[Cod-bugs] Feature suggest COD search with sketcher

[Antanas Vaitkus]

Dear Norwid,

thank you for the bug reports. The COD team is quite swamped at the moment
so it may take us some time to
implement the fixes, but the suggested usability improvements indeed seem
useful.

As a side note, I do not mind you writing directly to this e-mail, but in
the future it would be better to send any bug
reports or feature requests to the COD support e-mail (cod-bugs at ibt.lt).
This way it becomes visible to the entire
COD team and is slightly easier for us to track. In this spirit, I will
also forward my reply to the support e-mail.

Sincerely,
Antanas


On Wed, 3 Jun 2020 at 12:04, Norwid Behrnd <nbehrnd at yahoo.com> wrote:

> Dear Antanas,
>
> based on a previous helpful exchange with you as one of the curators of
> the COD, I would like to suggest an addition of the features the data
> base offers when searching with the sketcher by Ertl et al.
>
>
> Point #1:
> A lecture about alkylated polythiophenes / polythiophene polymers (e.g.,
> slide #4 of the reprinted .pdf attached) lead me to check if the COD would
> contain similar models -- maybe not polymers, but tri- or tetramers fitting
> better into the scope of the database's criterion of «small molecules».
> One of the structure motifs for example was translated on the «search
> results» page into the SMILES string of 'CCc3csc(c2sc(c1sccc1CC)cc2CC)c3',
> with two model data indexed.
>
> I notice that the bottom of the page listing COD entries offers a link
> to return to the search form to refine the query.  In my case, however, the
> SMILES string was not retained; in other words, I _speculated_ the search
> mask's second field «OpenBabel FastSearch» would contain this string to
> continue further.  This however, was not (yet) the case and I would like to
> suggest that this piece of information is transferred to the text-based
> search automatically.
>
>
> Point #2:
> In this case, retrieving the two models was iterative.  With a dimer at
> hand, for example ('CCc2csc(c1sccc1CC)c2' as motif), there already are
> three
> indexed models.  Not knowing (enough / at all) about the technical
> background
> of the COD to bring a solution to the table, I would like to suggest to
> add a second function to the list of results:  If a query was based on a
> structure formula, to offer a return to the page with sketcher where this
> query structure is «still alive» for an adjustment / refinement.
>
> E.g., if you would like to query the COD of halonitrostilbenes; here, I'm
> not aware if the sketcher allows the definition of a «placeholder» then
> covering the set of (F .or. Cl .or. Br .or. I) as in CCDC's conquest GUI.
> So far -- if not simply querying the database with nitrostilbene as
> substructure -- this requires to draw the molecular structure again from
> the beginning.  And again if one of the arenes were substituted by pyridine
> or an other heterocycle where conquest permits to define a arene atom to be
> either (C .or. N); this would not be a simple sub-structure search possibly
> addressed by one query.
>
> With best regards,
>
> Norwid
>


-- 
Antanas Vaitkus,
PhD student at Vilnius University Institute of Biotechnology,
room V325, Saulėtekio al. 7,
LT-10257 Vilnius, Lithuania

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