(Apologies to list, my first response was accidentally off-list)
Ashika sent me a sample, which is below. If the tag of interest is "mol.id"
(i.e. dot in string), babel hangs with
*** Open Babel Error in GetValues
mol not recognized as a property or a descriptor
But if the tag is changed to "mol_id", -m and -append "mol_id" produce the
expected results.
I (quickly, not exhaustively) tried some different quoting and escaping of "
mol.id" but got no joy. Didn't see anything with cursory read of bug list.
Best,
Phil
SAMPLE SDF
-IDBS- 120620101130
5 4 0 0 0 0 0 0 0 0999 V2000
0.2500 -6.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9625 -5.9208 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1.6750 -6.3333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3875 -5.9167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1000 -5.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0
1 2 2 0 0 0
3 4 1 0 0 0
4 5 3 0 0 0
M END
> <mol.id>
AB-00010674
> <mol.weight>
68.07734
$$$$
On Thu, Dec 3, 2015 at 11:29 PM, Fredrik Wallner <[email protected]> wrote:
> Hi,
>
> The information is key within open babel, so whether you see it in the end
> depends on the output format. If you keep the files as SDFiles the
> information should be preserved. If there are a few properties you would
> like to keep, you can also add them to the title with the option --append,
> see http://openbabel.org/wiki/--append
>
> Kind regards,
> Fredrik
> > 2 dec. 2015 kl. 16:55 skrev ashika <[email protected]>:
> >
> > Hello all,
> >
> > I am in the possession of an SDF file containing a chemical library. In
> this
> > file, each molecule is identified by and id number. I am wondering if
> this
> > information can be kept when splitting or acting upon this file. So far I
> > have not found a way.
> >
> > Thanks,
> > Ashika
> >
> >
> >
> > --
> > View this message in context:
> http://forums.openbabel.org/How-do-you-keep-comment-type-information-from-an-SDF-file-tp4659076.html
> > Sent from the General discussion mailing list archive at Nabble.com.
> >
> >
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