[Cod-bugs] {Filename?} feature suggestion COD's display array of results
Norwid Behrnd
nbehrnd at yahoo.com
Mon Jun 8 15:03:11 EEST 2020
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Dear Ladies and Gentlemen,
today I searched in the COD for entries sharing a motif expressed by the
SMILES string of c1scc2OCCOc12. As anticipated, the database successfully
indicated multiple entries. Based on this and earlier queries in the COD,
I would like to suggest a modification of the GUI of your database, namely
a rearrangement of the initial array of results displayed shown prior to
accessing the individual structure cards. To document observations and
suggestions, a there are twelve attachements to this e-mail, too.
I would like to suggest to move the very left-hand column with links to
the homepage of COD and different documentations would be pivoted into an
horizontal arrangement, preferably just below the «title line» of «COD
Crystallographic Open Database», however before the search-dependent array
«Search results» starts (motif_rearrange.png). The currently four topics
of «COD Home», «Accessing COD Data», «Add Your Data», and «Documentation»
could, yet need not to be organized in pull-down menus. This move may then
offer additional overall width for the array about the results to follow.
Inspired by the line-drawings CCDC's interface conquest offers to document
a search in a .pdf file, I subsequently suggest the addition of similar
illustrations intended as a preview of the structure models. As shown in
motif_a.png and motiv_b.png, this possibly could be either just below the
COD ID number, or in a separate column currently the layout not contains.
Publications in Acta Cryst E typically include the chemical name of the
molecule or complex studied; yet sometimes, these names may be long.
COD's data sources sources thankfully include publications «not typically» crystallographic one where the title offers less information about the
model deposit; e.g. if it is about a catalyst, or a synthetic intermediate.
Equally, a publication may cover multiple models, too. Thus, a preview --
at low dimension -- may accelerate the identification of an interesting
entry in the COD for a query departing from a motif in common.
This suggestion partially overlaps with a suggestion sent to one of you,
Antanas Vaitkus on June 3rd, which should have been deposited here instead.
With openbabel (version 3.1.0) and cod-tools (version 2.10) accessible to
Linux Debian 10 / bullseye (branch testing), I searched for a programmatic
generation of «conquest-like» structure formulae as already used within the
Python API of the CSD. As observed, however, this first approach lacks speed
of execution. Larger, possibly conformational flexible ring systems (like
entry 1505735.cif / 1505735.cif.rdf.png) actually yield representations which
are not quite helpful.
Perhaps there are options in openbabel or other program libraries more
suitable to generate these illustrations both reliably and rapidly, too.
With best regards,
Norwid Behrnd
---- 8>< ---- md5sum ---- ---- file attached ----
b173f254b7e49d9732d64c926198f403 1505735.cif
8156c5804818eade5976502b5173def8 1505735.cif.sdf.png
ccf225ac9cf9be328c271d26a543e1f1 1512220.cif
a5c1148d077a67a904cd72e2571b365a 1512220.cif.sdf.png
6baa2a3b0021bb4ca2c34b1c0459f6a9 1512247.cif
b0cc52edca7d7d0bb730413341ec5da1 1512247.cif.sdf.png
9ed542c6424f28512152c9a2d9135622 1513289.cif
3cbf4af5e13344a716f1f85b42dc2a9a 1513289.cif.sdf.png
b1c761142b2b142ac197243007113c1a motif_a.png
739fdee133e5979639fdef3d5f517292 motif_b.png
5d3967f597d2047a43c4e6e9fdc2266b motif_rearrange.png
182323e992968304136708fcd25fe62f test_convert.sh
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