Egon,
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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