Indigo - SData groups problem

[Hinnerk Rey]

Hi,
I use Indigo with Knime. When I import a structure from MOL into
Indigo and export this structure back to MOL, some SData groups (at
least the ones of my MOL-entry) are not included any more. I think
this is due to the conversion to Smiles.
Is it possible to preserver the SData groups?
Of course I can add columns, but this will increase memory usage.
Best, Hinnerk

[Mikhail Rybalkin]

Hello Hinnerk,

Yes, we know about this issue. There is no conversion into SMILES.
Indigo converts molecules into its internal compact format, and we
haven't added support of SGroups there yet. But as you have such
request, we will it add it soon. Sorry, that it wasn't documented.
With the current version it is not possible to preserve SGroups.

Best regards,
Mikhail

[Hinnerk Rey]

Hi Mikhail,
I have quite a lot of structures with various SData groups. Some of
them do carry information from the cheminformatic point of view (e.g.
direction of optical rotation, e.g. "(+)"), others do have
information, which might be usable (like charges on fragments,
coefficients of fragments). Is it possible to convert the later ones
to the indigo internal representation, that they could be processed?
Best, Hinnerk

e.g uracil monoanion
----------------

R>Mv4.0009170720502D 1 1.00000 0.00000 0

8 8 0 0 0 0 0 0 0 0999 V2000
2.6040 2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.4700 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6040 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3361 2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.4700 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.4700 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7380 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.3361 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
2 4 1 0 0 0 0
2 5 2 0 0 0 0
3 6 1 0 0 0 0
3 7 2 0 0 0 0
4 8 1 0 0 0 0
6 8 2 0 0 0 0
M STY 1 1 DAT
M SAL 1 8 1 2 3 4 5 6 7 8
M SBL 1 8 1 2 3 4 5 6 7 8
M SDT 1 MDLBG_FRAGMENT_CHARGE F
M SDD 1 4.9361 4.1600 DA ALL 1 5
M SED 1 -1
M END
-------------------------------

[Mikhail Rybalkin]

Hello Hinnerk,

Indigo toolkit supports SData groups, and it can render them. But in
KNIME all the date are saved on the disk, and them reloaded on demand
(when the workflow is loaded). We have small unimplemented part: SData
groups are not saved into our internal format now, and thus
information about SData groups are discarded when the molecule is
converted into Indigo format. But it is not a natural limitation, we
just have not implemented it. With the current version you cannot
restore them, after the molecule was converted into Indigo cell. It is
not a hard work to add such support, and I think on the next week we
will add a support of sgroups in the Indigo nodes.

And what kind of processing are you interested in? Because these is no
specific methods for working with SData groups in Indigo.

Best regards,
Mikhail

[Hinnerk Rey]

Typos: of course it should be:
> Some of
> them do NOT carry information from the cheminformatic point of view (e.g.

> direction of optical rotation, e.g. "(+)"), others do have
> information, which might be usable