.0306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 6.8654 -0.4452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 7.5767 -0.0306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 1 2 1 0 0 0 0
> > 3 5 1 0 0 0 0
> > 4 1 1 0 0 0 0
> > 5 6 1 0 0 0 0
> > 2 3 1 0 0 0 0
> > 6 7 2 0 0 0 0
> > M STY 1 1 SRU
> > M SCN 1 1 HT
> > M SAL 1 3 1 2 3
> > M SDI 1 4 3.3640 -0.8608 3.3640 0.3938
> > M SDI 1 4 5.6399 0.3938 5.6399 -0.8608
> > M END
> > <CAS>
> > 27274-31-3
> > $$$$
> > NAME: Laureth-11 carboxylic acid, sodium salt RN: 33939-64-9
> >
> > Marvin 05210520372D
> >
> > 20 19 0 0 0 0 999 V2000
> > -9.2408 2.5672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > -8.5287 2.9844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > -7.8240 2.5672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > -7.1122 2.9844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > -6.4074 2.5672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > -5.6955 2.9844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > -4.9908 2.5672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > -4.2788 2.9844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > -3.5741 2.5672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > -2.8693 2.9844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > -2.1574 2.5672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > -1.4455 2.9844 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> > -0.5609 2.5672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 0.1510 2.9844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 0.8559 2.5744 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> > 1.7761 2.9915 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 2.4882 2.5816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 3.2002 2.9988 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> > 2.4882 1.7618 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> > -9.9527 2.9844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 2 3 1 0 0 0 0
> > 10 11 1 0 0 0 0
> > 5 6 1 0 0 0 0
> > 11 12 1 0 0 0 0
> > 1 2 1 0 0 0 0
> > 12 13 1 0 0 0 0
> > 6 7 1 0 0 0 0
> > 13 14 1 0 0 0 0
> > 3 4 1 0 0 0 0
> > 14 15 1 0 0 0 0
> > 7 8 1 0 0 0 0
> > 15 16 1 0 0 0 0
> > 16 17 1 0 0 0 0
> > 8 9 1 0 0 0 0
> > 17 18 1 0 0 0 0
> > 4 5 1 0 0 0 0
> > 17 19 2 0 0 0 0
> > 9 10 1 0 0 0 0
> > 1 20 1 0 0 0 0
> > M STY 1 1 SRU
> > M SCN 1 1 HT
> > M SAL 1 3 13 14 15
> > M SDI 1 4 -0.9809 2.1472 -0.9809 3.4044
> > M SDI 1 4 1.2759 3.4044 1.2759 2.1472
> > M END
> > <CAS>
> > 33939-64-9
> > $$$$
> >
> > Regards,
> > Nina
>
--
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Assoc. Prof. Dr. Nina Nikolova-Jeliazkova
* * Institute for Parallel Processing
* * Bulgarian Academy of Sciences
* IST Foundation * Acad. G. Bonchev St 25-A
* The Bulgarian NREN * 1113 Sofia, Bulgaria
* * Tel: +359 886 802011
* * ICQ: 10705013
http://www.ist.bg www: http://ambit.acad.bg/nina
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PGP Public Key
http://cert.acad.bg/pgp-keys/keys/nina-nikolova-0xEEABA669.asc
8E99 8BAD D804 1A43 27B7 7F87 CF04 C7D1 EEAB A669
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27274-31-3.png
Description: PNG image
33939-64-9.png
Description: PNG image
